1,281 research outputs found
Expanding the Portfolio by a Novel Monomeric Oleate Hydratase from Pediococcus parvulus
Oleate hydratases convert oleic acid into 10-hydroxy stearic acid, a valuable fine chemical, useful in lubricant and surfactant formulations. They are of large interest due to their high expression rates and solubility, however, they differ drastically by their overall stability and pH- and temperature ranges. To expand their portfolio, another oleate hydratase named OhyPp (originating from Pediococcus parvulus) was characterized. It is a close relative of the well-known oleate hydratase OhyRe from Rhodococcus erythropolis. OhyPp is only the second member of the monomeric oleate hydratase family with some surprising catalytic features. A distinct characteristic is OhyPp's higher affinity towards FAD compared to OhyRe's helping to understand and improve FAD binding in the future, which is a current drawback for the industrial application of oleate hydratases
Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics
This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014
Single-artificial-atom lasing using a voltage-biased superconducting charge qubit
We consider a system composed of a single artificial atom coupled to a cavity
mode. The artificial atom is biased such that the most dominant relaxation
process in the system takes the atom from its ground state to its excited
state, thus ensuring population inversion. A recent experimental manifestation
of this situation was achieved using a voltage-biased superconducting charge
qubit. Even under the condition of `inverted relaxation', lasing action can be
suppressed if the `relaxation' rate is larger than a certain threshold value.
Using simple transition-rate arguments and a semiclassical calculation, we
derive analytic expressions for the lasing suppression condition and the state
of the cavity in both the lasing and suppressed-lasing regimes. The results of
numerical calculations agree very well with the analytically derived results.
We start by analyzing a simplified two-level-atom model, and we then analyze a
three-level-atom model that should describe accurately the recently realized
superconducting artificial-atom laser.Comment: 21 pages in preprint format, 6 figure
Measuring surface-area-to-volume ratios in soft porous materials using laser-polarized xenon interphase exchange NMR
We demonstrate a minimally invasive nuclear magnetic resonance (NMR)
technique that enables determination of the surface-area-to-volume ratio (S/V)
of soft porous materials from measurements of the diffusive exchange of
laser-polarized 129Xe between gas in the pore space and 129Xe dissolved in the
solid phase. We apply this NMR technique to porous polymer samples and find
approximate agreement with destructive stereological measurements of S/V
obtained with optical confocal microscopy. Potential applications of
laser-polarized xenon interphase exchange NMR include measurements of in vivo
lung function in humans and characterization of gas chromatography columns.Comment: 14 pages of text, 4 figure
COVID-19 and genetic variants of protein involved in the SARS-CoV-2 entry into the host cells
The recent global COVID-19 public health emergency is caused by SARS-CoV-2 infections and can manifest extremely variable clinical symptoms. Host human genetic variability could influence susceptibility and response to infection. It is known that ACE2 acts as a receptor for this pathogen, but the viral entry into the target cell also depends on other proteins. The aim of this study was to investigate the variability of genes coding for these proteins involved in the SARS-CoV-2 entry into the cells. We analyzed 131 COVID-19 patients by exome sequencing and examined the genetic variants of TMPRSS2, PCSK3, DPP4, and BSG genes. In total we identified seventeen variants. In PCSK3 gene, we observed a missense variant (c.893G>A) statistically more frequent compared to the EUR GnomAD reference population and a missense mutation (c.1906A>G) not found in the GnomAD database. In TMPRSS2 gene, we observed a significant difference in the frequency of c.331G>A, c.23G>T, and c.589G>A variant alleles in COVID-19 patients, compared to the corresponding allelic frequency in GnomAD. Genetic variants in these genes could influence the entry of the SARS-CoV-2. These data also support the hypothesis that host genetic variability may contribute to the variability in infection susceptibility and severity
Time-optimal CNOT between indirectly coupled qubits in a linear Ising chain
We give analytical solutions for the time-optimal synthesis of entangling
gates between indirectly coupled qubits 1 and 3 in a linear spin chain of three
qubits subject to an Ising Hamiltonian interaction with equal coupling plus
a local magnetic field acting on the intermediate qubit. The energy available
is fixed, but we relax the standard assumption of instantaneous unitary
operations acting on single qubits. The time required for performing an
entangling gate which is equivalent, modulo local unitary operations, to the
between the indirectly coupled qubits 1 and 3 is
, i.e. faster than a previous estimate based on a similar
Hamiltonian and the assumption of local unitaries with zero time cost.
Furthermore, performing a simple Walsh-Hadamard rotation in the Hlibert space
of qubit 3 shows that the time-optimal synthesis of the (which acts as the identity when the control qubit 1 is in the state
, while if the control qubit is in the state the target
qubit 3 is flipped as ) also requires the same
time .Comment: 9 pages; minor modification
Bonn Potential and Shell-Model Calculations for 206,205,204Pb
The structure of the nuclei 206,205,204Pb is studied interms of shell model
employing a realistic effective interaction derived from the Bonn A
nucleon-nucleon potential. The energy spectra, binding energies and
electromagnetic properties are calculated and compared with experiment. A very
good overall agreement is obtained. This evidences the reliability of our
realistic effective interaction and encourages use of modern realistic
potentials in shell-model calculations for heavy-mass nuclei.Comment: 4 pages, 4 figures, submitted to Physical Review
A database of immunoglobulins with integrated tools: DIGIT
The DIGIT (Database of ImmunoGlobulins with Integrated Tools) database (http://biocomputing.it/digit) is an integrated resource storing sequences of annotated immunoglobulin variable domains and enriched with tools for searching and analyzing them. The annotations in the database include information on the type of antigen, the respective germline sequences and on pairing information between light and heavy chains. Other annotations, such as the identification of the complementarity determining regions, assignment of their structural class and identification of mutations with respect to the germline, are computed on the fly and can also be obtained for user-submitted sequences. The system allows customized BLAST searches and automatic building of 3D models of the domains to be performed
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