472 research outputs found
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><sub><it>cat </it></sub>of this enzyme was 325 s<sup>-1 </sup>and the <it>K</it><sub><it>m </it></sub>values for 6-phosphogluconate, NADP<sup>+</sup>, and NAD<sup>+ </sup>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 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
dark energy, constant , 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 , 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 and
are obtained. The correlation amplitude is proportional to the galactic mass,
and is oscillating over large scales 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
to 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 \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 d after core-collapse reaching a bolometric luminosity of Lp
\ergs. Spectral models, including the nebular epoch, show
that the SN ejected \msun\ of material, with \msun\ below
5000 \kms, and with a kinetic energy of erg. The
explosion synthesised \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 of \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
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