Nanoscale Magnetic Arrays through Block Copolymer Templating of Polyoxometalates.

Magnetic nanoarrays promise to enable new energy-efficient computations based on spintronics or magnonics. In this work, we present a block copolymer-assisted strategy for fabricating ordered magnetic nanostructures on silicon and permalloy substrates. Block copolymer micelle-like structures were used as a template in which polyoxometalate (POM) clusters could assemble in an opal-like structure. A combination of microscopy and scattering techniques was used to confirm the structural and organizational features of the fabricated materials. The magnetic properties of these materials were investigated by polarized neutron reflectometry, nuclear magnetic resonance, and magnetometry measurements. The data show that a magnetic structural design was achieved and that a thin layer of patterned POMs strongly influenced an underlying permalloy layer. This work demonstrates that the bottom-up pathway is a potentially viable method for patterning magnetic substrates on a sub-100 nm scale, toward the magnetic nanostructures needed for spintronic or magnonic crystal devices.

Causal mediation analysis with multiple mediators.

In diverse fields of empirical research-including many in the biological sciences-attempts are made to decompose the effect of an exposure on an outcome into its effects via a number of different pathways. For example, we may wish to separate the effect of heavy alcohol consumption on systolic blood pressure (SBP) into effects via body mass index (BMI), via gamma-glutamyl transpeptidase (GGT), and via other pathways. Much progress has been made, mainly due to contributions from the field of causal inference, in understanding the precise nature of statistical estimands that capture such intuitive effects, the assumptions under which they can be identified, and statistical methods for doing so. These contributions have focused almost entirely on settings with a single mediator, or a set of mediators considered en bloc; in many applications, however, researchers attempt a much more ambitious decomposition into numerous path-specific effects through many mediators. In this article, we give counterfactual definitions of such path-specific estimands in settings with multiple mediators, when earlier mediators may affect later ones, showing that there are many ways in which decomposition can be done. We discuss the strong assumptions under which the effects are identified, suggesting a sensitivity analysis approach when a particular subset of the assumptions cannot be justified. These ideas are illustrated using data on alcohol consumption, SBP, BMI, and GGT from the Izhevsk Family Study. We aim to bridge the gap from "single mediator theory" to "multiple mediator practice," highlighting the ambitious nature of this endeavor and giving practical suggestions on how to proceed.

On regression adjustment for the propensity score.

Propensity scores are widely adopted in observational research because they enable adjustment for high-dimensional confounders without requiring models for their association with the outcome of interest. The results of statistical analyses based on stratification, matching or inverse weighting by the propensity score are therefore less susceptible to model extrapolation than those based solely on outcome regression models. This is attractive because extrapolation in outcome regression models may be alarming, yet difficult to diagnose, when the exposed and unexposed individuals have very different covariate distributions. Standard regression adjustment for the propensity score forms an alternative to the aforementioned propensity score methods, but the benefits of this are less clear because it still involves modelling the outcome in addition to the propensity score. In this article, we develop novel insights into the properties of this adjustment method. We demonstrate that standard tests of the null hypothesis of no exposure effect (based on robust variance estimators), as well as particular standardised effects obtained from such adjusted regression models, are robust against misspecification of the outcome model when a propensity score model is correctly specified; they are thus not vulnerable to the aforementioned problem of extrapolation. We moreover propose efficient estimators for these standardised effects, which retain a useful causal interpretation even when the propensity score model is misspecified, provided the outcome regression model is correctly specified.

Methods for dealing with time-dependent confounding.

Longitudinal studies, where data are repeatedly collected on subjects over a period, are common in medical research. When estimating the effect of a time-varying treatment or exposure on an outcome of interest measured at a later time, standard methods fail to give consistent estimators in the presence of time-varying confounders if those confounders are themselves affected by the treatment. Robins and colleagues have proposed several alternative methods that, provided certain assumptions hold, avoid the problems associated with standard approaches. They include the g-computation formula, inverse probability weighted estimation of marginal structural models and g-estimation of structural nested models. In this tutorial, we give a description of each of these methods, exploring the links and differences between them and the reasons for choosing one over the others in different settings.

Missing at random: a stochastic process perspective.

We offer a natural and extensible measure-theoretic treatment of missingness at random. Within the standard missing-data framework, we give a novel characterization of the observed data as a stopping-set sigma algebra. We demonstrate that the usual missingness-at-random conditions are equivalent to requiring particular stochastic processes to be adapted to a set-indexed filtration. These measurability conditions ensure the usual factorization of likelihood ratios. We illustrate how the theory can be extended easily to incorporate explanatory variables, to describe longitudinal data in continuous time, and to admit more general coarsening of observations.

The temperature optima of enzymes: a new perspective on an old phenomenon.

Careful analysis of the dependence of enzyme activity on assay temperature has revealed that some enzymes might have real temperature optima in which the decrease in catalytic rate at temperatures above the optimum is not primarily a result of irreversible thermal inactivation. The 'equilibrium model' has been formulated to describe genuine temperature optima, and to suggest a simple experimental method by which to distinguish these cases from those in which enzyme instability is the major determinant of temperature optima.

Investigating the effects of long-term dornase alfa use on lung function using registry data.

BACKGROUND: Dornase alfa (DNase) is one of the commonest cystic fibrosis (CF) treatments and is often used for many years. However, studies have not evaluated the effectiveness of its long-term use. We aimed to use UK CF Registry data to investigate the effects of one-, two-, three-, four- and five-years of DNase use on lung function to see if the benefits of short-term treatment use are sustained long term. METHODS: We analysed data from 4,198 people in the UK CF Registry from 2007 to 2015 using g-estimation. By controlling for time-dependent confounding we estimated the effects of long-term DNase use on percent predicted FEV1 (ppFEV1) and investigated whether the effect differed by ppFEV1 at treatment initiation or by age. RESULTS: Considering the population as a whole, there was no significant effect of one-year's use of DNase; change in ppFEV1 over one year was -0.1% in the treated compared to the untreated (p = 0.51) and this did not change with long-term use. However, treatment was estimated to be more beneficial in people with lower lung function (p < 0.001); those with ppFEV1 < 70% at treatment initiation, showed an increase in lung function over one year that was sustained out to five years. The estimated effect of DNase did not depend on age (p = 0.35). CONCLUSIONS: DNase improved lung function in individuals with reduced lung function, bringing a step-change in lung function, but no change in the slope of decline. There was no evidence for a benefit in lung function in those initiating treatment with ppFEV1 > 70%.

[Fluoride concentrations in typical Brazilian foods and in infant foods]. / Concentração de fluoreto em arroz, feijão e alimentos infantis industrializados.

OBJECTIVE: To determine fluoride concentrations in the typical Brazilian meal (rice with beans) and in processed infant foods, and to estimate their contribution towards dental fluorosis. METHODS: The foods were purchased at supermarkets in the cities of Piracicaba and Campinas, Southeastern Brazil. The processed infant foods were bought in 2001 and the rice and beans in 2003, and they were analyzed immediately. Three brands of rice, three brands of beans and 36 samples of infant foods were analyzed, divided into five groups: ready-to-eat, porridges, formulated foods, powdered milk and others. For the rice and beans, fluoride concentrations were determined in the raw grains and after they were cooked with fluoridated (0.7 ppm) or distilled water. All the fluoride analyses were performed using a specific electrode. A dose of 0.07 mg/kg/day was considered to be the upper limit of fluoride exposure in terms of fluorosis risks. RESULTS: The fluoride concentrations found in the grains of rice and beans were low. However, they increased 100 to 200-fold after cooking in fluoridated water. Even so, they were lower than what is found in some processed foods. A meal of rice and beans prepared with fluoridated water would be responsible for 29% of the threshold dose for fluoride intake in terms of acceptable fluorosis; the contribution from some processed foods reaches 45%. CONCLUSIONS: The typical Brazilian food, even when prepared with fluoridated water, is safer in terms of the risk of dental fluorosis than are some processed infant foods.

Thermostable beta-glucosidase and beta-xylosidase from Thermotoga sp. strain FjSS3-B.1.

A beta-D-glucosidase and a beta-D-xylosidase were purified to homogeneity from the thermophilic eubacterium Thermotoga sp. strain FjSS3-B.1. Both enzymes were largely cell-associated and were probably associated with the 'toga' structures of this organism. Using SDS-PAGE they were found to have M(r) values of 75,000 and 92,000, respectively. The beta-glucosidase was active against cellobiose, sophorose and gentiobiose with Km values of 59 mM, 2.7 mM and 6 mM, respectively. The beta-xylosidase had a Km of 2 mM for xylobiose, showed strong activity against p-nitrophenyl alpha-L-arabinofuranoside and p-nitrophenyl alpha-L-arabinopyranoside, but was subject to strong substrate inhibition by p-nitrophenyl beta-D-xylopyranoside. Both enzymes were extremely thermostable, with half-lives of several hours at 98 degrees C. The thermostabilities of both enzymes were increased further by the addition of either trehalose or betaine.

Steady state kinetics of the glutamate dehydrogenase from an archaebacterial extreme thermophile, isolate AN1.

A steady state kinetic study was carried out with the glutamate dehydrogenase from the thermophilic, archaebacterial isolate AN1. Initial velocity studies of the oxidative deamination reaction showed the mechanism is sequential and indicated that the order of substrate addition is random, while inhibition studies with products and substrate analogues suggested a strong preference for NADP+ to bind first. Initial velocity studies of the reductive amination reaction showed that the mechanism is sequential and indicated that the order of substrate addition is random, while product inhibition studies and the effect of substrate saturation on the initial velocity suggested that the preferred order of substrate addition is NADPH, 2-ketoglutarate, ammonia.

Purification and some properties of an extracellular protease (caldolysin) from an extreme thermophile.

An extracellular metal-chelator-sensitive lytic protease (assigned the trivial name caldolysin) was isolated from a Thermus-like organism, Thermus T-351. Caldolysin was purified by affinity chromatography on Cbz-D-phenylalanine-TETA-Sepharose 4B and by gel filtration. It contained 13% carbohydrate, a single zinc atom, had a molecular weight of approx. 21,000, a pH optimum of 8 (azocasein substrate), and an isoelectric point of about 8.5. It was capable of hydrolysing many soluble and insoluble protein substrates, including collagen and elastin. No esterase activity was detected, and small peptides (less than four amino acids) and low molecular weight chromogenic substrates were not hydrolysed. A specificity for small aliphatic amino acids on either side of the splitting point was indicated. Caldolysin lysed heat-killed Gram-negative bacterial cells, but had little effect on Gram-positive organisms. Caldolysin exhibited a very high degree of thermostability (t 1/2(80 degrees C) approximately 30 h, t 1/2(90 degrees C) = 1 h). The stability (but not activity) was shown to be dependent on the presence of Ca2+ (t 1/2(75 degrees C, 10 mM calcium) greater than 193 h; t 1/2(75 degrees C, no calcium) = 4.8 min). None of the other metal ions tested (Co, Zn, Sr, Mg, Ba and Cu) was as effective as calcium in conferring thermostability of EDTA-treated caldolysin. Caldolysin was stable at room temperature in moderately acid and alkaline (pH 5 to 11) buffers for periods of greater than 90 days. Little loss of enzyme activity was detected after the incubation of caldolysin at 18 degrees C in the presence of 8 M urea, 6 M guanidine hydrochloride or 1% sodium dodecyl sulphate for 24 h. At 75 degrees C, the activity half-life of caldolysin in these denaturing agents was reduced to approx. 1 h, 1 h and more than 5 h, respectively.

Properties and stabilization of an extracellular alpha-glucosidase from the extremely thermophilic archaebacteria Thermococcus strain AN1: enzyme activity at 130 degrees C.

An extracellular alpha-glucosidase from the thermophilic archaebacterium Thermococcus strain AN1 was purified 875-fold in five steps (Hiload Q-Sepharose, phenyl Sepharose, HPHT-hydroxyapatite, gel filtration and Mono Q chromatography) with a yield of 4%. It is a monomer with a molecular mass of about 60 kDa and a pI around 5. At 98 degrees C, the purified enzyme in buffer has a half-life around 35 min, which is increased to around 215 min in presence of 1% (w/v) dithiothreitol and 1% (w/v) BSA. Dithiothreitol (1%, w/v) and BSA (0.4%, w/v) also substantially increase the enzyme activity. The Km at 75 degrees C is 0.41 mM with pNP-alpha-D-glucopyranoside as substrate. The substrate preference of the enzyme is: pNP-alpha-D-glucoside > nigerose > panose > palatinose > isomaltose > maltose and turanose. No activity was found against starch, pullulan, amylose, maltotriose, maltotetraose, isomaltotriose, cellobiose and beta-gentiobiose. A variety of techniques including immobolization (e.g., on epoxy and glass beads), chemical modification (cross- and cocross-linking) and the use of additives (including polyhydroxylic molecules, BSA, salts, etc.) were applied to enhance stability at temperatures above 100 degrees C. The half-life could be increased from about 4 min at 100 degrees C to 30-60 min at 130 degrees C in presence of 90% (w/v) sorbitol, 1% (w/v) dithiothreitol and 1% (w/v) BSA, and by cross-linking with BSA in the presence of 90% (w/v) sorbitol. The stabilized enzyme showed good activity at 130 degrees C.

Characterisation of arginase from the extreme thermophile 'Bacillus caldovelox'.

A thermostable arginase (L-arginine amidinohydrolase, EC 3.5.3.1) was purified from the extreme thermophile 'Bacillus caldovelox' (DSM 411) by a procedure including DEAE-Sepharose chromatography, and gel filtration, anion exchange and hydrophobic-interaction fast-protein liquid chromatography, with substantial retention of the metal ion cofactor. The purified enzyme is a hexamer with a subunit Mr of 31,000 +/- 2000 and contains greater than or equal to 1 Mn atom per subunit. Maximum activation on incubation with Mn2+ is 29%. Activity is optimal at pH 9 and at 60 degrees C the Km for arginine is 3.4 mM and Ki(ornithine) is 0.55 mM. Incubation in 0.1 M Mops/NaOH buffer (pH 7) causes rapid inactivation at 60 degrees C (t1/2 (half life) = 4.5 min) and individually 0.1 mM Mn2+ or 1 mg/ml BSA (bovine serum albumin) increase the t1/2 of arginase activity 4-fold, but combined they produce greater than 1000-fold increase and a t1/2 = 105 min at 95 degrees C. Aspartic acid and other species that bind Mn2+ can replace BSA, and it is suggested that arginase can be inactivated by free Mn2+. A strong chelating agent causes inactivation without subunit dissociation, but arginase dissociates rapidly at pH 2.5. Reassociation occurs at pH 9 and is unusual in that it does not require Mn2+.

Glutamate dehydrogenase from the extremely thermophilic archaebacterial isolate AN1.

Glutamate dehydrogenase (L-glutamate:NADP+ oxidoreductase, deaminating and transaminating, EC 1.4.1.4) was purified to homogeneity from the extremely thermophilic archaebacterial isolate AN1 (a member of the Thermococcales). The enzyme comprised a large proportion of the soluble cell protein (11%) and was purified in high yield. The molecular mass of the native enzyme was 204 kDa, while the subunit molecular mass was 47 kDa, indicating a tetrameric structure. The enzyme is specific for NADP(H) rather than NAD(H) by a factor of greater than 1000, as judged by Vmax/Km. Glutamate synthase activity was about 50% of the glutamate dehydrogenase activity. Activity was markedly enhanced by calcium, magnesium and manganese ions. The enzyme was highly thermostable with t1/2 values of 12.5 h and 47 min at 90 degrees C and 103 degrees C, respectively.

Enzyme activity down to -100 degrees C.

The activities of two enzymes, beef liver catalase (EC 1.11.1.6) and calf intestine alkaline phosphatase (EC 3.1.3.1), have been measured down to -97 degrees C and -100 degrees C, respectively. Enzyme activity has not previously been measured at such low temperatures. For catalase, the cryosolvents used were methanol:ethylene glycol:water (70:10:20) and DMSO:ethylene glycol:water (60:20:20). For alkaline phosphatase, methanol:ethylene glycol:water (70:10:20) was used. All of the Arrhenius plots were linear over the whole of the temperature range examined. Since the lowest temperatures at which activity was measured are well below the dynamic transition observed for proteins, the results indicate that the motions which cease below the dynamic transition are not essential for enzyme activity. In all cases the use of cryosolvent led to substantial increases in Arrhenius activation energies, and this imposed practical limitations on the measurement of enzyme activity below -100 degrees C. At even lower temperatures, enzyme activity may be limited by the effect of solvent fluidity on substrate/product diffusion, but overall there is no evidence that any intrinsic enzyme property imposes a lower temperature limit for enzyme activity.

Immunological evidence for the capability of free-living Rhizobium japonicum to synthesize a portion of a nitrogenase component.

Immunodiffusion tests conducted under aerobic conditions demonstrated that cross-reactive material to antiserum prepared against the Mo-Fe protein component of nitrogenase from soybean nodule bacteroids was detectable in extracts of free-living Rhizobium japonicum cells cultured in a standard medium under: aerobic conditions; aerobic conditions with nitrate; aerobic conditions with ammonia; anaerobic conditions with nitrate; and anaerobic conditions with nitrate and ammonia. The most intense precipitin bands resulted from cross-reaction of the antiserum with extracts of cells cultured anaerobically with nitrate or anaerobically with ammonia and nitrate. Immunodiffusion experiments with crude bacteroid extract and purified Mo-Fe protein revealed a greater number of precipitin bands in tests conducted under aerobic conditions than those conducted under anaerobic conditions. These results indicate that some of the cross-reactive material observed under aerobic conditions resulted from breakdown of the Mo-Fe protein. Bacteroid extracts of nodules from plants supplied with ammonia exhibited only a trace of nitrogenase activity. The addition of an excess of the Fe protein component of nitrogenase, however, resulted in 270-fold enhancement of activity indication the presence of active Mo-Fe protein in these extracts. Our experiments together with results published elsewhere provide evidence that the genetic information for synthesis of a part of the Mo-Fe component of nitrogenase is carried by Rhizobium.

Sequence of the gene encoding a highly thermostable neutral proteinase from Bacillus sp. strain EA1: expression in Escherichia coli and characterisation.

The gene for a highly thermostable neutral proteinase (Npr) was isolated from Bacillus sp. strain EA1 by the polymerase chain reaction using consensus primers based on the sequences of npr genes from related species. The gene was sequenced and shown to be closely related to a neutral proteinase gene from Bacillus caldolyticus strain YP-T; the mature form of the enzyme differing by only a single amino acid. Enzyme samples were prepared from both the native organisms and also from recombinant Escherichia coli expressing the two npr genes. The proteinase from strain EA1 was shown to be significantly more thermostable than that from B. caldolyticus and that this difference is the result of a single amino acid substitution which is situated proximal to a region of the enzyme known to be crucial to conferring thermal stability. The phylogenetic relationship of EA1 to other Bacilli is also described.

Calcium-mediated thermostability in the subtilisin superfamily: the crystal structure of Bacillus Ak.1 protease at 1.8 A resolution.

Proteins of the subtilisin superfamily (subtilases) are widely distributed through many living species, where they perform a variety of processing functions. They are also used extensively in industry. In many of these enzymes, bound calcium ions play a key role in protecting against autolysis and thermal denaturation. We have determined the crystal structure of a highly thermostable protease from Bacillus sp. Ak.1 that is strongly stabilized by calcium. The crystal structure, determined at 1.8 A resolution (R=0. 182, Rfree=0.247), reveals the presence of four bound cations, three Ca(2+) and one Na(+). Two of the Ca(2+) binding sites, Ca-1 and Ca-2, correspond to sites also found in thermitase and the mesophilic subtilisins. The third calcium ion, however, is at a novel site that is created by two key amino acid substitutions near Ca-1, and has not been observed in any other subtilase. This site, acting cooperatively with Ca-1, appears to give substantially enhanced thermostability, compared with thermitase. Comparisons with the mesophilic subtilisins also point to the importance of aromatic clusters, reduced hydrophobic surface and constrained N and C termini in enhancing the thermostability of thermitase and Ak.1 protease. The Ak.1 protease also contains an unusual Cys-X-Cys disulfide bridge that modifies the active site cleft geometry.

Characterisation of a thermostable pepstatin-insensitive acid proteinase from a Bacillus sp.

An acid proteinase, Wai 21a, produced by a thermophilic Bacillus species (strain Wai 21a) has been purified to homogeneity by cation-exchange chromatography, phenyl-Sepharose chromatography and anion-exchange chromatography. A pI of 3.8 was determined by isoelectric focussing. The protein contained some associated carbohydrate (20 mol hexose equiv/mol proteinase). Optimal proteolytic activity was observed at pH 3.0 (at 60 degrees C). The Leu15-Tyr16 bond was the major site of hydrolysis for the oxidized B chain of insulin. Enzyme activity was not affected by inhibitors of the cysteine, metallo or serine class of proteinases. The aspartate proteinase inhibitor, pepstatin, did not inhibit enzyme activity. Inhibition of enzyme activity by 1,2-epoxy-3-(p-nitrophenoxy)-propane indicated the presence of at least one carboxyl group essential to the catalytic mechanism of the enzyme. Proteinase activity was inhibited by diazoacetyl-DL-norleucine methyl ester in a slow and non-specific manner atypical of pepstatin-sensitive aspartate proteinases. Wai 21a proteinase may be classified as member of the pepstatin-insensitive group of aspartate proteinases. The thermal stability at pH 3.0 and 60 degrees C increased 2.1-fold (t1/2, 4.5-9.7 hr) in the presence of 5 mM Ca++. An increase in both pH (3.0-4.5) and Ca++ concentration (0-30 mM) resulted in a 15-fold increase (t1/2, 15-230 min) in thermal stability at 75 degrees C. The amino acid composition of Wai 21a proteinase was found to be similar to other pepstatin-insensitive proteinases from bacterial sources and in particular similar to the other pepstatin-insensitive proteinases from bacterial sources and in particular similar to the thermostable enzyme, kumamolysin.

Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium.

A new obligately anaerobic, extremely thermophilic, cellulolytic bacterium is described. The strain designated Tp8T 6331 is differentiated from thermophilic cellulolytic clostridia on the basis of physiological characteristics and phylogenetic position within the Bacillus/Clostridium subphylum of the Gram-positive bacteria. Strain Tp8T 6331 is assigned to a new genus Caldicellulosiruptor, as Caldicellulosiruptor saccharolyticus gen., nov., sp. nov.