Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.

New antibacterials are needed to tackle antibiotic-resistant bacteria. Type IIA topoisomerases (topo2As), the targets of fluoroquinolones, regulate DNA topology by creating transient double-strand DNA breaks. Here we report the first co-crystal structures of the antibacterial QPT-1 and the anticancer drug etoposide with Staphylococcus aureus DNA gyrase, showing binding at the same sites in the cleaved DNA as the fluoroquinolone moxifloxacin. Unlike moxifloxacin, QPT-1 and etoposide interact with conserved GyrB TOPRIM residues rationalizing why QPT-1 can overcome fluoroquinolone resistance. Our data show etoposide's antibacterial activity is due to DNA gyrase inhibition and suggests other anticancer agents act similarly. Analysis of multiple DNA gyrase co-crystal structures, including asymmetric cleavage complexes, led to a 'pair of swing-doors' hypothesis in which the movement of one DNA segment regulates cleavage and religation of the second DNA duplex. This mechanism can explain QPT-1's bacterial specificity. Structure-based strategies for developing topo2A antibacterials are suggested.

Thermopressurized diluted phosphoric acid pretreatment of ligno(hemi)cellulose to make free sugars and nutraceutical oligosaccharides.

Ligno(hemi)cellulosics (L(h)Cs) as sugarcane bagasse and loblolly pine sawdust are currently being used to produce biofuels such as bioethanol and biobutanol through fermentation of free sugars that are often obtained enzymatically. However, this bioconversion requires a pretreatment to solubilize the hemicellulose fractions, thus facilitating the action of the cellulolytic enzymes. Instead of the main free monosaccharides used in these current models, the modulation of thermopressurized orthophosphoric acid as a pretreatment, in the ranges of 3-12 atm and pH 1.5-2.5, can produce nondigestible oligosaccharides (NDOS) such as xylo-oligosaccharides (XOS) because heteroxylan is present in both types of hardwood and softwood hemicelluloses. A comparative thin-layer chromatographic analysis of the hydrolytic products showed the best conditions for NDOS production to be 7 atm/water, pH 2.25 and 2.50, and 8.5 atm/water for both sources. Particular hydrolysates from 7 atm (171 °C) at pHs 2.25 and 2.50 both for cane bagasse and pine sawdust, with respective oligosaccharide contents of 57 and 59 %, once mixed in a proportion of 1:1 for each plant source, were used in vitro as carbon sources for Bifidobacterium or Lactobacillus. Once both bacteria attained the stationary phase of growth, an unforeseen feature emerged: the preference of B. animalis for bagasse hydrolysates and, conversely, the preference of L. casei for pine hydrolysates. Considering the fact that nutraceutical oligosaccharides from both hemicelluloses correspond to higher value-added byproducts, the technology using a much diluted thermopressurized orthophosphoric acid pretreatment becomes an attractive choice for L(h)Cs.

Impacts of an invasive non-native annual weed, Impatiens glandulifera, on above- and below-ground invertebrate communities in the United Kingdom.

Vegetation community composition and the above- and below-ground invertebrate communities are linked intrinsically, though few studies have assessed the impact of non-native plants on both these parts of the community together. We evaluated the differences in the above- (foliage- and ground-dwelling) and below-ground invertebrate communities in nine uninvaded plots and nine plots invaded by the annual invasive species Impatiens glandulifera, in the UK during 2007 and 2008. Over 139,000 invertebrates were identified into distinct taxa and categorised into functional feeding groups. The impact of I. glandulifera on the vegetation and invertebrate community composition was evaluated using multivariate statistics including principal response curves (PRC) and redundancy analysis (RDA). In the foliage-dwelling community, all functional feeding groups were less abundant in the invaded plots, and the species richness of Coleoptera and Heteroptera was significantly reduced. In the ground-dwelling community, herbivores, detritivores, and predators were all significantly less abundant in the invaded plots. In contrast, these functional groups in the below-ground community appeared to be largely unaffected, and even positively associated with the presence of I. glandulifera. Although the cover of I. glandulifera decreased in the invaded plots in the second year of the study, only the below-ground invertebrate community showed a significant response. These results indicate that the above- and below-ground invertebrate communities respond differently to the presence of I. glandulifera, and these community shifts can potentially lead to a habitat less biologically diverse than surrounding native communities; which could have negative impacts on higher trophic levels and ecosystem functioning.

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.

The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.

Estimating the turnover number in enzyme kinetic reactions using transient and stationary state data / Número estimando de turnover das reações cinéticas de enzimas utilizando os dados de estado transiente e estacionária

Substrate and product concentration data obtained by simulating enzyme-substrate reaction rate equations were used to test two proposed kinetic rate constant estimation techniques in this study. In the first technique, the turnover number, k3, was calculated using early transient time domain data, which are difficult to obtain experimentally. The technique used an iterative approach to calculate k3 with a pair of data and the value of k3 could be retrieved with 35 percent error. The second technique calculated k3 using stationary domain data and the value of k3 could be retrieved with less than 5 percent error. This second technique also offered internal consistency in the calculation of k3 by calculating k3 both from the intercept and the slope of the linear plot derived in this study. A series of sensitivity analyses was conducted to understand the robustness of the second technique in estimating k3 from simulated data to the changes in the reaction rate constants (k1, k2, and k3) and the initial concentration of enzyme used for simulation. It was found that the second technique generally worked well in the estimation of k3 except for the simulated data for fast substrate conversions such as in the large k3 and [E]0 cases . This latter method, thus, shows promise for the use of late time experimental substrate/product concentration data to obtain k3. Exclusively using late time data avoids the need for difficult and expensive rapid early time measurement techniques for estimating k3. Once a reasonable estimate for k3 is obtained, the initial enzyme value can easily be determined from the maximum velocity constant established from fitting the Michaelis-Menten or Briggs-Haldane equations to substrate and product stationary state domain (late time) data. While the first technique can estimate k3 with only one point in the transient domain, it is suggested that the second method generally be favored since it only requires late-time stationary...

Dados de concentração de substrato e de produto obtidos por simulação de equações de velocidade de reação enzima-substrato foram usados neste estudo para testar duas técnicas para estimar constantes cinéticas. Na primeira técnica, a constante, k3, foi calculada utilizando os dados de domínio do tempo inicial de transição, que são difíceis de serem obtidos experimentalmente. A técnica usou uma aproximação iterativa para calcular k3 cujo valor pôde ser estimado com erro de 33 por cento. A segunda técnica calculou k3 usando dados de domínio no estado estacionário e o valor de k3 pôde ser estimado com erro de 5 por cento. Esta segunda técnica também ofereceu uma consistência interna no cálculo de k3, por calculá-lo tanto pela intersecção quanto pela inclinação da reta derivada deste estudo. Uma série de análises de sensibilidade foi realizada para avaliar a robustez da segunda técnica na estimativa de k3 utilizando dados que foram simulados quanto às mudanças nas constantes de taxa de reação (k1, k2 e k3) e na concentração inicial de enzima. Foi encontrado que a segunda técnica, em geral, proporcionou boa estimativa de k3, exceto para os dados simulados para as conversões rápidas de substrato, como no caso de valores elevados de k3 e de [E]o. Este último método, portanto, mostra ser promissor quando se usam dados experimentais tardios da concentração de substrato/produto para obter k3. O uso dados de tempo tardio evita a necessidade do uso de técnicas difíceis e caras na medida de tempo iniciais para estimativa de k3. Uma vez que é obtida uma estimativa razoável de k3, o valor inicial da enzima pode ser facilmente determinado a partir da constante de velocidade máxima estabelecida por ajuste das equações de Michaelis-Menten ou de Briggs-Haldane e partir de dados de substrato e de produtos no estado estacionário (tempo tardio). Enquanto a primeira técnica pode estimar k3 com somente um ponto no regime transiente, sugere-se que o segundo método...

Exploring the perceptions of out-of-hours training for GP registrars in Wales.

This paper explores the perceptions of GP registrars about the quality of the training that they receive within out-of-hours (OOH) settings. Focus groups with trainers, clinical supervisors and GP registrars revealed three areas of interest: supervision, educational experience and system factors. Implications for OOH training are discussed.

Periodic fermentor yield and enhanced product enrichment from autonomous oscillations.

Four decades of work have clearly established the existence of autonomous oscillations in budding yeast culture across a range of operational parameters and in a few strains. Autonomous oscillations impact substrate conversion to biomass and products. Relatively little work has been done to quantify yield in this case. We have analyzed the yield of autonomously oscillating systems, grown under different conditions, and demonstrate that it too oscillates. Using experimental data and mathematical models of yeast growth and division, we demonstrate strategies to increase the efficient recovery of products. The analysis makes advantage of the population structure and synchrony of the system and our ability to target production within the cell cycle. While oscillatory phenomena in culture have generally been regarded with trepidation in the engineering art of bioprocess control, our results provide further evidence that autonomously oscillating systems can be a powerful tool, rather than an obstruction.

Development of activity-based cost functions for cellulase, invertase, and other enzymes.

As enzyme chemistry plays an increasingly important role in the chemical industry, cost analysis of these enzymes becomes a necessity. In this paper, we examine the aspects that affect the cost of enzymes based upon enzyme activity. The basis for this study stems from a previously developed objective function that quantifies the tradeoffs in enzyme purification via the foam fractionation process (Cherry et al., Braz J Chem Eng 17:233-238, 2000). A generalized cost function is developed from our results that could be used to aid in both industrial and lab scale chemical processing. The generalized cost function shows several nonobvious results that could lead to significant savings. Additionally, the parameters involved in the operation and scaling up of enzyme processing could be optimized to minimize costs. We show that there are typically three regimes in the enzyme cost analysis function: the low activity prelinear region, the moderate activity linear region, and high activity power-law region. The overall form of the cost analysis function appears to robustly fit the power law form.

A proposed mechanism for detergent-assisted foam fractionation of lysozyme and cellulase restored with beta-cyclodextrin.

Foam fractionation by itself cannot effectively concentrate hydrophilic proteins such as lysozyme and cellulase. However, the addition of a detergent to a protein solution can increase the foam volume, and thus, the performance of the foam fractionation process. In this article, we propose a possible protein concentration mechanism of this detergent-assisted foam fractionation: A detergent binds to an oppositely charged protein, followed by the detergent-protein complex being adsorbed onto a bubble during aeration. The formation of this complex is inferred by a decrease in surface tension of the detergent-protein solution. The surface tension of a solution with the complex is lower than the surface tension of a protein or a detergent solution alone. The detergent can then be stripped from the adsorbed protein, such as cellulase, by an artificial chaperone such as beta-cyclodextrin. Stripping the detergent from the protein allows the protein to return to its original conformation and to potentially retain all of its original activity following the foam fractionation process. Low-cost alternatives to beta-cyclodextrin such as corn dextrin were tested experimentally to restore the protein activity through detergent stripping, but without success.

Separating a mixture of egg yolk and egg white using foam fractionation.

A mixture created by blending with a spatula, an egg yolk and an egg white from the same egg can serve as a binary system for testing to see how well foam fractionation can be used to separate two different groups of proteins naturally found together. This mixture of two phases is particularly attractive for such a study because the two phases can be visualized distinctly when in their separated states. It has been shown that air alone at a low flow rate and with little or no water added can effect visually clean separations of egg yolk from egg white, making this a "green" separation process. The white precedes the yolk in the process, which takes less than 10 min at a laboratory scale.

Effect of beta-cyclodextrin in artificial chaperones assisted foam fractionation of cellulase.

Foam fractionation has the potential to be a low-cost protein separation process; however, it may cause protein denaturation during the foaming process. In previous work with cellulase, artificial chaperones were integrated into the foam fractionation process in order to reduce the loss of enzymatic activity. In this study, other factors were introduced to further reduce the loss of cellulase activity: type of cyclodextrin, cyclodextrin concentration, dilution ratio cyclodextrin to the foamate and holding time. alpha-Cyclodextrin was almost as effective as beta-cyclodextrin in refolding the foamed cellulase-Cetyltrimethylammonium bromide mixture. beta-Cyclodextrin (6.5 mM) was almost as effective as 13 mM beta-cyclodextrin in refolding. The dilution ratio, seven parts foamate and three parts beta-cyclodextrin solution, was found to be most effective among the three ratios tested (7:3, 1:1, and 3:7). The activity after refolding at this dilution ratio is around 0.14 unit/mL. The refolding time study showed that the refolding process was found to be most effective for the short refolding times (within 1 h).

Enhancing cellulase foam fractionation with addition of surfactant.

Foam fractionation cannot be used to recover cellulase from an aerated water solution effectively because cellulase by itself can produce only a small amount of foam. The addition of a surfactant can, however, increase the foamate volume and enhance the concentration of cellulase. We studied three detergents individually added to a 200 mg/L cellulase solution to promote foaming. These detergents were anionic, cationic, and nonionic surfactants, respectively. Although contributing to foam production, it was observed that nonionic surfactant (Pluronic F-68) barely concentrated cellulase, leaving the enrichment ratio unchanged, near 1. With anionic surfactant, sodium dedecyl sulfate, and cationic surfactant, cetyltrimethylammonium bromide (CTAB), the enrichment ratio became much larger, but cellulase denaturation occurred, reducing the activity of the enzyme. When CTAB was used to help foam cellulase, beta-cyclodextrin was subsequently added to the foamate to help restore the enzyme activity.

Removing proteins from an aerated yeast fermentation by pulsing carbon dioxide: replacing salting-out as a method of protein precipitation.

Salting-out is a common technique used for precipitating proteins and other materials from fermentation and tissue culture processes. It leaves a salt residue in the system. Foam fractionation can also be used to remove proteins by protein precipitation from a dilute solution. In doing so, there is usually a trade-off between enrichment and recovery. An increase in the airflow rate will increase the recovery, but only at the expense of the enrichment. A new method for increasing the recovery in foam fractionations and in yeast fermentations is to add a burst of CO2 to the process and then restore the air. This CO2 acts like a temporary salt, but it does not leave behind a residue. The recovery increases as a result of the joint use of these gases, perhaps by more than 10-fold, without sacrificing the enrichment. Chicken egg albumin in a foam fractionation column can serve as a simple, experimental model for the proposed recovery process in lieu of the fermentation process.

Degeneration of beta-glucosidase activity in a foam fractionation process.

Foam fractionation is a promising technique for concentrating proteins because of its simplicity and low operating cost. One such protein that can be foamed is the enzyme cellulase. The use of inexpensively purified cellulase may be a key step in the economical production of ethanol from biomass. We conducted foam fractionation experiments at total reflux using the cellulase component beta-glucosidase to study how continuous shear affects beta-glucosidase in a foam such as a fermentation or foam fractionation process. The experiments were conducted at pH 2.4, 5.4, and 11.6 and airflow rates of 3, 6, 15, 20, and 32 cc/min to determine how beta-glucosidase activity changes in time at these different conditions. This is apparently a novel and simple way of testing for changes in enzyme activity within a protein foam. The activity did not degenerate during 5 min of reflux at pH 5.4 at an airflow rate of 10 cc/min. It was established that at 10 min of refluxing, the beta-glucosidase denatured more as the flow rate increased. At pH 2.4 and a flow rate of 10 cc/min, the activity remained constant for at least 15 min.

Effect of lidocaine on ovalbumin and egg albumin foam stability.

Foam fractionation is a simple separation process that can remove and concentrate hydrophobic molecules such as proteins, surfactants, and organic wastes from an aqueous solution. Bovine serum albumin and ovalbumin have been widely used as model proteins due to their strong foaming potential and low price. Here, we study the effect of lidocaine on albumin foam, since drugs like lidocaine are known to bind with albumin. We observed that lidocaine not only enhances the amount of foam produced but also the stability of that foam as well. The foam stability was evaluated as the decay rate constant of the foam, determined from a change in height (or volume) of the foam over a given time period.

Breathing air from protein foam.

Protein foams can be used to extinguish fires. If foams are to be used to extinguish fires where people are present, such as in high-rise buildings or ships, then a method for allowing people to breathe in a foam-filled environment is needed. It is proposed that the air, used to create the foam be used for breathing. A canister that will break incoming air-filled foam has been designed for attachment to a standard gas mask, in order to provide breathable air to a trapped person. Preliminary results for the modified mask indicate feasibility of breathing air from air-filled protein foam.

Variation of bubble size distribution in a protein foam fractionation column measured using a capillary probe with photoelectric sensors.

Bubble size is used to characterize not only bubble-specific interfacial area but also bubble coalescence in a foam column. The bubble size distributions were obtained in a continuous foam fractionation process for concentrating ovalbumin using a developed photoelectric probe. When the continuous process reached steady state, the bubble size distribution pattern remained stable. Bubble size distribution data above (+1 cm) or below (-1 cm) the bulk liquid-foam interface showed symmetry along the diameter of the column (14 cm ID). The bubble size distribution was affected by the column wall. The nearly constant protein concentration distribution across the column cross-section indicated that the bubble flow distribution approached a flat profile across the column. A log-normal bubble distribution pattern best fit the weighted range of bubbles in the column at column lengths above and below the liquid-foam interface. These observations may prove to be useful in understanding the mechanisms underlying the foam fractionation of proteins.

The effect of pH on the foam fractionation of beta-glucosidase and cellulase.

The surface tension-pH profile of beta-glucosidase was established to determine its relationship to the corresponding profile of cellulase and to the foam fractionation of that cellulase. The goal of this work was to determine the optimal foaming points for both cellulase and cellobiase. This data may prove useful in the separation of certain components of cellulase, since the non-foaming hydrophilic beta-glucosidase does not foam as well as the hydrophobic components of cellulase at low concentrations. A key finding from these experiments was that there are two local minima in the surface tension-pH trajectory for Trichoderma reesei cellulase, as contrasted to the usual single minimum. The lower of these minimum points corresponds to the cellulase isoelectric point. The double minimum surface tension-pH profile was also observed for cellobiase alone. The optimal foaming pH for cellobiase alone was determined to be around 10.5, while for cellulase it was between 6 and 9.

Effect of bubble size on foam fractionation of ovalbumin.

The bubble size distribution and void fraction (epsilong) (at two bulk liquid pool positions below the bulk liquid-foam interface and one lower foam phase position) in a continuous foam fractionation column containing ovalbumin were obtained using a photoelectric capillary probe. The bubble size and epsilong data were gathered for different operating conditions (including the changes in the superficial gas velocity and feed flow rate) at a feed solution of pH 6.5 and used to calculate the specific area, a, of the bubbles. Thus, local enrichment (ERl), values of ovalbumin could be estimated and compared with directly obtained experimental results. The ERl results were also correlated with the bubble size and epsilong to understand better the concentration mechanisms of foam fractionation. The high ERl in the lower foam phase was largely attributable to the abrupt increase in epsilong (from 0.25 to 0.75), or the a (from about 12 to 25 cm2/cm3) from the bulk liquid to the foam phase. These changes correspond with enhanced gravity drainage. With an increase in the superficial gas velocity, the bubble size increased and the a decreased in both the bulk liquid and lower foam phases, resulting in a decrease in the local experimentally determined enrichments at high superficial gas velocities. At intermediate feed flow rates, the bubble size reached the maximum. The epsilong and a, on the other hand, were the largest for the largest feed flow rate. The ERl in the lower foam phase was maximized at the lowest feed flow rate. It follows, therefore, that a alone is not sufficient to determine the magnitude of the ERl in the foam phase.