Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serine/threonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.

Molecular modelling of human CYP1B1 substrate interactions and investigation of allelic variant effects on metabolism

Molecular modelling of human CYP1B1 based on homology with the mammalian P450, CYP2C5, of known three-dimensional structure is reported. The enzyme model has been used to investigate the likely mode of binding for selected CYP1B1 substrates, particularly with regard to the possible effects of allelic variants of CYP1B1 on metabolism. In general, it appears that the CYP1B1 model is consistent with known substrate selectivity for the enzyme, and the sites of metabolism can be rationalized in terms of specific contacts with key amino acid residues within the CYP1B1 heme locus. Further-more, a mode of binding interaction for the inhibitor, a-naphthoflavone, is presented which accords with currently available information. The current paper shows that a combination of molecular modelling and experimental determinations on the substrate metabolism for CYP1B1 allelic variants can aid in the understanding of structure-function relationships within P450 enzymes. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved.

The source of the Great Dyke, Zimbabwe, and its tectonic significance: Evidence from Re-Os isotopes

Re-Os data for chromite separates from 10 massive chromitite seams sampled along the 550-km length of the 2.58-Ga Great Dyke layered igneous complex, Zimbabwe, record initial 187Os/188Os ratios in the relatively narrow range between 0.1106 and 0.1126. This range of initial 187Os/188Os values is only slightly higher than the value for the coeval primitive upper mantle (0.1107) as modeled from the Re-Os evolution of chondrites and data of modern mantle melts and mantle derived xenoliths. Analyses of Archean granitoid and gneiss samples from the Zimbabwe Craton show extremely low Os concentrations (3-9 ppt) with surprisingly unradiogenic present-day 187Os/188Os signatures between 0.167 and 0.297. Only one sample yields an elevated 187Os/188Os ratio of 1.008. Using these data, the range of crustal contamination of the Great Dyke magma would be minimally 0%-33% if the magma source was the primitive upper mantle, whereas the range estimated from Nd and Pb isotope systematics is 5%-25%. If it is assumed that the primary Great Dyke magma derived from an enriched deep mantle reservoir (via a plume), a better agreement can be obtained. A significant contribution from a long-lived subcontinental lithospheric mantle (SCLM) reservoir with subchondritic Re/Os to the Great Dyke melts cannot be reconciled with the Os isotope results at all. However, Os isotope data on pre-Great Dyke ultramafic complexes of the Zimbabwe Craton and thermal modeling show that such an SCLM existed below the Zimbabwe Craton at the time of the Great Dyke intrusion. It is therefore concluded that large melt volumes such as that giving rise to the Great Dyke were able to pass lithospheric mantle keels without significant contamination in the late Archean. Because the ultramafic-mafic melts forming the Great Dyke must have originated below the SCLM (which extends to at least a 200-km depth ), the absence of an SCLM signature precludes a subduction-related magma-generation process.

Petrology and geochemistry of early cretaceous bimodal continental flood volcanism of the NW Etendeka, Namibia. Part 1: Introduction, mafic lavas and re-evaluation of mantle source components

The bimodal NW Etendeka province is located at the continental end of the Tristan plume trace in coastal Namibia. It comprises a high-Ti (Khumib type) and three low-Ti basalt (Tafelberg, Kuidas and Esmeralda types) suites, with, at stratigraphically higher level, interstratified high-Ti latites (three units) and quartz latites (five units), and one low-Ti quartz latite. Khumib basalts are enriched in high field strength elements and light rare earth elements relative to low-Ti types and exhibit trace element affinities with Tristan da Cunha lavas. The unradiogenic Pb-206/Pb-204 ratios of Khumib basalts are distinctive, most plotting to the left of the 132 Ma Geochron, together with elevated Pb-207/Pb-204 ratios, and Sr-Nd isotopic compositions plotting in the lower Nd-143/Nd-144 part of mantle array (EM1-like). The low-Ti basalts have less coherent trace element patterns and variable, radiogenic initial Sr (similar to0.707-0.717) and Pb isotope compositions, implying crustal contamination. Four samples, however, have less radiogenic Pb and Sr that we suggest approximate their uncontaminated source. All basalt types, but particularly the low-Ti types, contain samples with trace element characteristics (e.g. Nb/Nb-*) suggesting metasediment input, considered source-related. Radiogenic isotope compositions of these samples require long-term isolation of the source in the mantle and depletions (relative to unmodified sediment) in certain elements (e.g. Cs, Pb, U), which are possibly subduction-related. A geodynamic model is proposed in which the emerging Tristan plume entrained subducted material in the Transition Zone region, and further entrained asthenosphere during plume head expansion. Mixing calculations suggest that the main features of the Etendeka basalt types can be explained without sub-continental lithospheric mantle input. Crustal contamination is evident in most low-Ti basalts, but is distinct from the incorporation of a metasedimentary source component at mantle depths.

Adult CNS explants as a source of neural progenitors

Adult neural progenitors have been isolated from diverse regions of the CNS using methods which primarily involve the enzymatic digestion of tissue pieces; however, interpretation of these experiments can be complicated by the loss of anatomical resolution during the isolation procedures. We have developed a novel, explant-based technique for the isolation of neural progenitors, Living CNS regions were sectioned using a vibratome and small, well-defined discs of tissue punched out. When Cultured. explants from the cortex, hippocampus, cerebellum, spinal cord, hypothalamus, and caudate nucleus all robustly gave rise to proliferating progenitors. These progenitors were similar in behaviour and morphology to previously characterised multipotent hippocampal progenitor lines. Clones from all regions examined could proliferate from single cells and give rise to secondary neurospheres at a low but consistent frequency. Immunostaining demonstrated that clonal cortical progenitors were able to differentiate into both neurons and glial cells, indicating their multipotent characteristics. These results demonstrate it is possible to isolate anatomically resolved adult neural progenitors from small amounts of tissue throughout the CNS, thus, providing a tool for investigating the frequency and characteristics of progenitor cells from different regions. (c) 2005 Elsevier B.V. All rights reserved.

Simultaneous saccharification and fermentation of potato starch wastewater to lactic acid by Rhizopus oryzae and Rhizopus arrhizus

The biochemical kinetic of simultaneous saccharification and fermentation (SSF) for lactic acid production by fungal species of Rhizopus arrhizus 36017 and Rhizopus oryzae 2062 was studied with respect to growth pH, temperature and substrate. Both R. arrhizus 36017 and R. oryzae 2062 had a capacity to carry out a single stage SSF process for lactic acid production from potato starch wastewater. The kinetic characteristics, termed as starch hydrolysis, accumulation of reducing sugars, lactic acid production and fungal biomass formation, were affected with variations in pH, temperature, and starch source and concentration. A growth condition with starch concentration approximately 20 g/l at pH 6.0 and 30 degrees C was favourable for both starch saccharification and lactic acid fermentation, resulting in lactic acid yield of 0.85-0.92 g/g associated with 1.5-3.5 g/l fungal biomass produced in 36-48 h fermentation. R. arrhizus 36017 had a higher capacity to produce lactic acid, while R. oryzae 2062 produced more fungal biomass under similar conditions. (c) 2005 Elsevier B.V. All rights reserved.

Susceptibility of source plants to Sugarcane Fiji disease virus influences the acquisition and transmission of the virus by the planthopper vector Perkinsiella saccharicida

Fiji leaf gall (FLG) caused by Sugarcane Fiji disease virus (SCFDV) is transmitted by the planthopper Perkinsiella saccharicida. FLG is managed through the identification and exploitation of plant resistance. The glasshouse-based resistance screening produced inconsistent transmission results and the factors responsible for that are not known. A series of glasshouse trials conducted over a 2-year period was compared to identify the factors responsible for the erratic transmission results. SCFDV transmission was greater when the virus was acquired by the vector from a cultivar that was susceptible to the virus than when the virus was acquired from a resistant cultivar. Virus acquisition by the vector was also greater when the vector was exposed to the susceptible cultivars than when exposed to the resistant cultivar. Results suggest that the variation in transmission levels is due to variation in susceptibility of sugarcane cultivars to SCFDV used for virus acquisition by the vector.

The subcellular fractionation properties and function of insulin receptor substrate-1 (IRS-1) are independent of cytoskeletal integrity

Efficient insulin action requires spatial and temporal coordination of signaling cascades. The prototypical insulin receptor substrate, IRS-1 plays a central role in insulin signaling. By subcellular fractionation IRS-1 is enriched in a particulate fraction, termed the high speed pellet (HSP), and its redistribution from this fraction is associated with signal attenuation and insulin resistance. Anecdotal evidence suggests the cytoskeleton may underpin the localization of IRS-1 to the HSP. In the present study we have taken a systematic approach to examine whether the cytoskeleton contributes to the subcellular fractionation properties and function of IRS-1. By standard microscopy or immunoprecipitation we were unable to detect evidence to support a specific interaction between IRS-1 and the major cytoskeletal components actin (microfilaments), vimentin (intermediate filaments), and tubulin (microtubules) in 3T3-L1 adipocytes or in CHO.IR.IRS-1 cells. Pharmacological disruption of microfilaments and microtubules, individually or in combination, was without effect on the subcellular distribution of IRS-1 or insulin-stimulated tyrosine phosphorylation in either cell type. Phosphorylation of Akt was modestly reduced (20-35%) in 3T3-L1 adipocytes but not in CHO.IR.IRS-1 cells. In cells lacking intermediate filaments (Vim(-/-)) IRS-1 expression, distribution and insulin-stimulated phosphorylation appeared normal. Even after depolymerisation of microfilaments and microtubules, insulin-stimulated phosphorylation of IRS-1 and Akt were maintained in Vim-/- cells. Taken together these data indicate that the characteristic subcellular fractionation properties and function of IRS-1 are unlikely to be mediated by cytoskeletal networks and that proximal insulin signaling does not require an intact cytoskeleton. (c) 2006 Elsevier Ltd. All rights reserved.

Particle number emissions and source signatures of an industrial facility

The work presented was conducted within the scope of a larger study investigating impacts of the Stuart Oil Shale project, a facility operating to the north of the industrial city of Gladstone, Australia. The aims of the investigations were threefold: (a) the identification of the plant signatures in terms of particle size distributions in the submicrometer range (13-830 nm) through stack measurements, (b) exploring the applicability of these signatures in tracing the source contributions at locations of interest, at a distance from the plant, and (c) assessing the contribution of the plant to the total particle number concentration at locations of interest. The stack measurements conducted for three different conditions of plant operation showed that the particle size distributions were bimodal with average modal count median diameters (CMDs) of 24 (SD 4) and 52 (SD 9) nm. The average of all the particle size distributions recorded within the plant sector at a site located 4.5 km from the plant, over the sampling period when the plant was operating, also showed a bimodal distribution. The modal CMDs in this case were 27 and 50 nm, similar to those at the stack. This bimodal size distribution is distinct from the size distribution of the most common ambient anthropogenic emission source, which is vehicle emissions, and can be considered as a signature of this source. The average contribution of the plant (for plant sector winds) was estimated to be (10.0 +/- 3.8) x 10(2) particles cm(-3) and constituted approximately a 50% increase over the local particle ambient concentration for plant sector winds. This increase in particle number concentration compared to the local background concentration, while high compared to the clean environment concentration, is not significant when compared to concentrations generally encountered in the urban environment of Brisbane.