Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration

<p>Abstract</p> <p>Background</p> <p>Thermostable enzymes from thermophilic microorganisms are playing more and more important roles in molecular biology R&D and industrial applications. However, over-production of recombinant soluble proteins from thermophilic microorganisms in mesophilic hosts (e.g. <it>E. coli</it>) remains challenging sometimes.</p> <p>Results</p> <p>An open reading frame TM0438 from a hyperthermophilic bacterium <it>Thermotoga maritima </it>putatively encoding 6-phosphogluconate dehydrogenase (6PGDH) was cloned and expressed in <it>E. coli</it>. The purified protein was confirmed to have 6PGDH activity with a molecular mass of 53 kDa. The <it>k</it>_{<it>cat </it>}of this enzyme was 325 s^-1and the <it>K</it>_{<it>m </it>}values for 6-phosphogluconate, NADP⁺, and NAD⁺were 11, 10 and 380 μM, respectively, at 80°C. This enzyme had half-life times of 48 and 140 h at 90 and 80°C, respectively. Through numerous approaches including expression vectors, hosts, cultivation conditions, inducers, and codon-optimization of the <it>6pgdh </it>gene, the soluble 6PGDH expression levels were enhanced to ~250 mg per liter of culture by more than 500-fold. The recombinant 6PGDH accounted for >30% of total <it>E. coli </it>cellular proteins when lactose was used as a low-cost inducer. In addition, this enzyme coupled with glucose-6-phosphate dehydrogenase for the first time was demonstrated to generate two moles of NADPH per mole of glucose-6-phosphate.</p> <p>Conclusion</p> <p>We have achieved a more than 500-fold improvement in the expression of soluble <it>T. maritima </it>6PGDH in <it>E. coli</it>, characterized its basic biochemical properties, and demonstrated its applicability for NADPH regeneration by a new enzyme cocktail. The methodology for over-expression and simple purification of this thermostable protein would be useful for the production of other thermostable proteins in <it>E. coli</it>.</p

Bailout Embeddings, Targeting of KAM Orbits, and the Control of Hamiltonian Chaos

We present a novel technique, which we term bailout embedding, that can be used to target orbits having particular properties out of all orbits in a flow or map. We explicitly construct a bailout embedding for Hamiltonian systems so as to target KAM orbits. We show how the bailout dynamics is able to lock onto extremely small KAM islands in an ergodic sea.Comment: 3 figures, 9 subpanel

Comparison of dark energy models: A perspective from the latest observational data

In this paper, we compare some popular dark energy models under the assumption of a flat universe by using the latest observational data including the type Ia supernovae Constitution compilation, the baryon acoustic oscillation measurement from the Sloan Digital Sky Survey, the cosmic microwave background measurement given by the seven-year Wilkinson Microwave Anisotropy Probe observations and the determination of $H_0$ from the Hubble Space Telescope. Model comparison statistics such as the Bayesian and Akaike information criteria are applied to assess the worth of the models. These statistics favor models that give a good fit with fewer parameters. Based on this analysis, we find that the simplest cosmological constant model that has only one free parameter is still preferred by the current data. For other dynamical dark energy models, we find that some of them, such as the $\alpha$ dark energy, constant $w$, generalized Chaplygin gas, Chevalliear-Polarski-Linder parametrization, and holographic dark energy models, can provide good fits to the current data, and three of them, namely, the Ricci dark energy, agegraphic dark energy, and Dvali-Gabadadze-Porrati models, are clearly disfavored by the data.Comment: 19 pages, 10 figures; new data used, typos fixed; version for publication in SCIENCE CHINA Physics, Mechanics & Astronom

The SDSS-IV extended Baryon Oscillation Spectroscopic Survey: selecting emission line galaxies using the Fisher discriminant

We present a new selection technique of producing spectroscopic target catalogues for massive spectroscopic surveys for cosmology. This work was conducted in the context of the extended Baryon Oscillation Spectroscopic Survey (eBOSS), which will use ~200 000 emission line galaxies (ELGs) at 0.6<zspec<1.0 to obtain a precise baryon acoustic oscillation measurement. Our proposed selection technique is based on optical and near-infrared broad-band filter photometry. We used a training sample to define a quantity, the Fisher discriminant (linear combination of colours), which correlates best with the desired properties of the target: redshift and [OII] flux. The proposed selections are simply done by applying a cut on magnitudes and this Fisher discriminant. We used public data and dedicated SDSS spectroscopy to quantify the redshift distribution and [OII] flux of our ELG target selections. We demonstrate that two of our selections fulfil the initial eBOSS/ELG redshift requirements: for a target density of 180 deg^2, ~70% of the selected objects have 0.6<zspec<1.0 and only ~1% of those galaxies in the range 0.6<zspec<1.0 are expected to have a catastrophic zspec estimate. Additionally, the stacked spectra and stacked deep images for those two selections show characteristic features of star-forming galaxies. The proposed approach using the Fisher discriminant could, however, be used to efficiently select other galaxy populations, based on multi-band photometry, providing that spectroscopic information is available. This technique could thus be useful for other future massive spectroscopic surveys such as PFS, DESI, and 4MOST.Comment: Version published in A&

Production of N2O5 and ClNO2 in summer in urban Beijing, China

The heterogeneous hydrolysis of dinitrogen pentoxide (N2O5) has a significant impact on both nocturnal particulate nitrate formation and photochemistry on the following day through the photolysis of nitryl chloride (ClNO2), yet these processes in highly polluted urban areas remain poorly understood. Here we present measurements of gas-phase N2O5 and ClNO2 by high-resolution time-of-flight chemical ionization mass spectrometer (ToF-CIMS) during summer in urban Beijing, China as part of the Air Pollution and Human Health (APHH) campaign. N2O5 and ClNO2 show large day-to-day variations with average (±1σ ) mixing ratios of 79.2±157.1 and 174.3±262.0 pptv, respectively. High reactivity of N2O5, with ., (N2O5)'1 ranging from 0.20 × 10'2 to 1.46 × 10'2 s'1, suggests active nocturnal chemistry and a large nocturnal nitrate formation potential via N2O5 heterogeneous uptake. The lifetime of N2O5, ., (N2O5), decreases rapidly with the increase in aerosol surface area, yet it varies differently as a function of relative humidity with the highest value peaking at 1/4 40 %. The N2O5 uptake coefficients estimated from the product formation rates of ClNO2 and particulate nitrate are in the range of 0.017-0.19, corresponding to direct N2O5 loss rates of 0.00044-0.0034 s'1. Further analysis indicates that the fast N2O5 loss in the nocturnal boundary layer in urban Beijing is mainly attributed to its indirect loss via NO3, for example through the reactions with volatile organic compounds and NO, while the contribution of the heterogeneous uptake of N2O5 is comparably small (7-33 %). High ClNO2 yields ranging from 0.10 to 0.35 were also observed, which might have important implications for air quality by affecting nitrate and ozone formation

High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway

BACKGROUND: The future hydrogen economy offers a compelling energy vision, but there are four main obstacles: hydrogen production, storage, and distribution, as well as fuel cells. Hydrogen production from inexpensive abundant renewable biomass can produce cheaper hydrogen, decrease reliance on fossil fuels, and achieve zero net greenhouse gas emissions, but current chemical and biological means suffer from low hydrogen yields and/or severe reaction conditions. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate a synthetic enzymatic pathway consisting of 13 enzymes for producing hydrogen from starch and water. The stoichiometric reaction is C(6)H(10)O(5) (l)+7 H(2)O (l)→12 H(2) (g)+6 CO(2) (g). The overall process is spontaneous and unidirectional because of a negative Gibbs free energy and separation of the gaseous products with the aqueous reactants. CONCLUSIONS: Enzymatic hydrogen production from starch and water mediated by 13 enzymes occurred at 30°C as expected, and the hydrogen yields were much higher than the theoretical limit (4 H(2)/glucose) of anaerobic fermentations. SIGNIFICANCE: The unique features, such as mild reaction conditions (30°C and atmospheric pressure), high hydrogen yields, likely low production costs ($∼2/kg H(2)), and a high energy-density carrier starch (14.8 H(2)-based mass%), provide great potential for mobile applications. With technology improvements and integration with fuel cells, this technology also solves the challenges associated with hydrogen storage, distribution, and infrastructure in the hydrogen economy

Comparison of Standard Ruler and Standard Candle constraints on Dark Energy Models

We compare the dark energy model constraints obtained by using recent standard ruler data (Baryon Acoustic Oscillations (BAO) at z=0.2 and z=0.35 and Cosmic Microwave Background (CMB) shift parameters R and l_a) with the corresponding constraints obtained by using recent Type Ia Supernovae (SnIa) standard candle data (ESSENCE+SNLS+HST from Davis et. al.). We find that, even though both classes of data are consistent with LCDM at the 2\sigma level, there is a systematic difference between the two classes of data. In particular, we find that for practically all values of the parameters (\Omega_0m,\Omega_b) in the 2\sigma range of the the 3-year WMAP data (WMAP3) best fit, LCDM is significantly more consistent with the SnIa data than with the CMB+BAO data. For example for (\Omega_0m,\Omega_b)=(0.24,0.042) corresponding to the best fit values of WMAP3, the dark energy equation of state parametrization w(z)=w_0 + w_1 (z/(1+z)) best fit is at a 0.5\sigma distance from LCDM (w_0=-1,w_1=0) using the SnIa data and 1.7\sigma away from LCDM using the CMB+BAO data. There is a similar trend in the earlier data (SNLS vs CMB+BAO at z=0.35). This trend is such that the standard ruler CMB+BAO data show a mild preference for crossing of the phantom divide line w=-1, while the recent SnIa data favor LCDM. Despite of this mild difference in trends, we find no statistically significant evidence for violation of the cosmic distance duality relation \eta \equiv d_L(z)/(d_A(z) (1+z)^2)=1. For example, using a prior of \Omega_0m=0.24, we find \eta=0.95 \pm 0.025 in the redshift range 0<z<2, which is consistent with distance duality at the 2\sigma level.Comment: References added. 9 pages, 7 figures. The Mathematica files with the numerical analysis of the paper can be found at http://leandros.physics.uoi.gr/rulcand/rulcand.ht

Cosmological parameters constraints from galaxy cluster mass function measurements in combination with other cosmological data

We present the cosmological parameters constraints obtained from the combination of galaxy cluster mass function measurements (Vikhlinin et al., 2009a,b) with new cosmological data obtained during last three years: updated measurements of cosmic microwave background anisotropy with Wilkinson Microwave Anisotropy Probe (WMAP) observatory, and at smaller angular scales with South Pole Telescope (SPT), new Hubble constant measurements, baryon acoustic oscillations and supernovae Type Ia observations. New constraints on total neutrino mass and effective number of neutrino species are obtained. In models with free number of massive neutrinos the constraints on these parameters are notably less strong, and all considered cosmological data are consistent with non-zero total neutrino mass \Sigma m_\nu \approx 0.4 eV and larger than standard effective number of neutrino species, N_eff \approx 4. These constraints are compared to the results of neutrino oscillations searches at short baselines. The updated dark energy equation of state parameters constraints are presented. We show that taking in account systematic uncertainties, current cluster mass function data provide similarly powerful constraints on dark energy equation of state, as compared to the constraints from supernovae Type Ia observations.Comment: Accepted for publication in Astronomy Letter

Statefinder diagnosis and the interacting ghost model of dark energy

A new model of dark energy namely "ghost dark energy model" has recently been suggested to interpret the positive acceleration of cosmic expansion. The energy density of ghost dark energy is proportional to the hubble parameter. In this paper we perform the statefinder diagnostic tool for this model both in flat and non-flat universe. We discuss the dependency of the evolutionary trajectories in $s-r$ and $q-r$ planes on the interaction parameter between dark matter and dark energy as well as the spatial curvature parameter of the universe. Eventually, in the light of SNe+BAO+OHD+CMB observational data, we plot the evolutionary trajectories in $s-r$ and $q-r$ planes for the best fit values of the cosmological parameters and compare the interacting ghost model with other dynamical dark energy models. We show that the evolutionary trajectory of ghost dark energy in statefinder diagram is similar to holographic dark energy model. It has been shown that the statefinder location of $\Lambda$CDM is in good agreement with observation and therefore the dark energy models whose current statefinder values are far from the $\Lambda$CDM point can be ruled out.Comment: 23 pages, 6 figure