A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03), representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs), Bacteroidetes (868 OTUs), Acidobacteria (731 OTUs), Firmicutes (540 OTUs), and Actinobacteria (418 OTUs). The genus Flavobacterium (11.6% of bacterial sequences) was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03), representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs), Bacteroidetes (868 OTUs), Acidobacteria (731 OTUs), Firmicutes (540 OTUs), and Actinobacteria (418 OTUs). The genus Flavobacterium (11.6% of bacterial sequences) was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands

低溫SQUID應用於人體心臟磁場測量之研究

[[abstract]]摘要 此研究主要是量測人體的心磁圖(magnetocardiography，MCG)，使用的儀器是多通道心磁儀系統(multichannel SQUID magnetometer system)，在磁屏蔽屋(Magnetically-shielded room，MSR)的環境下，進行測量。 我們找180位心電圖 (electrocardiograms，ECG) 檢驗結果為心臟健康的自願者與100位心臟有疾病的患者，進行MCG量測。觀察正常人與患者之MCG，在不同的參數分析下所得的生理學參數之分佈情形。這些患者是要接受運動心電圖的檢測，檢查是否有心肌缺氧(ischemia)的症狀，而在這100位患者之中，運動心電圖正常( Positive )的有14位，異常(Negative)的有65位，無法判斷(Bolder line)的有11位；利用運動心電圖結果異常與正常的79位病人所得的心磁訊號資料，進行了十一種參數的分析，其中CMDyn(current moment dynamics) 、MAmax(map angle maximum)、MADyn(map angle dynamics)以及SIQTC有最明顯的差異性，此時所計算出的敏感性(Sensitivity)為、明確性(Specificity)皆有達到六成以上；同時也計算出靜態心電圖判讀後的敏感性為64.2 %及明確性為75.3 %，因此心磁圖分析在臨床檢驗上是具有價值的，是一個非侵入性、無輻射及其他傷害，測量的時間只需30秒，是一種快速而安全的前瞻性檢測方式。

Structure-Based Redesign of a Methanol Oxidase into an “Aryl Alcohol Oxidase” for Enzymatic Synthesis of Aromatic Flavor Compounds

Alcohol oxidases (AOxs) catalyze the aerobic oxidation of alcohols to the corresponding carbonyl products (aldehydes or ketones), producing only H2O2 as the byproduct. The majority of known AOxs, however, have a strong preference for small, primary alcohols, limiting their broad applicability, e.g., in the food industry. To broaden the product scope of AOxs, we performed structure-guided enzyme engineering of a methanol oxidase from Phanerochaete chrysosporium (PcAOx). The substrate preference was extended from methanol to a broad range of benzylic alcohols by modifying the substrate binding pocket. A mutant (PcAOx-EFMH) with four substitutions exhibited improved catalytic activity toward benzyl alcohols with increased conversion and kcat toward the benzyl alcohol from 11.3 to 88.9% and from 0.5 to 2.6 s-1, respectively. The molecular basis for the change of substrate selectivity was analyzed by molecular simulation.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.BT/Biocatalysi

Dynamic responses of the aero-engine rotor system to bird strike on fan blades at different rotational speeds

To study the effect of a bird striking engine fan on the rotor system, a low-pressure rotor system dynamic model based on a real aero-engine structure was established. Dynamic equations were derived considering the case of the bird strike force which transferred to the rotor system. The bird strike force was obtained from the bird strike process simulation in LS-DYNA, where a smoothed particle hydrodynamics (SPH) mallard model was constructed using a computed tomog-raphy (CT) scanner, and finite element method (FEM) was used to simulate the bird strike on an actual fan model. The dynamic equations were solved using the Newmark-β method. The effect of rotational speeds on the rotor system dynamics after bird strike was investigated and discussed. Results show that the maximum bird impact force can reach 104 kN at 3772 r/min. Impact time is only 0.06 s, but the bird strike on fan blades lead to a transient shock on the rotor system. Under the action of transient shocks, the rotor system displacement in the horizontal and vertical directions increase sharply, and the closer the mass point is to the fan, the more it is affected; the vibration amplitude at the fan will increase 15 times within 0.1 s of the bird strike and will gradually decrease with the effect of damping. The dynamics of the rotor system changes from a stable single periodic motion to a complex irregular quasi-periodic motion after a bird strike, and the strike force excites the first-order vibrational mode of the rotor system. This phenomenon occurs at all speeds when bird strikes occur. Bird strikes will cause resonance in the rotor system, which may cause damage to the engine. It was also seen that the bird strike force, and hence the effects on the rotor system, increases as the engine rotational speed increases; the peak force is larger and the number of peaks has increased. The impact force at 3772 r/min is 99.5 kN higher than at 836 r/min, and three additional peaks emerged. This effect is more reflected in the amplitude, and the overall vibration characteristics do not change. Combining the bird strike with the rotor dynamics calculation, the dynamic response of the aero-engine rotor system to bird strike is studied at different flight stages, which is of guiding significance for power evaluation of aero engines after bird strike.Novel Aerospace Material

Biosynthesis of cyclic ketones by a H₂O₂ self-sufficient cascade reaction

In the present work we propose a bienzymatic cascade for the oxyfunctionalisation of cycloalkanes to cyclic alcohols/cyclic ketones. By combining a H2O2-dependent peroxygenase with a O2-consuming and H2O2-producing alcohol oxidase an overall aerobic oxidation system was established. A convincing proof-of-concept is presented and some current limitations are outlined.BT/Biocatalysi

A novel unspecific peroxygenase from Agaricus bisporus var. bisporus for biocatalytic oxyfunctionalisation reactions

Unspecific peroxygenases (UPOs) represent an emerging class of catalysts for the selective oxyfunctionalisation of C–H- and C = C groups. Until now, only a few UPOs have been characterised. In this study, we report a new peroxygenase identified from the Unspecific Peroxygenase Database. The UPO from Agaricus bisporus var. bisporus (AbvbUPO) has been heterologously expressed in Aspergillus niger and initially characterised with respect to its basic biochemical features. Furthermore, its catalytic properties were evaluated with enzymatic cascade reactions of choline oxidase (AnChOx) and AbvbUPO, which the AnChOx provided H2O2 necessary via reductive activation of oxygen in situ. Three types of oxyfunctionalizations, such as hydroxylation of ethylbenzene, epoxidations of styrene and cyclohexene, sulfoxidations of methyl phenyl sulfide and phenyl vinyl sulfide, were successfully achieved. We also investigated the activity of AbvbUPO on fatty acids in some more detail. The experimental results show that Under the above conditions, AbvbUPO had the higher activity for cyclohexene epoxidation and sulfonation of sulfide substrates. The concentration of epoxy cyclohexane was 2.91 mM, and the concentration of methyl phenyl sulfoxide was 3.69 mM. The regioselectivity of AbvbUPO was ω-1 bonds position of linear saturated fatty acid. All in all, AbvbUPO exhibits some interesting differences which may put the basis for further understanding of the factors determining peroxygenase selectivity.BT/Biocatalysi

A Novel Unspecific Peroxygenase from Galatian marginata for Biocatalytic Oxyfunctionalization Reactions

Unspecific peroxygenases (UPOs, EC 1.11.2.1) are promising oxyfunctionalization catalysts because of their unique stereoselectivity. However, so far only a few UPOs have been reported. In this study, gene mining was used to identify a gene from Galerina marginata that coded for a novel UPO (GmaUPO). GmaUPO was expressed in Pichia pastoris X-33 by scale-up fermentation (the UPO activity of the culture supernatant was 118 U/L). GmaUPO exhibited a molecular weight of 40 kDa and exhibited highest activity at 35°C and pH 9, respectively. Furthermore, GmaUPO was demonstrated to catalyze the epoxidation, sulfoxidation, and hydroxylation of common substrates, particularly fatty acids such as tridecanoic acid. The molecular basis for GmaUPO regioselectivity for fatty acid hydroxylation was explored by molecular modelling. The regioselectivity was mostly governed by the architecture of the enzyme's active site.BT/Biocatalysi

Effect of Impact and Bearing Parameters on Bird Strike with Aero-Engine Fan Blades

Bird strikes are one major accident for aircraft engines and can inflict heavy casualties and economic losses. In this study, a smoothed particle hydrodynamics (SPH) mallard model has been used to simulate bird impact to rotary aero-engine fan blades. The simulations were performed using the finite element method (FEM) at LS-DYNA. The reliability of the material model and numerical method was verified by comparing the numerical results withWilberk’s experimental results. The effects of impact and bearing parameters, including bird impact location, bird impact orientation, initial bird velocity, fan rotational speeds, stiffness of the bearing, and the damping of the bearing on the bird impact to aero-engine fan blade are studied and discussed. The results show that both the impact location and bird orientation have significant effects on the bird strike results. Bird impact to blade roots is the most dangerous scenario causing the impact force to reach 390 kN. The most dangerous orientation is the case where the bird’s head is tilted 45° horizontally, which leads to huge fan kinetic energy loss as high as 64.73 kJ. The bird’s initial velocity affects blade deformations. The von Mises stress during the bird strike process can reach 1238 MPa for an initial bird velocity of 225 m/s. The fan’s rotational speed and the bearing stiffness affect the rotor stability significantly. The value of bearing damping has little effect on the bird strike process. This paper gives an idea of how to evaluate the strength of fan blades in the design period.Novel Aerospace Material

More efficient enzymatic cascade reactions by spatially confining enzymes via the SpyTag/SpyCatcher technology

Hydrocarbon synthesis from (waste)oils enabled by a cascade of lipase-catalysed hydrolysis and decarboxylase-catalysed decarboxylation has become an active area of research en route to alternative, biobased fuels. However, Poor substrate transport efficiency is a major issue causing low reaction rates. This study focused on a protein self-assembly strategy based on SpyTag/SpyCatcher to overcome diffusion limitations. For this, two fusion proteins, TLL-Linker-SpyCatcher based on the lipase from Thermomyces lanuginosus and CvFAP-Linker-SpyTag based on the fatty acid photodecarboxylase from Chlorella variabilis were designed. A covalent multi-enzyme complex (TLL-CvFAP) was formed spontaneously by self-assembly of each enzyme. The effects of temperature, pH and molar ratio of self-assembled components on assembly efficiency were investigated. The results showed that the multi-enzyme complex TLL-CvFAP reached about 60% after 12 h of assembly, and the enzyme activity of the multienzyme complex was increased by about 50% compared to that of the corresponding non-assembled enzymes. Under optimized conditions 10 mM soybean oil were converted into 25 mM of the corresponding hydrocarbons, suggesting a good potential of biofuel synthesis.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.BT/Biocatalysi

Modeling thermodynamic properties of propane or tetrahydrofuran mixed with carbon dioxide or methane in structure-II clathrate hydrates

A sound knowledge of thermodynamic properties of sII hydrates is of great importance to understand the stability of sII gas hydrates in petroleum pipelines and in natural settings. Here, we report direct molecular dynamics (MD) simulations of the thermal expansion coefficient, the compressibility, and the specific heat capacity of C3H8, or tetrahydrofuran (THF), in mixtures of CH4 or CO2, in sII hydrates under a wide, relevant range of pressure and temperature conditions. The simulations were started with guest molecules positioned at the cage center of the hydrate. Annealing simulations were additionally performed for hydrates with THF. For the isobaric thermal expansion coefficient, an effective correction method was used to modify the lattice parameters, and the corrected lattice parameters were subsequently used to obtain thermal expansion coefficients in good agreement with experimental measurements. The simulations indicated that the isothermal expansion coefficient and the specific heat capacity of C3H8-pure hydrates were comparable but slightly larger than those of THF-pure hydrates, which could form Bjerrum defects. The considerable variation in the compressibility between the two appeared to be due to crystallographic defects. However, when a second guest molecule occupied the small cages of the THF hydrate, the deviation was smaller, because the subtle guest-guest interactions can offset an unfavorable configuration of unstable THF hydrates, caused by local defects in free energy. Unlike the methane molecule, the carbon dioxide molecule, when filling the small cage, can increase the expansion coefficient and compressibility as well as decrease the heat capacity of the binary hydrate, similar to the case of sI hydrates. The calculated bulk modulus for C3H8-pure and binary hydrates with CH4 or CO2 molecule varied between 8.7 and 10.6 GPa at 287.15K between 10 and 100 MPa. The results for the specific heat capacities varied from 3155 to 3750.0 J kg-1 K-1 for C3H8-pure and binary hydrates with CH4 or CO2 at 287.15K. These results are the first of this kind reported so far. The simulations show that the thermodynamic properties of hydrates largely depend on the enclathrated compounds. This provides a much-needed atomistic characterization of the sII hydrate properties and gives an essential input for large-scale discoveries of hydrates and processing as a potential energy source.Accepted Author ManuscriptEngineering Thermodynamic