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.

Candidatus "Scalindua brodae", spec. nov., Candidatus "Scalindua wagneri", spec. nov., two new species of anaerobic ammonium oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus Scalindua brodae and Scalindua wagneri considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus Scalindua sorokinii, was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.

Using the flexibility index to compare batch and continuous activated sludge processes

This paper considers the question of which is better: the batch or the continuous activated sludge processes? It is an important question because dissension still exists in the wastewater industry as to the relative merits of each of the processes. A review of perceived differences in the processes from the point of view of two related disciplines, process engineering and biotechnology, is presented together with the results of previous comparative studies. These reviews highlight possible areas where more understanding is required. This is provided in the paper by application of the flexibility index to two case studies. The flexibility index is a useful process design tool that measures the ability of the process to cope with long term changes in operation.

Metabolic model for glycogen-accumulating organisms in anaerobic/aerobic activated sludge systems

Glycogen-accumulating organisms (GAO) have the potential to directly compete with polyphosphate-accumulating organisms (PAO) in EBPR systems as both are able to take up VFA anaerobically and grow on the intracellular storage products aerobically. Under anaerobic conditions GAO hydrolyse glycogen to gain energy and reducing equivalents to take up VFA and to synthesise polyhydroxyalkanoate (PHA). In the subsequent aerobic stage, PHA is being oxidised to gain energy for glycogen replenishment (from PHA) and for cell growth. This article describes a complete anaerobic and aerobic model for GAO based on the understanding of their metabolic pathways. The anaerobic model has been developed and reported previously, while the aerobic metabolic model was developed in this study. It is based on the assumption that acetyl-CoA and propionyl-CoA go through the catabolic and anabolic processes independently. Experimental validation shows that the integrated model can predict the anaerobic and aerobic results very well. It was found in this study that at pH 7 the maximum acetate uptake rate of GAO was slower than that reported for PAO in the anaerobic stage. On the other hand, the net biomass production per C-mol acetate added is about 9% higher for GAO than for PAO. This would indicate that PAO and GAO each have certain competitive advantages during different parts of the anaerobic/aerobic process cycle. (C) 2002 Wiley Periodicals, Inc.

Synthesis and characterization of delta-atracotoxin-ar1a, the lethal neurotoxin from venom of the Sydney funnel-web spider (Atrax robustus)

delta-Atracotoxin-Ar1a (delta-ACTX-Ar1a) is the major polypeptide neurotoxin isolated from the venom of the male Sydney funnel-web spider, Atrax robustus. This neurotoxin targets both insect and mammalian voltage-gated sodium channels, where it competes with scorpion alpha-toxins for neurotoxin receptor site-3 to slow sodium-channel inactivation. Progress in characterizing the structure and mechanism of action of this toxin has been hampered by the limited supply of pure toxin from natural sources. In this paper, we describe the first successful chemical synthesis and oxidative refolding of the four-disulfide bond containing delta-ACTX-Ar1a. This synthesis involved solid-phase Boc chemistry using double coupling, followed by oxidative folding of purified peptide using a buffer of 2 M GdnHCl and glutathione/glutathiol in a 1:1 mixture of 2-propanol (pH 8.5). Successful oxidation and refolding was confirmed using both chemical and pharmacological characterization. Ion spray mass spectrometry was employed to confirm the molecular weight. H-1 NMR analysis showed identical chemical shifts for native and synthetic toxins, indicating that the synthetic toxin adopts the native fold. Pharmacological studies employing whole-cell patch clamp recordings from rat dorsal root ganglion neurons confirmed that synthetic delta-ACTX-Ar1a produced a slowing of the sodium current inactivation and hyperpolarizing shifts in the voltage-dependence of activation and inactivation similar to native toxin. Under current clamp conditions, we show for the first time that delta-ACTX-Ar1a produces spontaneous repetitive plateau potentials underlying the clinical symptoms seen during envenomation. This successful oxidative refolding of synthetic delta-ACTX-Ar1a paves the way for future structure-activity studies to determine the toxin pharmacophore.

A comprehensive insight into floc characteristics and their impact on compressibility and settleability of activated sludge

This paper presents a comprehensive study of sludge floc characteristics and their impact on compressibility and settleability of activated sludge in full scale wastewater treatment processes. The sludge flocs were characterised by morphological (floc size distribution, fractal dimension, filament index), physical (flocculating ability, viscosity, hydrophobicity and surface charge) and chemical (polymeric constituents and metal content) parameters. Compressibility and settleability were defined in terms of the sludge volume index (SVI) and zone settling velocity (ZSV). The floc morphological and physical properties had important influence on the sludge compressibility and settleability. Sludges containing large flocs and high quantities of filaments, corresponding to lower values of fractal dimension (D-f), demonstrated poor compressibility and settleability. Sludge flocs with high flocculating ability had lower SVI and higher ZSV, whereas high values of hydrophobicity, negative surface charge and viscosity of the sludge flocs correlated to high SVI and low ZSV. The quantity of the polymeric compounds protein. humic substances and carbohydrate in the sludge and the extracted extracellular polymeric substances (EPS) had significant positive correlations with SVI. The ZSV was quantitatively independent of the polymeric constituents. High concentrations of the extracted EPS were related to poor compressibility and settleability. The cationic ions Ca, Mg, Al and Fe in the sludge improved significantly the sludge compressibility and settleability. (C) 2003 Elsevier Science B.V. All rights reserved.

The influence of key chemical constituents in activated sludge on surface and flocculating properties

This paper examines the influence of the chemical constituents of activated sludge and extracted extracellular polymeric substances (EPS) on the surface properties, hydrophobicity, surface charge (SC) and flocculating ability (FA) of activated sludge floes. Activated sludge samples from 7 different full-scale wastewater treatment plants were examined. Protein and humic substances were found to be the dominant polymeric compounds in the activated sludges and the extracted EPS, and they significantly affected the FA and surface properties, hydrophobicity and SC, of the sludge floes. The polymeric compounds proteins, humic substances and carbohydrates in the sludge floes and the extracted EPS contributed to the negative SC, but correlated negatively to the hydrophobicity of sludge floes. The quantity of protein and carbohydrate within the sludge and the extracted EPS was correlated positively to the FA of the sludge floes, while increased amounts of humic substances resulted in lower FA. In contrast, increased amounts of total extracted EPS had a negative correlation to FA. The results reveal that the quality and quantity of the polymeric compounds within the sludge floes is more informative, with respect to understanding the mechanisms involved in flocculation, than if only the extracted EPS are considered. This is an important finding as it indicates that extracting EPS may be insufficient to characterise the EPS. This is due to the low extraction efficiency and difficulties involved in the separation of EPS from other organic compounds. Correlations were observed between the surface properties and FA of the sludge floes., This confirms that the surface properties of the, sludge flocs play an important role in the bioflocculation process but that also other interactions like polymer entanglement are important. (C) 2002 Elsevier Science Ltd. All rights reserved.

Impacts of structural characteristics on activated sludge floc stability

Activated sludge samples from seven full-scale plants were investigated in order to determine the relationship between floc structure and floc stability. Floc stability was determined by shear sensitivity and floc strength. Floc structure was considered in terms of two size scales, the micro- and macrostructure. The microstructure refers to the organization of the floc components, such as the individual microorganisms. The macrostructure refers to the overall floc. The floc macrostructure was characterized by filament index, sludge volume index, size, and fractal dimension. It had a significant impact on floc stability. Large and open floes with low fractal dimensions containing large number of filaments were more shear sensitive and had lower floc strength compared to small and dense floes. Fluorescent in situ hybridization analysis indicated that the organization of the bacterial cells might also have an effect on the floc stability. (C) 2003 Elsevier Ltd. All rights reserved.

Relationship between flocculation of activated sludge and composition of extracellular polymeric substances

Activated sludge floes are a flocculated mass of microorganisms, extracellular polymeric substances (EPS) and adsorbed organic and inorganic material. The structure of the floes is very heterogeneous and floes with very different properties and morphologies may occur, depending on the conditions in the activated sludge treatment plant and wastewater composition. Present thinking suggests that cations, such as calcium, create cationic bridges with EPS excreted by the bacteria and thereby hold the various floe constituents together. However, due to the complex and heterogeneous nature of activated sludge, the mechanisms have neither been thoroughly investigated nor successfully quantified. A better understanding and description of the biological flocculation process is necessary in order to establish more efficient operational strategies. The main aim of this study was to get a comprehensive and unique insight into the floe properties of activated sludge and to assess the relative impact of chemical and physical parameters. A variety of sludges from full scale treatment plants with different settling properties were characterised. The interrelationships between floe parameters such as composition of EPS, surface properties and floe structure, and their effect on the flocculation and separation properties were assessed. The results indicate that the EPS, both in terms of quantity and quality, are very important for the floe properties of the activated sludge. However, presence of filaments may alter the physical properties of the floes considerably. The EPS showed positive correlations to sludge volume index (SVI) if only sludges with low or moderate numbers of filaments were included. The surface properties were more affected by the composition of the EPS than by the number of filaments. The EPS showed positive correlation to negative surface charge and a negative correlation to relative hydrophobicity and flocculation ability. The negative correlation between flocculation ability and amount of EPS was surprising. The shear sensitivity, measured as degree of erosion of floes when subjected to shear, was more affected by floe size and number of filaments than amount of EPS.

χ-conopeptide MrIA partially overlaps desipramine and cocaine binding sites on the human norepinephrine transporter

The interactions of chi-conopeptide MrIA with the human norepinephrine transporter (hNET) were investigated by determining the effects of hNET point mutations on the inhibitory potency of MrIA. The mutants were produced by site-directed mutagenesis and expressed in COS-7 cells. The potency of MrIA was greater for inhibition of uptake by hNET of [H-3] norepinephrine (K-i 1.89 muM) than [H-3] dopamine (K-i 4.33 muM), and the human dopamine transporter and serotonin transporter were not inhibited by MrIA ( to 7 muM). Of 18 mutations where hNET amino acid residues were exchanged with those of the human dopamine transporter, MrIA had increased potency for inhibition of [H-3] norepinephrine uptake for three mutations ( in predicted extracellular loops 3 and 4 and transmembrane domain (TMD) 8) and decreased potency for one mutation (in TMD6 and intracellular loop (IL) 3). Of the 12 additional mutations in TMDs 2, 4, 5, and 11 and IL1, three mutations (in TMD2 and IL1) had reduced MrIA inhibitory potency. All of the other mutations tested had no influence on MrIA potency. A comparison of the results with previous data for desipramine and cocaine inhibition of norepinephrine uptake by the mutant hNETs reveals that MrIA binding to hNET occurs at a site that is distinct from but overlaps with the binding sites for tricyclic antidepressants and cocaine.

Therapeutic potential of venom peptides

Venomous animals have evolved a vast array of peptide toxins for prey capture and defence. These peptides are directed against a wide variety of pharmacological targets, making them an invaluable source of ligands for studying the properties of these targets in different experimental paradigms. A number of these peptides have been used in vivo for proof-of-concept studies, with several having undergone preclinical or clinical development for the treatment of pain, diabetes, multiple sclerosis and cardiovascular diseases. Here we survey the pharmacology of venom peptides and assess their therapeutic prospects.

Compositional changes of Australia-grown Western Schley pecans [Carya illinoinensis (Wangenh.) K. Koch] during maturation

Changes in composition during the maturation of Western Schley pecans [Carya illinoinensis (Wangenh.) K. Koch] grown in Australia were investigated. Pecans of different maturity levels were collected at monthly intervals between March and June in. 1999 and 2000 and analyzed for the concentrations of moisture, total lipid, sucrose, raffinose, protein, and the minerals aluminum, boron, calcium, copper, iron, potassium, magnesium, manganese, sodium, phosphorus, sulfur, and zinc. Moisture, total lipid, and calcium contents changed significantly (p < 0.05) with harvest time and maturity, whereas the other components did not. Western Schley pecans grown in Australia should be harvested after the shuck has opened and it is either green or brown in color to maximize total lipid content and quality. This occurred after May 11 in 1999 and after May 17 in 2000.

The peroxisome proliferator-activated receptor beta/delta agonist, GW501516, regulates the expression of genes involved in lipid catabolism and energy uncoupling in skeletal muscle cells

Lipid homeostasis is controlled by the peroxisome proliferator-activated receptors (PPARalpha, -beta/delta, and -gamma) that function as fatty acid-dependent DNA-binding proteins that regulate lipid metabolism. In vitro and in vivo genetic and pharmacological studies have demonstrated PPARalpha regulates lipid catabolism. In contrast, PPARgamma regulates the conflicting process of lipid storage. However, relatively little is known about PPARbeta/delta in the context of target tissues, target genes, lipid homeostasis, and functional overlap with PPARalpha and -gamma. PPARbeta/delta, a very low-density lipoprotein sensor, is abundantly expressed in skeletal muscle, a major mass peripheral tissue that accounts for approximately 40% of total body weight. Skeletal muscle is a metabolically active tissue, and a primary site of glucose metabolism, fatty acid oxidation, and cholesterol efflux. Consequently, it has a significant role in insulin sensitivity, the blood-lipid profile, and lipid homeostasis. Surprisingly, the role of PPARbeta/delta in skeletal muscle has not been investigated. We utilize selective PPARalpha, -beta/delta, -gamma, and liver X receptor agonists in skeletal muscle cells to understand the functional role of PPARbeta/delta, and the complementary and/or contrasting roles of PPARs in this major mass peripheral tissue. Activation of PPARbeta/delta by GW501516 in skeletal muscle cells induces the expression of genes involved in preferential lipid utilization, beta-oxidation, cholesterol efflux, and energy uncoupling. Furthermore, we show that treatment of muscle cells with GW501516 increases apolipoprotein-A1 specific efflux of intracellular cholesterol, thus identifying this tissue as an important target of PPARbeta/delta agonists. Interestingly, fenofibrate induces genes involved in fructose uptake, and glycogen formation. In contrast, rosiglitazone-mediated activation of PPARgamma induces gene expression associated with glucose uptake, fatty acid synthesis, and lipid storage. Furthermore, we show that the PPAR-dependent reporter in the muscle carnitine palmitoyltransferase-1 promoter is directly regulated by PPARbeta/delta, and not PPARalpha in skeletal muscle cells in a PPARgamma coactivator-1-dependent manner. This study demonstrates that PPARs have distinct roles in skeletal muscle cells with respect to the regulation of lipid, carbohydrate, and energy homeostasis. Moreover, we surmise that PPARgamma/delta agonists would increase fatty acid catabolism, cholesterol efflux, and energy expenditure in muscle, and speculate selective activators of PPARbeta/delta may have therapeutic utility in the treatment of hyperlipidemia, atherosclerosis, and obesity.

Water sorption into poly[(2-hydroxyethyl methacrylate)-co-(1-vinyl-2-pyrrolidone]at 310 K

Poly(2-hydroxyethyl methacrylate) and copolymers of 2-hydroxyethyl methacrylate (HEMA) and 1-vinyl-2-pyrrolidone (VP) in the form of cylindrical samples (approximate to8mm x 20mm) have been prepared and the sorption of water into these cylinders has been studied by the mass-uptake methods and by magnetic-resonance imaging. The equilibrium water contents for the cylinders were found to vary systematically with the copolymer composition. Diffusion of water into the cylinders was found to follow Fickian behaviour for cylinders with high HEMA contents, with the diffusion coefficients obtained from mass-uptake studies dependent on the copolymer composition, varying from 1.7 x 10(-11) m(2) s(-1) for poly(HEMA) to 2.0 x 10(-11) m(2) s(-1) for poly(HEMA-co-VP) with a composition of 1:1. However, NMR-imaging studies showed that, while the profiles of the water diffusion fronts for cylinders with high HEMA contents were Fickian, that for the 1:1 copolymer was not and indicated that the mechanism was Case III. The polymers which were rich in VP were characterized by a water-sorption process which follows Case-III behaviour. (C) 2003 Society of Chemical Industry.