Identification of residues and domains of Raf important for function in vivo and in vitro

Random mutagenesis and genetic screens for impaired Raf function in Caenorhabditis elegans were used to identify six loss-of-function alleles of lin-45 raf that result in a substitution of a single amino acid. The mutations were classified as weak, intermediate, and strong based on phenotypic severity. We engineered these mutations into the homologous residues of vertebrate Raf-1 and analyzed the mutant proteins for their underlying biochemical defects. Surprisingly, phenotype strength did not correlate with the catalytic activity of the mutant proteins. Amino acid substitutions Val-589 and Ser-619 severely compromised Raf kinase activity, yet these mutants displayed weak phenotypes in the genetic screen. Interestingly, this is because these mutant Raf proteins efficiently activate the MAPK (mitogen-activated protein kinase) cascade in living cells, a result that may inform the analysis of knockout mice. Equally intriguing was the observation that mutant proteins with non-functional Ras-binding domains, and thereby deficient in Ras-mediated membrane recruitment, displayed only intermediate strength phenotypes. This confirms that secondary mechanisms exist to couple Ras to Raf in vivo. The strongest phenotype in the genetic screens was displayed by a S508N mutation that again did not correlate with a significant loss of kinase activity or membrane recruitment by oncogenic Ras in biochemical assays. Ser-508 lies within the Raf-1 activation loop, and mutation of this residue in Raf-1 and the equivalent Ser-615 in B-Raf revealed that this residue regulates Raf binding to MEK. Further characterization revealed that in response to activation by epidermal growth factor, the Raf-S508N mutant protein displayed both reduced catalytic activity and aberrant activation kinetics: characteristics that may explain the C. elegans phenotype.

Core outcome domains for chronic pain clinical trials: IMMPACT recommendations

Objective. To provide recommendations for the core outcome domains that should be considered by investigators conducting clinical trials of the efficacy and effectiveness of treatments for chronic pain. Development of a core set of outcome domains would facilitate comparison and pooling of data, encourage more complete reporting of outcomes, simplify the preparation and review of research proposals and manuscripts, and allow clinicians to make informed decisions regarding the risks and benefits of treatment. Methods. Under the auspices of the Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (IMMPACT), 27 specialists from academia. governmental agencies, and the pharmaceutical industry participated in a consensus meeting and identified core outcome domains that should be considered in clinical trials of treatments for chronic pain. Conclusions. There was a consensus that chronic pain clinical trials should assess outcomes representing six core domains: (1) pain, (2) physical functioning, (3) emotional functioning, (4) participant ratings of improvement and satisfaction with treatment, (5) symptoms and adverse events, (6) participant disposition (e.g. adherence to the treatment regimen and reasons for premature withdrawal from the trial). Although consideration should be given to the assessment of each of these domains, there may be exceptions to the general recommendation to include all of these domains in chronic pain trials. When this occurs, the rationale for not including domains should be provided. It is not the intention of these recommendations that assessment of the core domains should be considered a requirement for approval of product applications by regulatory agencies or that a treatment must demonstrate statistically significant effects for all of the relevant core domains to establish evidence of its efficacy. (C) 2003 International Association for the Study of Pain.

Genomic screen for genes involved in mammalian craniofacial development

Using a subtractive hybridisation approach, we enriched for genes likely to play a role in embryonic development of the mammalian face and other structures. This was achieved by subtracting cDNA derived from adult mouse liver from that derived from 10.5 dpc mouse embryonic branchial arches 1 and 2. Random sequencing of clones from the resultant library revealed that a high percentage correspond to genes with a previously established role in embryonic development and disease, while 15% represent novel or uncharacterised genes. Whole mount in situ hybridisation analysis of novel genes revealed that approximately 50% have restricted expression during embryonic development. In addition to expression in branchial arches, these genes showed a range of expression domains commonly including neural tube and somites. Notably, all genes analysed were found to be expressed not only in the branchial arches but also in the developing limb buds, providing support for the hypothesis that development of the limbs and face is likely to involve analogous molecular processes. (C) 2003 Wiley-Liss, Inc.

The trans-membrane protein p25 forms highly specialized domains that regulate membrane composition and dynamics

Trans-membrane proteins of the p24 family are abundant, oligomeric proteins predominantly found in cis-Golgi membranes. They are not easily studied in vivo and their functions are controversial. We found that p25 can be targeted to the plasma membrane after inactivation of its canonical KKXX motif (KK to SS, p25SS), and that p25SS causes the co-transport of other p24 proteins beyond the Golgi complex, indicating that wild-type p25 plays a crucial role in retaining p24 proteins in cis-Golgi membranes. We then made use of these observations to study the intrinsic properties of these proteins, when present in a different membrane context. At the cell surface, the p25SS mutant segregates away from both the transferrin receptor and markers of lipid rafts, which are enriched in cholesterol and glycosphingolipids. This suggests that p25SS localizes to, or contributes to form, specialized membrane domains, presumably corresponding to oligomers of p25SS and other p24 proteins. Once at the cell surface, p25SS is endocytosed, together with other p24 proteins, and eventually accumulates in late endosomes, where it remains confined to well-defined membrane regions visible by electron microscopy. We find that this p25SS accumulation causes a concomitant accumulation of cholesterol in late endosomes, and an inhibition of their motility - two processes that are functionally linked. Yet, the p25SS-rich regions themselves seem to-exclude not only Lamp1 but also accumulated cholesterol. One may envision that p25SS accumulation, by excluding cholesterol from oligomers, eventually overloads neighboring late endosomal membranes with cholesterol beyond their capacity (see Discussion). In any case, our data show that p25 and presumably other p24 proteins are endowed with the intrinsic capacity to form highly specialized domains that control membrane composition and dynamics. We propose that p25 and other p24 proteins control the fidelity of membrane transport by maintaining cholesterol-poor membranes in the Golgi complex.

Linking superiority bias in the interpersonal and intergroup domains

The author conducted 2 studies to explore the link between superiority bias in the interpersonal and intergroup domains. Australian university students evaluated the extent to which various personality traits were more or less applicable to themselves than to other Australian university students in general. They then evaluated the extent to which the same traits were more or less applicable to Australians than to people from other countries in general. As expected, the more participants evaluated themselves as superior to other university students, the more they evaluated Australians as a whole as superior to people from other countries. This link between interpersonal and intergroup superiority biases explained 22.1% of variance in Study 1 and 33.6% of variance in Study 2. The author interprets the results of the 2 studies as support for fundamental principles of social identity theory: (a) that self-concept consists of not only one's personal self but also the social groups to which one belongs and (b) that people are motivated to view both levels of self in a relatively positive fashion.

Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Inheritance of early Archaean Pb-isotope variability from long-lived Hadean protocrust

Comparison of initial Pb-isotope signatures of several early Archaean (3.65-3.82 Ga) lithologies (orthogneisses and metasediments) and minerals (feldspar and galena) documents the existence of substantial isotopic heterogeneity in the early Archaean, particularly in the Pb-207/Pb-204 ratio. The magnitude of isotopic variability at 3.82-3.65 Ga requires source separation between 4.3 and 4.1 Ga, depending on the extent of U/Pb fractionation possible in the early Earth. The isotopic heterogeneity could reflect the coexistence of enriched and depleted mantle domains or the separation of a terrestrial protocrust with a U-238/Pb-204 (mu) that was ca. 20-30% higher than coeval mantle. We prefer this latter explanation because the high-p signature is most evident in metasediments (that formed at the Earth's surface). This interpretation is strengthened by the fact that no straightforward mantle model can be constructed for these high-mu lithologies without violating bulk silicate Earth constraints. The Pb-isotope evidence for a long-lived protocrust complements similar Hf-isotope data from the Earth's oldest zircons, which also require an origin from an enriched (low Lu/Hf) environment. A model is developed in which greater than or equal to3.8-Ga tonalite and monzodiorite gneiss precursors (for one of which we provide zircon U-Pb data) are not mantle-derived but formed by remelting or differentiation of ancient (ca. 4.3 Ga) basaltic crust which had evolved with a higher U/Pb ratio than coeval mantle in the absence of the subduction process. With the initiation of terrestrial subduction at, we propose, ca. 3.75 Ga, most of the greater than or equal to3.8-Ga basaltic shell (and its differentiation products) was recycled into the mantle, because of the lack of a stabilising mantle lithosphere. We argue that the key event for preservation of all greater than or equal to3.8-Ga terrestrial crust was the intrusion of voluminous granitoids immediately after establishment of global subduction because of complementary creation of a lithospheric keel. Furthermore, we argue that preservation of !3.8-Ga material (in situ rocks and zircons) globally is restricted to cratons with a high U/Pb source character (North Atlantic, Slave, Zimbabwe, Yilgarn, and Wyoming), and that the Pb-isotope systematics of these provinces are ultimately explained by reworking of material that was derived from ca. 4.3 Ga (i.e. Hadean) basaltic crust.

Transparent boundary conditions for wave propagation on unbounded domains

The numerical solution of the time dependent wave equation in an unbounded domain generally leads to a truncation of this domain, which requires the introduction of an artificial boundary with associated boundary conditions. Such nonreflecting conditions ensure the equivalence between the solution of the original problem in the unbounded region and the solution inside the artificial boundary. We consider the acoustic wave equation and derive exact transparent boundary conditions that are local in time and can be directly used in explicit methods. These conditions annihilate wave harmonics up to a given order on a spherical artificial boundary, and we show how to combine the derived boundary condition with a finite difference method. The analysis is complemented by a numerical example in two spatial dimensions that illustrates the usefulness and accuracy of transparent boundary conditions.

A novel route to the synthesis of mesoporous Titania with full anatase nanocrystalline domains

A porous, high surface area TiO2 with anatase or rutile crystalline domains is advantageous for high efficiency photonic devices. Here, we report a new route to the synthesis of mesoporous titania with full anatase crystalline domains. This route involves the preparation of anatase nanocrystalline seed suspensions as the titania precursor and a block copolymer surfactant, Pluronic P123 as the template for the hydrothermal self-assembly process. A large pore (7 - 8 nm) mesoporous titania with a high surface area of 106 - 150 m(2)/g after calcination at 400degreesC for 4 h in air is achieved. Increasing the hydrothermal temperature decreases the surface area and creates larger pores. Characteristics of the seed precursors as well as the resultant mesoporous titania powder were studied using XRD analysis, N-2-adsorption/desorption analysis, and TEM. We believe these materials will be especially useful for photoelectrochemical solar cell and photocatalysis applications.

The cyclic antimicrobial peptide RTD-1 induces stabilized lipid-peptide domains more efficiently than its open-chain analogue

The effects of a mammalian cyclic antimicrobial peptide, rhesus theta defensin 1 (RTD-1) and its open chain analogue (oRTD-1), on the phase behaviour and structure of model membrane systems (dipalmitoyl phosphatidylcholine, DPPC and dipalmitoyl phosphatidylglycerol, DPPG) were studied. The increased selectivity of RTD-1 for anionic DPPG over zwitterionic DPPC was shown by differential scanning calorimetry. RTD-1, at a molar peptide-lipid ratio of 1:100, induced considerable changes in the phase behaviour of DPPG, but not of DPPC. The main transition temperature, T-m, Was unchanged, but additional phase transitions appeared above T-m. oRTD-1 induced similar effects. However, the effects were not observable below a peptide:lipid molar ratio of 1:50, which correlates with the weaker biological activity of oRTD-1. Small-and wide-angle X-ray scattering revealed for DPPG the appearance of additional structural features induced by RTP-1 above T-m, which were interpreted as correlated lamellar structures, with increased order of the fatty acyl side chains of the lipid. It is proposed that after initial electrostatic interaction of the cationic rim of the peptide with the anionic DPPG headgroups, leading to stabilized lipid-peptide clusters, the hydrophobic face of the peptide assists in its interaction with the fatty acyl side chains eventually leading to membrane disruption. (C) 2004 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Mammalian GRIP domain proteins differ in their membrane binding properties and are recruited to distinct domains of the TGN

The four mammalian golgins, p230/golgin-245, golgin-97, GCC88 and GCC185 are targeted to trans-Golgi network ITGN) membranes by their C-terminal GRIP domain in a G-protein-dependent process. The Arf-like GTPase, Arl1, has been shown to mediate TGN recruitment of p230/golgin245 and golgin-97 by interaction with their GRIP domains; however, it is not known whether all the TGN golgins bind to Arl1 and whether they are all recruited to the same or different TGN domains. Here we demonstrate differences in membrane binding properties and TGN domain recruitment of the mammalian GRIP domain proteins. Overexpression of full-length GCC185 resulted in the appearance of small punctate structures dispersed in the cytoplasm of transfected cells that were identified as membrane tubular structures by immunoelectron microscopy. The cytoplasmic GCC185-labelled structures were enriched for membrane binding determinants of GCC185 GRIP, whereas the three other mammalian GRIP family members did not colocalize with the GCC185-labelled structures. These GCC185-labelled structures included the TGN resident protein alpha2,6 sialyltransferase and excluded the recycling TGN protein, TGN46. The Golgi stack was unaffected by overexpression of GCC185. Overexpression of both full-length GCC185 and GCC88 showed distinct and nonoverlapping structures. We also show that the GRIP domains of GCC185 and GCC88 differ in membrane binding properties from each other and, in contrast to p230/golgin245 and golgin-97, do not interact with Arl1 in vivo. Collectively these results show that GCC88, GCC185 and p230/golgin245 are recruited to functionally distinct domains of the TGN and are likely to be important for the maintenance of TGN subdomain structure, a critical feature for mediating protein sorting and membrane transport.

Domains of the TGN: Coats, tethers and G proteins

The trans-Golgi network is the major sorting compartment of the secretory pathway for protein, lipid and membrane traffic. There is a constant flow of membrane and cargo to and from this compartment. Evidence is emerging that the trans-Golgi network has multiple biochemically and functionally distinct subdomains, each of which contributes to the combined sorting and transport requirements of this dynamic compartment. The recruitment of distinct arrays of protein complexes to trans-Golgi network membranes is likely to produce the diversity of structure and biochemistry observed amongst subdomains that serve to generate different carriers or maintain resident trans-Golgi network components. This review discusses how these subdomains may be formed and examines the molecular players involved, including G proteins, clathrin adaptors and golgin tethers. Diversity within these protein families is highlighted and shown to be critical for the functionality of the trans-Golgi network, as a mediator of protein sorting and membrane transport, and for the maintenance of Golgi structure.

Geochemistry of late Archaean stromatolites from Zimbabwe: evidence for microbial life in restricted epicontinental seas

We report comprehensive trace element and Sr-isotope data for microbial carbonates from the Archaean Mushandike limestone, Masvingo Greenstone Belt, Zimbabwe. The stromatolites have very coherent REE + Y patterns and share the essential shale-normalised characteristics of other Archaean marine precipitates (positive La and Gd anomalies, absence of a negative Cc anomaly and a strongly superchondritic Y/Ho ratio). Mixing models constrain the maximum amount of shale contamination to 0.25-1% and calculated detritus-free carbonate REE + Y systematics require precipitation from seawater. In terms of light-REE over heavy-REE depletion, however, the studied samples are very different from all other known Archaean marine precipitates. In shale-normalised plots, the Mushandike samples yield a negative slope. A very restricted, regional input source of the dissolved load is indicated because normalisation with locally occurring tonalite gneiss REE + Y data yields a pattern closely resembling typical shale-normalised Archaean marine chemical sediments. The disappearance of a negative Eu anomaly when patterns are normalised with local tonalite gneiss strengthens this interpretation. Sr-isotope ratios are strongly correlated with trace element contents and ratios, which explains the modest scatter in Sr-isotope ratios as representing (minor) clastic contamination. Importantly, even the least contaminated samples have very radiogenic initial Sr-87/Sr-86 ratios (0.7184) implying Sr input from an ancient high Rb/Sr source, such as the early Archaean gneisses of south-central Zimbabwe. A local ancient (3.5-3.8 Ga) source is also indicated by previously published Pb-isotope datasets for the Mushandike stromatolites. This is entirely compatible with the occurrence of 3.7-3.8 Ga zircons in quartzites and metapelites from comparably old greenstone belts within less than 150 km of the studied locality. Comparison of the Pb-isotope ratios of the Mushandike stromatolites with 2.7 and 2.6 Ga old stromatolites from the neighbouring, Belingwe Greenstone Belt demonstrates differences in initial isotope composition that relate to the extent of exchange with the open ocean. The development of numerous basins on old continental crust, with water masses variably restricted from the open ocean. suggests a lack of strong vertical topography on this late Archaean craton. (C) 2004 Elsevier B.V. All rights reserved.

Three separable domains regulate GTP-dependent association of H-ras with the plasma membrane

The microlocalization of Ras proteins to different microdomains of the plasma membrane is critical for signaling specificity. Here we examine the complex membrane interactions of H-ras with a combination of FRAP on live cells to measure membrane affinity and electron microscopy of intact plasma membrane sheets to spatially map microdomains. We show that three separable forces operate on H-ras at the plasma membrane. The lipid anchor, comprising a processed CAAX motif and two palmitic acid residues, generates one attractive force that provides a high-affinity interaction with lipid rafts. The adjacent hypervariable linker domain provides a second attractive force but for nonraft plasma membrane microdomains. Operating against the attractive interaction of the lipid anchor for lipid rafts is a repulsive force generated by the N-terminal catalytic domain that increases when H-ras is GTP loaded. These observations lead directly to a novel mechanism that explains how H-ras lateral segregation is regulated by activation state: GTP loading decreases H-ras affinity for lipid rafts and allows the hypervariable linker domain to target to nonraft microdomains, the primary site of H-ras signaling.