Sedimentology, volcanology and geodynamics of the Redbank Package, McArthur Basin, northern Australia

The 1815-1705 Ma Redbank package is a 3-6 km thick succession of shallow marine to braided fluvial sandstone and lesser conglomerate, mudstone, carbonates and rhyolitic-basaltic volcanics and high-level intrusions. It forms the base of the Palaeo proterozoic McArthur Basin in northern Australia. In the southern McArthur Basin, the Tawallah Group is the best exposed stratigraphic component of this package. Coarse-grained facies at the base of the Group formed in a proximal-medial braided fluvial environment and are overlain by widespread sheets of supermature quartzarenite and intervening flood basalt. These enigmatic sandstone sheets contain features consistent with deposition in a complex high-energy shallow marine, fluvial and aeolian setting on an extensive low-gradient shelf Overlying mudstones and carbonates were deposited on a shallow epeiric shelf and coastal sabkha fringe that onlapped basement tectonic ridges. A regional sequence boundary formed during subsequent regional uplift and local synsedimentary deformation, and was followed by deposition of another widespread quartzarenite sheet. The overlying succession of fine-grained sandstone, mudstone, carbonate and evaporitic redbeds suggest more diverse depositional settings. Marginal marine salina, near-shore peritidal, storm-dominated shelf and moderately deep water settings, with periodic restriction to the marine realm, fluctuating accommodation rates and minor synsedimentary faulting are all recorded. Regional-scale dolerite sills and an extensive stacked succession of basalt sheets were emplaced sequentially as widely-dispersed invasive flows under a thin blanket of wet unconsolidated sediment and peperite. Volcanism was locally associated with uplift and emplacement of polymict debris flows and breccia bodies. This was followed by deposition of a complex association of clastic sediments and felsic volcanics and intrusion of high-level plutons (upper Tawallah Group). Sheet-like rhyolitic lavas with abrupt talus-lined margins evolved via non-explosive eruption and long-term viscous flow. This was facilitated by low water content and high and continuous eruption temperature and effusion rate. Complex ephemeral alluvial and debris flow aprons formed adjacent to the lavas, recording the generation, erosional denudation and final burial of a dynamic high-relief volcano-tectonic landscape. Epiclastic materials were reworked in bordering lakes and low-relief braid plains that prograded radially away from the volcanic centres. Periods between magmatic events were characterised by deposition of widespread immature sandstone sheets in extensive high-energy ephemeral to perennial braided fluvial settings and the development of low-relief regional disconformities. Concurrent pluton emplacement in the northern McArthur Basin generated a series of structural domes with peripheral deformation. Accommodation space for intrusion was provided by decollement at ductility transitions, upward flexuring, outward gravity slide and vertical displacement of overlying sediments. Detailed stratigraphic and facies analysis of the Tawallah Group has enabled the development of a tectonostratigraphic framework for the entire Redbank package. Four second order subdivisions are recognised (Yirrumanja, Liverpool, Costello and Mitchell mesopackages) that facilitate a clearer, integrated regional understanding of the lithology, timing and geographic distribution of basin phases. The package concept is also applied to the composite McArthur Basin system as a whole. Five distinct and regionally coherent basin phases are recognised (Redbank, Goyder, Glyde, Favenc and Wilton packages). These were deposited in a dynamic tectonic environment over a period of -350 m.y. Geochemical characterisation of Proterozoic igneous phases in northern Australia has confirmed many lithostratigraphic correlations in the McArthur Basin. Felsic units show temporal and spatial variation in geochemistry that reflects partial melting of heterogeneous Archaean mafic lower crust due to the emplacement oflarge basaltic magma chambers and radiogenic heating. The McArthur Basin contains five main mafic igneous phases with typical flood basalt attributes, spanning a period of -480 m.y. Magmas were derived by partial melting of chemically-stratified lower lithosphere and do not exhibit a plume or rift signature. A convergent intracratonic setting is proposed for the Redbank package. Basin architecture reflects diverse subsidence mechanisms operating inboard of the active southern margin of the North Australian Craton (Strangways arc). Wedge-shaped and magmatic-related basin architectures formed during subduction. Subsidence was influenced by dynamic topography, thermally- and mechanically-driven viscoelastic behaviour of heterogeneous crust, magmatic underplating, lithospheric phase transformations, and local transtension and isostatic loading. Local growthfault architecture formed by incipient back-arc extension. Magmatism was driven by a persistent thermal anomaly related to insulative heating and a transient convective roll emanating from the Strangways arc, that eroded the lower lithosphere and generated a magma pool. Migration of magma into lower-crustal magma chambers and to the surface took place at transtensional sites along lithosphere-scale strike-slip faults. Regional unconformities and elongate and wedge basin architectures formed in the Redbank package during periodic terrane accretion events at the Strangways arc. Subsidence was influenced largely by transmission of in-plane stress through the lithosphere to produce lithosphere-scale folding, viscoelastic deflections of the lithosphere, and transtensional strike-slip and flexural back-bulge basins. Local elongate magmatic grabens are interpreted as impactogens resulting from indentor tectonics

The MEROPS Database

Many proteins undergo important post-translational proteolytic processing to remove targeting signals and activation peptides, and most proteins undergo proteolytic inactivation and catabolism. The enzymes that hydrolyse the peptide bonds in proteins and peptides are known as peptidases, proteases or proteolytic enzymes. The MEROPS database ("http://merops.sanger.ac.uk":http://merops.sanger.ac.uk) presents the classification and nomenclature of peptidases, their inhibitors and substrates. In 1993 we proposed the scheme for the classification of peptidases that has been internationally accepted, and in 1996 we established the MEROPS database. Protein inhibitors have been included in the database since 2004. About 2% of the genes in a genome encode peptidase homologues, and a further 1% encode protein inhibitors. For example, the human genome has 1037 genes encoding peptidase homologues (of which 643 are known or predicted to be active peptidases) and 433 protein inhibitor genes (of which 144 have been biochemically characterized as inhibitors). 

The MEROPS classification is hierarchical. Sequences are grouped into a peptidase species (each of which is given a unique identifier, for example C01.060 for cathepsin B); peptidase species are grouped into a family (for example C1); and families grouped into a clan (for example CA). To be included in the same protein species, sequences must be derived from the same node on a dendrogram derived from the family sequence alignment and known (or predicted) to share similar specificity. To be included in the same family sequences must be homologous over the sequence domain that contains the active site residues (peptidases) or reactive site (inhibitors). To be included in the same clan, the proteins must share similar tertiary structures (or the same linear arrangement of active site residues if the structure is unknown). Over 117,000 peptidase homologues are classified into 3114 protein species, 205 families and 52 clans, and 12,104 protein inhibitors are classified into 663 protein species, 64 families and 33 clans.

The database includes manually curated summaries for each clan, family and protein species. There are also sequence alignments and manually curated bibliographies (with over 41,000 references) at every level. In addition to protein inhibitors we also include 158 manually curated summaries for synthetic and naturally occurring small molecule inhibitors. There is also a summary page for each organism listing all known homologues and an analysis highlighting significant presences, absences or gene family expansions for organisms with a completely sequenced genome. 

The MEROPS database includes known peptidase substrates: naturally occurring peptides and proteins, and synthetic substrates. Currently there are 4091 cleavages of synthetic substrates and 95,413 cleavages of proteins (of which 74,740 are physiological). Cleavages in proteins are mapped to UniProt entries. An alignment of very close homologues of each substrate sequence is shown, highlighting residues around each cleavage site indicating whether the peptidase is known to accept the amino acid at that position or not. Cleavage sites that are conserved are likely to be physiological; cleavage sites that are not conserved may be pathological for the species in which they occur or coincidental.

The MEROPS data is freely available to download from our FTP site ("http://ftp.sanger.ac.uk/pub/MEROPS":http://ftp.sanger.ac.uk/pub/MEROPS) and via our Distributed Annotation System (DAS) server ("http://das.sanger.ac.uk/das/merops":http://das.sanger.ac.uk/das/merops).
&#xa

Molecular gas freeze-out in the pre-stellar core L1689B

C17O (J=2-1) observations have been carried out towards the pre-stellar core L1689B. By comparing the relative strengths of the hyperfine components of this line, the emission is shown to be optically thin. This allows accurate CO column densities to be determined and, for reference, this calculation is described in detail. The hydrogen column densities that these measurements imply are substantially smaller than those calculated from SCUBA dust emission data. Furthermore, the C17O column densities are approximately constant across L1689B whereas the SCUBA column densities are peaked towards the centre. The most likely explanation is that CO is depleted from the central regions of L1689B. Simple models of pre-stellar cores with an inner depleted region are compared with the results. This enables the magnitude of the CO depletion to be quantified and also allows the spatial extent of the freeze-out to be firmly established. We estimate that within about 5000 AU of the centre of L1689B, over 90% of the CO has frozen onto grains. This level of depletion can only be achieved after a duration that is at least comparable to the free-fall timescale.Comment: MNRAS letters. 5 pages, 5 figure

Rotation of the pre-stellar core L1689B

The search for the onset of star formation in pre-stellar cores has focussed on the identification of an infall signature in the molecular line profiles of tracer species. The classic infall signature is a double peaked line profile with an asymmetry in the strength of the peaks such that the blue peak is stronger. L1689B is a pre-stellar core and infall candidate but new JCMT HCO+ line profile data, presented here, confirms that both blue and red asymmetric line profiles are present in this source. Moreover, a dividing line can be drawn between the locations where each type of profile is found. It is argued that it is unlikely that the line profiles can be interpreted with simple models of infall or outflow and that rotation of the inner regions is the most likely explanation. A rotational model is developed in detail with a new 3D molecular line transport code and it is found that the best type of model is one in which the rotational velocity profile is in between solid body and Keplerian. It is firstly shown that red and blue asymmetric line profiles can be generated with a rotation model entirely in the absence of any infall motion. The model is then quantitively compared with the JCMT data and an iteration over a range of parameters is performed to minmize the difference between the data and model. The results indicate that rotation can dominate the line profile shape even before the onset of infall.Comment: Accepted by MNRAS, 7 pages, 4 figure

Haemoglobinopathies and health care provision for ethnic minorities

The level of training and competence in dealing with haemoglobinopathies (which mainly affect ethnic minorities in the UK) may not be totally adequate among nurses. Nurses indicated that they received little or no information in their teaching for working from a multiracial perspective and what they had learned was through experience and personal research since qualifying as nurses. Knowledge of the biological basis of inheritance, methods of acquisition of thalassaemia and sicklecell anaemia and the ethnic profile of people affected by these conditions may not be totally adequate among nurses. Many nurses wanted more training, including those who had already received instruction, since this was described as ‘far too vague’, ‘not constructive’, ‘minimal’, or ‘embarrassingly insufficient’, recommending that instruction be given by a sickle-cell anaemia/thalassaemia counsellor with a contribution from patients. A combination of poor quality, or lack, of instruction, together with time and resource pressures, is responsible for this limited understanding, resulting in insufficient awareness of the health needs of ethnic minorities leading to inequalities in healthcare provision

SKA HI end2end simulation

The current status of the HI simulation efforts is presented, in which a self consistent simulation path is described and basic equations to calculate array sensitivities are given. There is a summary of the SKA Design Study (SKADS) sky simulation and a method for implementing it into the array simulator is presented. A short overview of HI sensitivity requirements is discussed and expected results for a simulated HI survey are presented.Comment: 7 pages, 6 figues, need skads2009.cls file to late

Desorption From Interstellar Ices

The desorption of molecular species from ice mantles back into the gas phase in molecular clouds results from a variety of very poorly understood processes. We have investigated three mechanisms; desorption resulting from H_2 formation on grains, direct cosmic ray heating and cosmic ray induced photodesorption. Whilst qualitative differences exist between these processes (essentially deriving from the assumptions concerning the species-selectivity of the desorption and the assumed threshold adsorption energies, E_t) all three processes are found to be potentially very significant in dark cloud conditions. It is therefore important that all three mechanisms should be considered in studies of molecular clouds in which freeze-out and desorption are believed to be important. Employing a chemical model of a typical static molecular core and using likely estimates for the quantum yields of the three processes we find that desorption by H_2 formation probably dominates over the other two mechanisms. However, the physics of the desorption processes and the nature of the dust grains and ice mantles are very poorly constrained. We therefore conclude that the best approach is to set empirical constraints on the desorption, based on observed molecular depletions - rather than try to establish the desorption efficiencies from purely theoretical considerations. Applying this method to one such object (L1689B) yields upper limits to the desorption efficiencies that are consistent with our understanding of these mechanisms.Comment: 11 pages, 5 figures, accepted by MNRAS subject to minor revision which has been carried ou

Bacterial calpains and the evolution of the calpain (C2) family of peptidases

Homologues of calpain, often thought to be an essential, cytoplasmic, calcium-dependent cysteine endopeptidase found exclusively in eukaryotes, have been found in bacterial proteomes. The homologues lack calcium-binding sites, have differing domain architectures, and can be secreted or membrane-associated. Homologues are rare and occur in a minority of bacterial phyla and often in a minority of species in a genus. However, the differences in domain architecture argue against a recent, horizontal gene transfer from a eukaryote. From analysis of a phylogenetic tree and absence of homologues in archaea, calpains in eukaryotes may be derived from genes horizontally transferred from a bacterium. Reviewers: This article was reviewed by L. Aravind and Frank Eisenhaber. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13062-015-0095-0) contains supplementary material, which is available to authorized users