Biosynthetic gene cluster of the non-ribosomally synthesized cyclodepsipeptide skyllamycin: deciphering unprecedented ways of unusual hydroxylation reactions

The cyclic depsipeptide skyllamycin A is a potent inhibitor of the platelet-derived growth factor (PDGF) signaling pathway by inhibiting binding of homodimeric PDGF BB to the PDGF β-receptor. Its structure contains a cinnamoyl side chain and shows a high amount of β-hydroxylated amino acids as well as an unusual α-hydroxyglycine moiety as a rare structural modification. The skyllamycin biosynthetic gene cluster was cloned and sequenced from Streptomyces sp. Acta 2897. Its analysis revealed the presence of open reading frames encoding proteins for fatty acid precursor biosynthesis, non-ribosomal peptide synthetases, regulators, and transporters along with other modifying enzymes. Specific in-frame mutagenesis of these tailoring enzymes resulted in the production of novel skyllamycin derivatives revealing that β-hydroxy groups in skyllamycin A are introduced by a promiscuous cytochrome P450 monooxygenase, whereas a two-component flavin-dependent monooxygenase is involved in α-hydroxylation.     

Characterization of small interfering RNA by non-denaturing ion-pair reversed-phase liquid chromatography

Small interfering RNAs (siRNA) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. siRNA are typically formed by annealing of two complementary single stranded oligoribonucleotides. Compared to purity determination of non-hybridized single strands by denaturing chromatographic methods, characterization of the hybridized duplex is challenging. Here we are reporting a non-denaturing ion pairing-reversed phase (IP-RP) chromatography method capable of separating optimal duplex (full-length single strands only) from non-optimal duplex variants (containing shortmers, longmers and 2',5'-isomers) using ultraviolet- and mass spectrometric detection. The impact of different annealing conditions on siRNA composition was investigated. Optimized annealing conditions lead to a significant increase in optimal duplex, while total duplex content remained constant. The non-denaturing method reported herein showed high mass spectrometric sensitivity and superior separation efficiencies compared to other IP-RP buffer systems. The method is useful for in-process control and release testing of therapeutic double stranded nucleic acids such as siRNA.     

Trace analysis of small gas samples in sealed containers with mass spectrometry using static dilution

A sampling method for the analysis of small amounts of gases from sealed containers is described. Liquefied pressurised gas samples were expanded into a vacuum box and statically diluted with ultrapure nitrogen. The equations for the sample dilution were established, relating the measured impurity amount fractions in the sample mixture to their partial pressures in the sealed container and, in the case of oxygen, to the air pressure. Ion?Cmolecule reaction mass spectrometry allowed identification and measurement of trace impurities corresponding to partial pressures in the range of 1?hPa in the container. The method was applied for determining the identity and amount of gaseous impurities in n-butane used in implantable gas pressure?Coperated drug infusion pumps. Impurities from the n-butane supply cylinder or from decomposition products, for example due to the laser welding of the Ti plugs of the containers, could be excluded by the results of saturation vapour pressure measurements, FID gas chromatograms and IMR mass spectra. The variability in pressure versus volume among tested infusion pump samples was associated with excess oxygen, attributable to an excessive residual air pressure in the gas containers before they were filled with n-butane. The sample preparation method is principally applicable to measure the composition of small amounts of gas mixtures and gaseous impurities with identified IMR mass spectra down to trace levels??even for ubiquitous substances like oxygen. The volume of the produced gas mixtures allows characterisation of the gas by standard gas analytical methods and for impurities by trace gas analytical methods.     

Isolation and detection of single molecules on paramagnetic beads using sequential fluid flows in microfabricated polymer array assemblies

We report a method for isolating individual paramagnetic beads in arrays of femtolitre-sized wells and detecting single enzyme-labeled proteins on these beads using sequential fluid flows in microfabricated polymer array assemblies. Arrays of femtolitre-sized wells were fabricated in cyclic olefin polymer (COP) using injection moulding based on DVD manufacturing. These arrays were bonded to a complementary fluidic structure that was also moulded in COP to create an enclosed device to allow delivery of liquids to the arrays. Enzyme-associated, paramagnetic beads suspended in aqueous solutions of enzyme substrate were delivered fluidically to the array such that one bead per well was loaded by gravity. A fluorocarbon oil was then flowed into the device to remove excess beads from the surface of the array, and to seal and isolate the femtolitre-sized wells containing beads and enzyme substrate. The device was then imaged using standard fluorescence imaging to determine which wells contained single enzyme molecules. The analytical performance of this device as the detector for digital ELISA compared favourably to the standard method, i.e., glass arrays mechanically sealed against a silicone gasket; prostate specific antigen (PSA) could be detected from 0.011 pg mL(-1) up to 100 pg mL(-1). The use of an enclosed fluidic device to isolate beads in single-molecule arrays offers a multitude of advantages for low-cost manufacturing, ease of automation, and instrument development to enable applications in biomarker validation and medical diagnosis.     

Remarks on a nonlinear transport problem

A nonlinear transport problem of hyperbolic–elliptic type is studied. Estimates of potentials over varying domains and the method of characteristics enable one to treat the initial value problem for Hölder continuous data as an abstract evolution equation via Picard–Lindelöf theorem. In addition, existence for all times is proved. Similar techniques yield the existence of shock front solutions with smooth interfaces at least for a small time interval. By a priori estimates of approximating solutions, the results extend to the case of only bounded initial values. A modification of the system applies to the construction of a diffeomorphism with prescribed Jacobian determinant.     

Selection properties of uniform and related structures

In this paper we present some results on selection properties in asymmetric generalized metric and uniform spaces. We demonstrate differences between selection properties of these spaces and selection properties of metric and uniform spaces.     

MRI allows for longitudinal quantitative analysis of body fat composition in rats: An analysis of sibutramine-associated changes at the group level

Purpose

Body fat distribution changes are associated with multiple alterations in metabolism. Therefore, the assessment of body fat compartments by MRI in animal models is a promising approach to obesity research. Standard T1-weighted (T1w) whole body MRI was used here to quantify different effects in the subcutaneous and visceral fat compartments in rats under treatment with an anorexiant.

Materials and methods

Twenty rats on a high caloric diet were investigated by the identical MRI protocol at baseline and after seven weeks. Ten rats received a treatment with sibutramine, 10 rats served as vehicle control group. To longitudinally assess body fat components, MRI analysis was used with two approaches: 2D slicewise graphic analysis (SGA) was compared with an automated 3D analysis algorithm (3DA).

Results

At the group level, fat volume differences showed a longitudinal increase of subcutaneous and visceral fat volumes for the control group, whereas the sibutramine group showed stable subcutaneous fat volumes and decrease in visceral fat volumes. SGA and 3DA volume determination showed significant correlations for subcutaneous fat volume (C = 0.85, p < 0.001), visceral fat volume (C = 0.87, p < 0.001), and total fat volume (C = 0.90, p < 0.001).

Conclusion

It could be demonstrated that computer-based analysis of T1w MRI could be used to longitudinally assess changes in body fat compartments in rats at the group level. In detail, it was possible to investigate the effect of sibutramine separate on the fat compartments in rats.     

Aqua Ions. 2. Structural manifestations of the Jahn-Teller effect in the beta-alums

Variable-temperature single-crystal neutron diffraction structures of the alums CsM(III)(SO(4))(2).12D(2)O, where M(III) = Ti, V, Mn, and Ga, are reported. Structural differences are highlighted by the titanium and manganese alums, which undergo cubic (Pathremacr;) to orthorhombic (Pbca) phase transitions at approximately 13 and approximately 156 K, respectively. The structural instability exhibited by these salts is interpreted as arising from cooperative Jahn-Teller interactions, and these measurements characterize the structural changes that result from the coupling between the electronic and vibrational states. Although the symmetry changes associated with the phase transformations are analogous for the Ti and Mn alums, the low-temperature geometries of the tervalent hexaaqua cations are markedly different. Whereas the MnO(6) framework is subject to a pronounced tetragonal elongation, changes in the Ti-O bond lengths are very modest; but significant changes in the O-Ti-O bond angles and in the disposition of the coordinated water molecules are identified. The large differences in the transition temperatures and in the low-temperature stereochemistries of the [Ti(OD(2))(6)](3+) and [Mn(OD(2))(6)](3+) cations are related to the sensitivity of the energies of the t(2g) (O(h)) and e(g) (O(h)) orbitals to the various asymmetric vibrations of the hexaaqua complex.