Structural characterization of glycerophospholipids by combinations of ozone- and collision-induced dissociation mass spectrometry: The next step towards "top-down" lipidomics

The complete structural elucidation of complex lipids, including glycerophospholipids, using only mass spectrometry represents a major challenge to contemporary analytical technologies. Here, we demonstrate that product ions arising from the collision-induced dissociation (CID) of the [M + Na] + adduct ions of phospholipids can be isolated and subjected to subsequent gas-phase ozonolysis-known as ozone-induced dissociation (OzID)-in a linear ion-trap mass spectrometer. The resulting CID/OzID experiment yields abundant product ions that are characteristic of the acyl substitution on the glycerol backbone (i.e., sn-position). This approach is shown to differentiate sn-positional isomers, such as the regioisomeric phosphatidylcholine pair of PC 16:0/18:1 and PC 18:1/16:0. Importantly, CID/OzID provides a sensitive diagnostic for the existence of an isomeric mixture in a given sample. This is of very high value for the analysis of tissue extracts since CID/OzID analyses can reveal changes in the relative abundance of isomeric constituents even within different tissues from the same animal. Finally, we demonstrate the ability to assign carbon-carbon double bond positions to individual acyl chains at specific backbone positions by adding subsequent CID and/or OzID steps to the workflow and that this can be achieved in a single step using a hybrid triple quadrupole-linear ion trap mass spectrometer. This unique approach represents the most complete and specific structural analysis of lipids by mass spectrometry demonstrated to date and is a significant step towards comprehensive top-down lipidomics. This journal is © The Royal Society of Chemistry 2014. Grant Number ARC/DP0986628, ARC/FT110100249, ARC/LP110200648

Bisresorcinols and arbutin derivatives from Grevillea banksii R. Br

This work is part of a series of chemical investigations of the genus Grevillea. Two new arbutin derivatives, seven new bisresorcinols, including a mixture of two isomers, three known flavonol glycosides, and four known resorcinols, including a mixture of two homologous compounds, were isolated from the ethyl acetate extract of the leaves and methanol extract of the stems of Grevillea banksii. The new compounds were identified, on the basis of spectroscopic data, as 6'-O-(3-(2(hydroxymethyl)acryloyloxy)-2-methylpropanoyl)arbutin (1), 6'-O-(2-methylacryloyl)arbutin (2), 5,5'-(4(Z)-dodecen-1,12diyl)bisresorcinol (6), 2'-methyl-5,5'-(4(Z)-tetradecen-1,14-diyl)bisresorcinol (8), 2,2'-di(4-hydroxyprenyl)-5,5'-(6(Z)-tetradecen-1,14-diyl)bisresorcinol (9), 2-(4-acetoxyprenyl)-2'-(4-hydroxyprenyl) 5,5'-(6(Z)-tetradecen-1,14-diyl)bisresorcinol (10), 2-(4-acetoxyprenyl)-2'-(4-hydroxyprenyl)5,5'-(8(Z)-tetradecen-l,14-diyl)bisresorcinol (11), 5,5'-(10(Z)-tetradecen-1-on-diyl)bisresorcinol (12) and 5,5'-(4(Z)-tetradecen-1-on-diyl)bisresorcinol (13).

Approximate Bayesian computation using auxiliary model based estimates

We present a novel approach for developing summary statistics for use in approximate Bayesian computation (ABC) algorithms using indirect infer- ence. We embed this approach within a sequential Monte Carlo algorithm that is completely adaptive. This methodological development was motivated by an application involving data on macroparasite population evolution modelled with a trivariate Markov process. The main objective of the analysis is to compare inferences on the Markov process when considering two di®erent indirect mod- els. The two indirect models are based on a Beta-Binomial model and a three component mixture of Binomials, with the former providing a better ¯t to the observed data.

Lattice mixing and vanishing trapdoors : a framework for fully secure short signatures and more

We propose a framework for adaptive security from hard random lattices in the standard model. Our approach borrows from the recent Agrawal-Boneh-Boyen families of lattices, which can admit reliable and punctured trapdoors, respectively used in reality and in simulation. We extend this idea to make the simulation trapdoors cancel not for a specific forgery but on a non-negligible subset of the possible challenges. Conceptually, we build a compactly representable, large family of input-dependent “mixture” lattices, set up with trapdoors that “vanish” for a secret subset which we hope the forger will target. Technically, we tweak the lattice structure to achieve “naturally nice” distributions for arbitrary choices of subset size. The framework is very general. Here we obtain fully secure signatures, and also IBE, that are compact, simple, and elegant.

Antibacterial anthranilic acid derivatives from Geijera parviflora

Five anthranilic acid derivatives, a mixture I of three new compounds 11′-hexadecenoylanthranilic acid (1), 9′-hexadecenoylanthranilic acid (2), and 7′-hexadecenoylanthranilic acid (3), as well as a new compound 9,12,15-octadecatrienoylanthranilic acid (4) together with a new natural product, hexadecanoylanthranilic acid (5), were isolated from Geijera parviflora Lindl. (Rutaceae). Their structures were elucidated by extensive spectroscopic measurements, and the positions of the double bonds in compounds 1-3 of the mixture I were determined by tandem mass spectrometry employing ozone-induced dissociation. The mixture I and compound 5 showed good antibacterial activity against several Gram-positive strains. © 2013 Elsevier B.V.

Bauxite residue neutralisation precipitate stability in acidic environments

This investigation used a combination of techniques, such as X-ray diffraction, inductively coupled plasma optical emission spectroscopy and infrared spectroscopy, to determine the dissolution mechanisms of the Bayer precipitate and the associated rate of dissolution in acetic, citric and oxalic acid environments. The Bayer precipitate is a mixture of hydrotalcite, calcium carbonate and sodium chloride that forms during the seawater neutralisation of Bayer liquors (waste residue of the alumina industry). The dissolution rate of a Bayer precipitate is found to be dependent on (1) the strength of the organic acid and (2) the number of donating H+ ions. The dissolution mechanism for a Bayer precipitate consists of several steps involving: (1) the dissolution of CaCO3, (2) formation of whewellite (calcium oxalate) when oxalic acid is used and (3) multiple dissolution steps for hydrotalcite that are highly dependent on the pH of solution. The decomposition of the Al–OH hydrotalcite layers resulted in the immediate formation of Al(OH)3, which is stable until the pH decreases below 5.5. This investigation has found that the Bayer precipitate is stable across a wide pH range in the presence of common organic acids found in the rhizosphere, and that initial decomposition steps are likely to be beneficial in supporting plant growth through the release of nutrients such as Ca2þ and Mg2þ.

Occupy Oakland and #oo : uses of Twitter within the Occupy movement

Social media have become crucial tools for political activists and protest movements, providing another channel for promoting messages and garnering support. Twitter, in particular, has been identified as a noteworthy medium for protests in countries including Iran and Egypt to receive global attention. The Occupy movement, originating with protests in, and the physical occupation of, Wall Street, and inspiring similar demonstrations in other U.S. cities and around the world, has been intrinsically linked with social media through location-specific hashtags: #ows for Occupy Wall Street, #occupysf for San Francisco, and so on. While the individual protests have a specific geographical focus-highlighted by the physical occupation of parks, buildings, and other urban areas-Twitter provides a means for these different movements to be linked and promoted through tweets containing multiple hashtags. It also serves as a channel for tactical communications during actions and as a space in which movement debates take place. This paper examines Twitter's use within the Occupy Oakland movement. We use a mixture of ethnographic research through interviews with activists and participant observation of the movements' activities, and a dataset of public tweets containing the #oo hashtag from early 2012. This research methodology allows us to develop a more accurate and nuanced understanding of how movement activists use Twitter by cross-checking trends in the online data with observations and activists' own reported use of Twitter. We also study the connections between a geographically focused movement such as Occupy Oakland and related, but physically distant, protests taking place concurrently in other cities. This study forms part of a wider research project, Mapping Movements, exploring the politics of place, investigating how social movements are composed and sustained, and the uses of online communication within these movements.

Stepwise engineering of a Pichia pastoris D-amino acid oxidase whole cell catalyst

Trigonopsis variabilis D-amino acid oxidase (TvDAO) is a well characterized enzyme used for cephalosporin C conversion on industrial scale. However, the demands on the enzyme with respect to activity, operational stability and costs also vary with the field of application. Processes that use the soluble enzyme suffer from fast inactivation of TvDAO while immobilized oxidase preparations raise issues related to expensive carriers and catalyst efficiency. Therefore, oxidase preparations that are more robust and active than those currently available would enable a much broader range of economically viable applications of this enzyme in fine chemical syntheses. A multi-step engineering approach was chosen here to develop a robust and highly active Pichia pastoris TvDAO whole-cell biocatalyst. As compared to the native T. variabilis host, a more than seven-fold enhancement of the intracellular level of oxidase activity was achieved in P. pastoris through expression optimization by codon redesign as well as efficient subcellular targeting of the enzyme to peroxisomes. Multi copy integration further doubled expression and the specific activity of the whole cell catalyst. From a multicopy production strain, about 1.3 x 103 U/g wet cell weight (wcw) were derived by standard induction conditions feeding pure methanol. A fed-batch cultivation protocol using a mixture of methanol and glycerol in the induction phase attenuated the apparent toxicity of the recombinant oxidase to yield final biomass concentrations in the bioreactor of >or= 200 g/L compared to only 117 g/L using the standard methanol feed. Permeabilization of P. pastoris using 10% isopropanol yielded a whole-cell enzyme preparation that showed 49% of the total available intracellular oxidase activity and was notably stabilized (by three times compared to a widely used TvDAO expressing Escherichia coli strain) under conditions of D-methionine conversion using vigorous aeration. Stepwise optimization using a multi-level engineering approach has delivered a new P. pastoris whole cell TvDAO biocatalyst showing substantially enhanced specific activity and stability under operational conditions as compared to previously reported preparations of the enzyme. The production of the oxidase through fed-batch bioreactor culture and subsequent cell permeabilization is high-yielding and efficient. Therefore this P. pastoris catalyst has been evaluated for industrial purposes.

Recursive pathways to marginal likelihood estimation with prior-sensitivity analysis

We investigate the utility to computational Bayesian analyses of a particular family of recursive marginal likelihood estimators characterized by the (equivalent) algorithms known as "biased sampling" or "reverse logistic regression" in the statistics literature and "the density of states" in physics. Through a pair of numerical examples (including mixture modeling of the well-known galaxy dataset) we highlight the remarkable diversity of sampling schemes amenable to such recursive normalization, as well as the notable efficiency of the resulting pseudo-mixture distributions for gauging prior-sensitivity in the Bayesian model selection context. Our key theoretical contributions are to introduce a novel heuristic ("thermodynamic integration via importance sampling") for qualifying the role of the bridging sequence in this procedure, and to reveal various connections between these recursive estimators and the nested sampling technique.

A new plasmid display technology for the in vitro selection of functional phenotype–genotype linked proteins

Background: Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype–genotype link between the displayed protein and the encoding gene. Results: A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50–DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein–plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype–genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions: A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins

Background Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor κB (NF-κB) p50 to establish a phenotype-genotype link between the displayed protein and the encoding gene. Results A range of model fusion proteins to either the amino- or carboxy-terminus of NF-κB p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-κB p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50-DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein-plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:108 and to enrich to near homogeneity a single functional protein from a phenotype-genotype linked Escherichia coli genomic library using in vitro functional selections. Conclusions A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.

A mass spectrometry study of XCO+, X = Si, Ge : Is SiCO+ a main group carbonyl? Comments on the bonding in ground state SiCO and the Si,C,O (+) potential energy surface

The cation\[Si,C,O](+) has been generated by 1) the electron ionisation (EI) of tetramethoxysilane and 2) chemical ionisation (CI) of a mixture of silane and carbon monoxide. Collisional activation (CA) experiments performed for mass-selected \[Si,C,O](+), generated by using both methods, indicate that the structure is not inserted OSiC+; however, a definitive structural assignment as Si+-CO, Si+-OC or some cyclic variant is impossible based on these results alone. Neutralisation-reionisation (+NR+) experiments for EI-generated \[Si,C,O](+) reveal a small peak corresponding to SiC+, but no detectable SiO+ signal, and thus establishes the existence of the Si+-CO isomer. CCSD(T)//B3LYP calculations employing a triple-zeta basis set have been used to explore the doublet and quartet potential-energy surfaces of the cation, as well as some important neutral states The results suggest that both Si+-CO and Si+ - OC isomers are feasible; however, the global minimum is (2)Pi SiCO+. Isomeric (2)Pi SiOC+ is 12.1 kcal mol(-1) less stable than (2)Pi SiCO+, and all quartet isomers are much higher in energy. The corresponding neutrals Si-CO and Si-OC are also feasible, but the lowest energy Si - OC isomer ((3)A") is bound by only 1.5 kcal mol(-1). We attribute most, if nor all, of the recovery signal in the +NR' experiment to SiCO+ survivor ions. The nature of the bonding in the lowest energy isomers of Si+ -(CO,OC) is interpreted with the aid of natural bond order analyses, and the ground stale bonding of SiCO+ is discussed in relation to classical analogues such as metal carbonyls and ketenes.

Implication of calcium hydroxide in the seawater neutralisation of bauxite refinery liquors

Tricalcium aluminate, hydrocalumite and residual lime have been identified as reversion contributing compounds after the seawater neutralisation of bauxite refinery residues. The formation of these compounds during the neutralisation process is dependent on the concentration of residual lime, pH and aluminate concentrations in the residue slurry. Therefore, the effect of calcium hydroxide (CaOH2) in bauxite refinery liquors was analysed and the degree of reversion monitored. This investigation found that the dissolution of tricalcium aluminate, hydrocalumite and CaOH2 caused reversion and continued to increase the pH of the neutralised residue until a state of equilibrium was reached at a solution pH of 10.5. The dissolution mechanism for each compound has been described and used to demonstrate the implications that this has on reversion in seawater neutralised Bayer liquor. This investigation describes the limiting factors for the dissolution and formation of these trigger compounds as well as confirming the formation of Bayer hydrotalcite (mixture of Mg6Al2(OH)16(CO32-,SO42-)•xH2O and Mg8Al2(OH)12(CO32-,SO42-)•xH2O) as the primary mechanism for reducing reversion during the neutralisation process. This knowledge then allowed for a simple but effective method (addition of magnesium chloride or increased seawater to Bayer liquor ratio) to be devised to reduce reversion occurring after the neutralisation of Bayer liquors. Both methods utilise the formation of Bayer hydrotalcite to permanently (stable in neutralised residue) remove hydroxyl (OH-) and aluminate (Al(OH)4-) ions from solution.

Characterization and novel activation of 72-kDa metalloproteinase in retinal interphotoreceptor matrix and Y-79 cell culture medium

Analysis of bovine interphotoreceptor matrix and conditioned medium from human Y-79 retinoblastoma cells by gelatin SDS-PAGE zymography reveals abundant activity of a 72-kDa M(r) gelatinase. The 72-kDa gelatinase from either source is inhibited by EDTA but not aprotinin or NEM, indicating that it is a metalloproteinase (MMP). The 72-kDa MMP is converted to a 62-kDa species with APMA treatment after gelatin sepharose affinity purification typical of previously described gelatinase MMP-2. The latent 72-kDa gelatinase from either bovine IPM or Y-79 media autoactivates without APMA in the presence of calcium and zinc after 72 hr at 37°C, producing a fully active mixture of proteinase species, 50 (48 in Y-79 medium), 38 and 35 kDa in size. The presence of inhibitory activity was examined in both whole bovine IPM and IPM fractions separated by SDS-PAGE. Whole IPM inhibited gelatinolytic activity of autoactivated Y-79-derived MMP in a dose-dependent manner. Inhibitory activities are observed in two protein fractions of 27-42 and 20-25 kDa. Western blots using antibodies to human tissue inhibitor of metalloproteinase 1 and 2 (TIMP-1 and -2) reveal the presence of two TIMP-1-like proteins at 21 and 29 kDa in inhibitory fractions of the bovine IPM. TIMP-2 was not detected in the inhibitory IPM fractions, consistent with the observed autoactivation of bovine IPM 72-kDa gelatinase. Potential roles for this IPM MMP-TIMP system include physiologic remodelling of the neural retina-RPE cell interface and digestion of shed rod outer segment as well as pathological processes such as retinal detachment, PE cell migration, neovascularization and tumor progression. Cultured Y-79 cells appear to be a good model for studying the production and regulation of this proteinase system.

Combined analysis of categorical and numerical descriptors of Australian groundnut accessions using nonlinear principal component analysis

For users of germplasm collections, the purpose of measuring characterization and evaluation descriptors, and subsequently using statistical methodology to summarize the data, is not only to interpret the relationships between the descriptors, but also to characterize the differences and similarities between accessions in relation to their phenotypic variability for each of the measured descriptors. The set of descriptors for the accessions of most germplasm collections consists of both numerical and categorical descriptors. This poses problems for a combined analysis of all descriptors because few statistical techniques deal with mixtures of measurement types. In this article, nonlinear principal component analysis was used to analyze the descriptors of the accessions in the Australian groundnut collection. It was demonstrated that the nonlinear variant of ordinary principal component analysis is an appropriate analytical tool because subspecies and botanical varieties could be identified on the basis of the analysis and characterized in terms of all descriptors. Moreover, outlying accessions could be easily spotted and their characteristics established. The statistical results and their interpretations provide users with a more efficient way to identify accessions of potential relevance for their plant improvement programs and encourage and improve the usefulness and utilization of germplasm collections.