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 $J$ 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 $\mathrm{CNOT}(1, 3)$ between the indirectly coupled qubits 1 and 3 is $T=\sqrt{3/2} J^{-1}$, 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 $\mathrm{CNOT}^{\pm}(1, 3)$ (which acts as the identity when the control qubit 1 is in the state $\ket{0}$, while if the control qubit is in the state $\ket{1}$ the target qubit 3 is flipped as $\ket{\pm}\rightarrow \ket{\mp}$) also requires the same time $T$.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