Average structure of an An (sub 48) plagioclase from the Hogarth Ranges

The average structure (CI) of a volcanic plagioclase megacryst with composition Ano, from the Hogarth Ranges, Australia, has been determined using three-dimensional, singlecrystal neutron and X-ray diffraction data. Least squaresr efinements, incorporating anisotropic thermal motion of all atoms and an extinction correction, resulted in weighted R factors (based on intensities) of 0.076 and 0.056, respectively, for the neutron and X-ray data. Very weak e reflections could be detected in long-exposure X-ray and electron diffraction photographs of this crystal, but the refined average structure is believed to be unaffected by the presence of such a weak superstructure. The ratio of the scattering power of Na to that of Ca is different for X ray and neutron radiation, and this radiation-dependence of scattering power has been used to determine the distribution of Na and Ca over a split-atom M site (two sites designated M' and M") in this Ano, plagioclase. Relative peak-height ratios M'/M", revealed in difference Fourier sections calculated from neutron and X-ray data, formed the basis for the cation-distribution analysis. As neutron and X-ray data sets were directly compared in this analysis, it was important that systematic bias between refined neutron and X-ray positional parameters could be demonstrated to be absent. In summary, with an M-site model constrained only by the electron-microprobedetermined bulk composition of the crystal, the following values were obtained for the M-site occupanciesN: ar, : 0.29(7),N ar. : 0.23(7),C ar, : 0.15(4),a nd Car" : 0.33(4). These results indicate that restrictive assumptions about M sites, on which previous plagioclase refinements have been based, are not applicable to this Ano, and possibly not to the entire compositional range. T-site ordering determined by (T-O) bond-length variation-t,o : 0.51(l), trm = t2o = t2m = 0.32(l)-is weak, as might be expectedf rom the volcanic origin of this megacryst.

Micrinite in Southern Hemisphere sub-bituminous and bituminous coals : redefined as fine grained kaolinite

A range of complementary analytical techniques including SEM/EDS, TEM/EDS and conventional optical microscopy has been rigorously applied to precisely defined areas of micrinite in polished coal samples from Australia and New Zealand. Elemental analyses of micrinite regions showed a high abundance of Al, Si and O and high resolution images of micrinite revealed a grain size < 1μm. Electron diffraction and elemental analyses from individual grains within the optically and electron-optically correlated micrinite regions are consistent with the occurence of fine-grained kaolinite. The optical properties of "dark clay" and "micrinite" (i.e. fine-grained kaolinite) can be understood in terms of the diffuse scattering of visible light from the surfaces of materials with different grain sizes in single-phase or multi-phase mixtures.

Protein monoubiquitination and polyubiquitination generate structural diversity to control distinct biological processes

Ubiquitination involves the attachment of ubiquitin (Ub) to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Polyubiquitination through different lysines (seven) or the N-terminus of Ub can generate different protein-Ub structures. These include monoubiquitinated proteins, polyubiqutinated proteins with homotypic chains through a particular lysine on Ub or mixed polyubiquitin chains generated by polymerization through different Ub lysines. The ability of the ubiquitination pathway to generate different protein-Ub structures provides versatility of this pathway to target proteins to different fates. Protein ubiquitination is catalyzed by Ub-conjugating and Ub-ligase enzymes, with different combinations of these enzymes specifying the type of Ub modification on protein substrates. How Ub-conjugating and Ub-ligase enzymes generate this structural diversity is not clearly understood. In the current review, we discuss mechanisms utilized by the Ub-conjugating and Ub-ligase enzymes to generate structural diversity during protein ubiquitination, with a focus on recent mechanistic insights into protein monoubiquitination and polyubiquitination.

Natural improvements of geochemical conditions of acid sulfate soils caused by free tidal inundation and its effects on the mangrove seedlings

Acid sulfate soils (ASS) are one of the stressor factors that cause many mangrove restoration projects to fail. Achieving successful rehabilitation in an ASS affected area requires an understanding of the geochemical conditions that influence the establishment and growth of mangrove seedlings. This study evaluated the effect of tidal inundation on geochemical conditions on sub layer to better understand their impacts on the density, establishment, and growth of mangrove seedlings. This study also examined the geochemical conditions under which mangrove seedlings can establish naturally, and/or be replanted in abandoned aquaculture ponds. The study area was in an area of abandoned aquaculture ponds situated in the Mare District, adjacent to Bone Bay, South Sulawesi, Indonesia.The pH, pHfox, redox potential, organic content, water soluble sulfate, SKCl, SPOS, and grain size of the soil from the sediment core at + 10 - 15 cm depth near roots were measured using. Pyrite analysis were conducted for the top and sub sediments. The density, establishment, and the relative root growth of Rhizophoraceae were also determined. Free tidal inundation at abandoned pond sites improved the sediment quality. The high density, establishment, and growth of mangrove seedlings were characterized by freely drained areas with a higher pH (field and oxidisable), lower organic content, and high proportion of silt/clay. Higher density and growth also correlated to reduced environments. Sulfur species did not influence the density, establishment, and growth of the seedlings directly. The supply of propagules from the mangrove stands, or access from good waterways were also important for seedlings to establish naturally.

Linking three-dimensional geological modelling and multivariate statistical analysis to define groundwater chemistry baseline and identify inter-aquifer connectivity within the Clarence-Moreton Basin, Southeast Queensland, Australia

The Clarence-Moreton Basin (CMB) covers approximately 26000 km2 and is the only sub-basin of the Great Artesian Basin (GAB) in which there is flow to both the south-west and the east, although flow to the south-west is predominant. In many parts of the basin, including catchments of the Bremer, Logan and upper Condamine Rivers in southeast Queensland, the Walloon Coal Measures are under exploration for Coal Seam Gas (CSG). In order to assess spatial variations in groundwater flow and hydrochemistry at a basin-wide scale, a 3D hydrogeological model of the Queensland section of the CMB has been developed using GoCAD modelling software. Prior to any large-scale CSG extraction, it is essential to understand the existing hydrochemical character of the different aquifers and to establish any potential linkage. To effectively use the large amount of water chemistry data existing for assessment of hydrochemical evolution within the different lithostratigraphic units, multivariate statistical techniques were employed.

Cellular model systems to study the tumor biological role of kallikrein-related peptidases in ovarian and prostate cancer

Since the identification of the gene family of kallikrein related peptidases (KLKs), their function has been robustly studied at the biochemical level. In vitro biochemical studies have shown that KLK proteases are involved in a number of extracellular processes that initiate intracellular signaling pathways by hydrolysis, as reviewed in Chapters 8, 9, and 15, Volume 1. These events have been associated with more invasive phenotypes of ovarian, prostate, and other cancers. Concomitantly, aberrant expression of KLKs has been associated with poor prognosis of patients with ovarian and prostate cancer (Borgoño and Diamandis, 2004; Clements et al., 2004; Yousef and Diamandis, 2009), with prostate-specific antigen (PSA, KLK3) being a long standing, clinically employed biomarker for prostate cancer (Lilja et al., 2008). Data generated from patient samples in clinical studies, alongwith biochemical activity, suggests that KLKs function in the development and progression of these diseases. To bridge the gap between their function at the molecular level and the clinical need for efficacious treatment and prognostic biomarkers, functional assessment at the in vitro cellular level, using various culture models, is increasing, particularly in a three-dimensional (3D) context (Abbott, 2003; Bissell and Radisky, 2001; Pampaloni et al., 2007; Yamada and Cukierman, 2007).

Applied sub-transmission & distribution reliability assessment of SEQEB network in Queensland

In this paper a combined subtransmission and distribution reliability analysis of SEQEB’s outer suburban network is presented. The reliability analysis was carried out with a commercial software package which evaluates both energy and customer indices. Various reinforcement options were investigated to ascertain the impact they have on the reliability of supply seen by the customers. The customer and energy indices produced by the combined subtransmission and distribution reliability studies contributed to optimise capital expenditure to the most effective areas of the network.

Soil N2O and CO2 emissions from cotton in Australia under varying irrigation management

Irrigation is known to stimulate soil microbial carbon and nitrogen turnover and potentially the emissions of nitrous oxide (N2O) and carbon dioxide (CO2). We conducted a study to evaluate the effect of three different irrigation intensities on soil N2O and CO2 fluxes and to determine if irrigation management can be used to mitigate N2O emissions from irrigated cotton on black vertisols in South-Eastern Queensland, Australia. Fluxes were measured over the entire 2009/2010 cotton growing season with a fully automated chamber system that measured emissions on a sub-daily basis. Irrigation intensity had a significant effect on CO2 emission. More frequent irrigation stimulated soil respiration and seasonal CO2 fluxes ranged from 2.7 to 4.1 Mg-C ha−1 for the treatments with the lowest and highest irrigation frequency, respectively. N2O emission happened episodic with highest emissions when heavy rainfall or irrigation coincided with elevated soil mineral N levels and seasonal emissions ranged from 0.80 to 1.07 kg N2O-N ha−1 for the different treatments. Emission factors (EF = proportion of N fertilizer emitted as N2O) over the cotton cropping season, uncorrected for background emissions, ranged from 0.40 to 0.53 % of total N applied for the different treatments. There was no significant effect of the different irrigation treatments on soil N2O fluxes because highest emission happened in all treatments following heavy rainfall caused by a series of summer thunderstorms which overrode the effect of the irrigation treatment. However, higher irrigation intensity increased the cotton yield and therefore reduced the N2O intensity (N2O emission per lint yield) of this cropping system. Our data suggest that there is only limited scope to reduce absolute N2O emissions by different irrigation intensities in irrigated cotton systems with summer dominated rainfall. However, the significant impact of the irrigation treatments on the N2O intensity clearly shows that irrigation can easily be used to optimize the N2O intensity of such a system.

Nitrous oxide emissions from irrigated wheat in Australia : impact of irrigation management

Background and Aims: Irrigation management affects soil water dynamics as well as the soil microbial carbon and nitrogen turnover and potentially the biosphere-atmosphere exchange of greenhouse gasses (GHG). We present a study on the effect of three irrigation treatments on the emissions of nitrous oxide (N2O) from irrigated wheat on black vertisols in South-Eastern Queensland, Australia. Methods: Soil N2O fluxes from wheat were monitored over one season with a fully automated system that measured emissions on a sub-daily basis. Measurements were taken from 3 subplots for each treatment within a randomized split-plot design. Results: Highest N2O emissions occurred after rainfall or irrigation and the amount of irrigation water applied was found to influence the magnitude of these “emission pulses”. Daily N2O emissions varied from -0.74 to 20.46 g N2O-N ha-1 day-1 resulting in seasonal losses ranging from 0.43 to 0.75 kg N2O N ha-1 season -1 for the different irrigation treatments. Emission factors (EF = proportion of N fertilizer emitted as N2O) over the wheat cropping season, uncorrected for background emissions, ranged from 0.2 to 0.4% of total N applied for the different treatments. Highest seasonal N2O emissions were observed in the treatment with the highest irrigation intensity; however, the N2O intensity (N2O emission per crop yield) was highest in the treatment with the lowest irrigation intensity. Conclusions: Our data suggest that timing and amount of irrigation can effectively be used to reduce N2O losses from irrigated agricultural systems; however, in order to develop sustainable mitigation strategies the N2O intensity of a cropping system is an important concept that needs to be taken into account.

Cryo-electron tomography of Marburg Virus particles and their morphogenesis within infected cells

Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible "Velcro-like" manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps.

Small signal stability analysis of a DFIG based wind power system with tuned damping controller under super/sub-synchronous mode of operation

This paper focuses on the super/sub-synchronous operation of the doubly fed induction generator (DFIG) system. The impact of a damping controller on the different modes of operation for the DFIG based wind generation system is investigated. The co-ordinated tuning of the damping controller to enhance the damping of the oscillatory modes using bacteria foraging (BF) technique is presented. The results from eigenvalue analysis are presented to elucidate the effectiveness of the tuned damping controller in the DFIG system. The robustness issue of the damping controller is also investigated

The legal nature of justice in REDD+

Formation of Reduced Emissions from Deforestation and Degradation (REDD+) policy within the international climate regime has raised a number of discussions about ‘justice’. REDD+ aims to provide an incentive for developing countries to preserve or increase the amount of carbon stored in their forested areas. Governance of REDD+ is multi-layered: at the international level, a guiding framework must be determined; at the national level, strong legal frameworks are a pre-requisite to ensure both public and private investor confidence and at the sub-national level, forest-dependent peoples need to agree to participate as stewards of forest carbon project areas. At the international level the overall objective of REDD+ is yet to be determined, with competing mitigation, biological and justice agendas. Existing international law pertaining to the environment (international environmental principles and law, IEL) and human rights (international human rights law, IHRL) should inform the development of international and national REDD+ policy especially in relation to ensuring the environmental integrity of projects and participation and benefit-sharing rights for forest dependent communities. National laws applicable to REDD+ must accommodate the needs of all stakeholders and articulate boundaries which define their interactions, paying particular attention to ensuring that vulnerable groups are protected. This paper i) examines justice theories and IEL and IHRL to inform our understanding of what ‘justice’ means in the context of REDD+, and ii) applies international law to create a reference tool for policy-makers dealing with the complex sub-debates within this emerging climate policy. We achieve this by: 1) Briefly outlining theories of justice (for example – perspectives offered by anthropogenic and ecocentric approaches, and views from ‘green economics’). 2) Commenting on what ‘climate justice’ means in the context of REDD+. 3) Outlining a selection of IEL and IHRL principles and laws to inform our understanding of ‘justice’ in this policy realm (for example – common but differentiated responsibilities, the precautionary principle, sovereignty and prevention drawn from the principles of IEL, the UNFCCC and CBD as relevant conventions of international environmental law; and UNDRIP and the Declaration on the Right to Development as applicable international human rights instruments) 4) Noting how this informs what ‘justice’ is for different REDD+ stakeholders 5) Considering how current law-making (at both the international and national levels) reflects these principles and rules drawn from international law 6) Presenting how international law can inform policy-making by providing a reference tool of applicable international law and how it could be applied to different issues linked to REDD+. As such, this paper will help scholars and policy-makers to understand how international law can assist us to both conceptualise and embody ‘justice’ within frameworks for REDD+ at both the international and national levels.

The effects of deep cracks on the rain-induced instability of slopes : A case study

Rainfall can disrupt the balance of natural soil slope. This imbalance will be accelerated by existence of cracks in soil slope, which lead to decreasing shear strength and increasing hydraulic conductivity of the soil slope. Some research works have been conducted on the effects of surface-cracks on slope stability. However, the influence of deep-cracks is yet to be investigated. Limited availability of deep crack data due to the lack of effective sub-soil investigation methods could be one of the obstacles. To emphasize the effects of deep cracks in soil slope on its rain-induced instability, a natural soil slope in Indonesia that failed in 31st October 2010 due to heavy rainfall was analyzed for stability with and without deep cracks in the slope. The slope stability analysis was conducted using SLOPE/W coupling with the results of transient seepage analysis (SEEP/W) that simulate the pore-water pressure development in the slope during the rainfall. The results of Electrical Resistivity Tomography (ERT) survey, bore-hole tests and geometrical survey conducted on the slope before its failure were used to identify the soil layers’ stratification including deep cracks, the properties of different soil layers, and geometrical parameters of the slope for the analysis. The results showed that it is vital to consider the existence of deep crack in soil slopes in analysing their instability induced by rainfalls.

Paleomagnetic data support Early Permian age for the Abor Volcanics in the lower Siang Valley, NE India; significance for Gondwana-related break-up models

Confusion exists as to the age of the Abor Volcanics of NE India. Some consider the unit to have been emplaced in the Early Permian, others the Early Eocene, a difference of ∼230 million years. The divergence in opinion is significant because fundamentally different models explaining the geotectonic evolution of India depend on the age designation of the unit. Paleomagnetic data reported here from several exposures in the type locality of the formation in the lower Siang Valley indicate that steep dipping primary magnetizations (mean = 72.7 ± 6.2°, equating to a paleo-latitude of 58.1°) are recorded in the formation. These are only consistent with the unit being of Permian age, possibly Artinskian based on a magnetostratigraphic argument. Plate tectonic models for this time consistently show the NE corner of the sub-continent >50°S; in the Early Eocene it was just north of the equator, which would have resulted in the unit recording shallow directions. The mean declination is counter-clockwise rotated by ∼94°, around half of which can be related to the motion of the Indian block; the remainder is likely due local Himalayan-age thrusting in the Eastern Syntaxis. Several workers have correlated the Abor Volcanics with broadly coeval mafic volcanic suites in Oman, NE Pakistan–NW India and southern Tibet–Nepal, which developed in response to the Cimmerian block peeling-off eastern Gondwana in the Early-Middle Permian, but we believe there are problems with this model. Instead, we suggest that the Abor basalts relate to India–Antarctica/India–Australia extension that was happening at about the same time. Such an explanation best accommodates the relevant stratigraphical and structural data (present-day position within the Himalayan thrust stack), as well as the plate tectonic model for Permian eastern Gondwana.