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

Recommendation model based on opinion diffusion

Information overload in the modern society calls for highly efficient recommendation algorithms. In this letter we present a novel diffusion based recommendation model, with users' ratings built into a transition matrix. To speed up computation we introduce a Green function method. The numerical tests on a benchmark database show that our prediction is superior to the standard recommendation methods.Comment: 5 pages, 2 figure

Partial Dynamical Symmetry and Mixed Dynamics

Partial dynamical symmetry describes a situation in which some eigenstates have a symmetry which the quantum Hamiltonian does not share. This property is shown to have a classical analogue in which some tori in phase space are associated with a symmetry which the classical Hamiltonian does not share. A local analysis in the vicinity of these special tori reveals a neighbourhood of phase space foliated by tori. This clarifies the suppression of classical chaos associated with partial dynamical symmetry. The results are used to divide the states of a mixed system into ``chaotic'' and ``regular'' classes.Comment: 10 pages, Revtex, 3 figures, Phys. Rev. Lett. in pres

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

A Coarse-Grained Field Theory for Density Fluctuations and Correlation Functions of Galactic Objects

We present a coarse-grained field theory of density fluctuations for a Newtonian self-gravitating many-body system and apply it to a homogeneous Universe with small density fluctuations. The theory treats the clustering of galaxies and clusters in terms of the field of density fluctuations. The Jeans length $\lambda_0$, a unique physical scale for a gravitating system, appears naturally as the characteristic scale underlying the large scale structure. Under Gaussian approximation the analytic expressions of $\xi(r)$ and $P(k)$ are obtained. The correlation amplitude is proportional to the galactic mass, and is oscillating over large scales $\sim 100$ $h^{-1}$ Mpc and damped to zero. The spectrum amplitude is inversely proportional to the galactic number density.The preliminary results qualitatively explain some pronounced features of large scale structures.Comment: 7 pages, 4 figures. to appear in A&

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&

SN 2016coi/ASASSN-16fp: An example of residual helium in a type Ic supernova?

The optical observations of Ic-4 supernova (SN) 2016coi/ASASSN-16fp, from $\sim 2$ to $\sim450$ days after explosion, are presented along with analysis of its physical properties. The SN shows the broad lines associated with SNe Ic-3/4 but with a key difference. The early spectra display a strong absorption feature at $\sim 5400$ \AA\ which is not seen in other SNe~Ic-3/4 at this epoch. This feature has been attributed to He I in the literature. Spectral modelling of the SN in the early photospheric phase suggests the presence of residual He in a C/O dominated shell. However, the behaviour of the He I lines are unusual when compared with He-rich SNe, showing relatively low velocities and weakening rather than strengthening over time. The SN is found to rise to peak $\sim 16$ d after core-collapse reaching a bolometric luminosity of Lp $\sim 3\times10^{42}$ \ergs. Spectral models, including the nebular epoch, show that the SN ejected $2.5-4$ \msun\ of material, with $\sim 1.5$ \msun\ below 5000 \kms, and with a kinetic energy of $(4.5-7)\times10^{51}$ erg. The explosion synthesised $\sim 0.14$ \msun\ of 56Ni. There are significant uncertainties in E(B-V)host and the distance however, which will affect Lp and MNi. SN 2016coi exploded in a host similar to the Large Magellanic Cloud (LMC) and away from star-forming regions. The properties of the SN and the host-galaxy suggest that the progenitor had $M_\mathrm{ZAMS}$ of $23-28$ \msun\ and was stripped almost entirely down to its C/O core at explosion.Comment: Accepted for publication in MNRAS. Updated to reflect the published version, minor typographical changes onl

Semiquantal dynamics of fluctuations: Ostensible quantum chaos

The time-dependent variational principle using generalized Gaussian trial functions yields a finite dimensional approximation to the full quantum dynamics and is used in many disciplines. It is shown how these 'semi-quantum' dynamics may be derived via the Ehrenfest theorem and recast as an extended classical gradient system with the fluctuation variables coupled to the average variables. An extended potential is constructed for a one-dimensional system. The semiquantal behavior is shown to be chaotic even though the system has regular classical behavior and the quantum behavior had been assumed regular.Comment: 9 pages, TeX, 2 figures (not attached; hard copies available immediately on request). To appear in Physical Review Letter