New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore model

TAR RNA is a potential target for AIDS therapy. Ligand-based virtual screening was performed to retrieve novel scaffolds for RNA-binding molecules capable of inhibiting the Tat-TAR interaction, which is essential for HIV replication. We used a "fuzzy" pharmacophore approach (SQUID) and an alignment-free pharmacophore method (CATS3D) to carry out virtual screening of a vendor database of small molecules and to perform "scaffold-hopping". A small subset of 19 candidate molecules were experimentally tested for TAR RNA binding in a fluorescence resonance energy transfer (FRET) assay. Both methods retrieved molecules that exhibited activities comparable to those of the reference molecules acetylpromazine and chlorpromazine, with the best molecule showing ten times better binding behavior (IC50 = 46 microM). The hits had molecular scaffolds different from those of the reference molecules.     

Free and esterified sterols of cotton buds and anthers

Capillary gas liquid chromatography analyses were conducted on free and esterified sterol fractions of cotton (Gossypium hirsutum cv. Stoneville 213) floral buds and anthers. The free sterols of both cotton buds and anthers consist mainly of the common plant sterols sitosterol, stigmasterol and 24ζ-methylcholest-5-en-3β-ol. The composition of esterified sterols of cotton buds and anthers were similar, and consisted of pollinastanol, 31-norcycloartanol, cycloartenol, 31-norcycloartenol, 24-dehydropolinastanol and sitosterol. Desmosterol was also present in both the free and esterified sterols of anthers. The identities of the sterols were confirmed by gas chromatography-mass spectrometry analyses. Esterified sterols accounted for 46.7 and 88.7% of total sterols of cotton bud and anthers, respectively. The ratio of esterified sterol to free sterol per gram of tissue is about 8∶1 in anthers. The Δ⁵-sterols of the esterified sterols of cotton buds and anthers account for only 17 and 9.2% of the total sterols, respectively.     

Abietoid seed fatty acid composition—A review of the genera Abies, Cedrus, Hesperopeuce, Keteleeria, Pseudolarix, and Tsuga and preliminary inferences on the taxonomy of Pinaceae

The seed fatty acid (FA) compositions of Abietoids (Abies, Cedrus, Hesperopeuce, Keteleeria, Pseudolarix, and Tsuga) are reviewed in the present study in conclusion to our survey of Pinaceae seed FA compositions. Many unpublished data are given. Abietoids and Pinoids (Pinus, Larix, Ficea, and Pseudotsuga)—constituting the family Pinaceae—are united by the presence of several Δ5-olefinic acids, taxoleic (5,9–18∶2), pinolenic (5,9,12–18∶3) coniferonic (5,9,12,15–18∶4), keteleeronic (5,11–20∶2), and sciadonic (5,11,14–20∶3) acids, and of 14-methyl hexadecanoic (anteiso-17∶0) acid. These acids seldom occur in angiosperm seeds. The proportions of individual Δ5-olefinic acids, however, differ between Pinoids and Abietoids. In the first group, pinolenic acid is much greater than taxoleic acid, whereas in the second group, pinolenic acid is greater than or equal to taxoleic acid. Moreover, taxoleic acid in Abietoids is much greater than taxoleic acid in Pinoids, an apparent limit between the two subfamilies being about 4.5% of that acid relative to total FA. Tsuga spp. appear to be a major exception, as their seed FA compositions are much like those of species from the Pinoid group. In this respect, Hesperopeuce mertensiana, also known as Tsuga mertensiana, has little in common with Abietoids and fits the general FA pattern of Pinoids well. Tsuga spp. and H. mertensiana, from their seed FA compositions, should perhaps be separated from the Abietoid group and their taxonomic position revised. It is suggested that a “Tsugoid” subfamily be created, with seed FA in compliance with the Pinoid pattern and other botanical and immunological criteria of the Abietoid type. All Pinaceae genera, with the exception of Pinus, are quite homogeneous when considering their overall seed FA compositions, including Δ5-olefinic acids. In all cases but one (Pinus), variations from one species to another inside a given genus are of small amplitude. Pinus spp., on the other hand, have highly variable levels of Δ5-olefinic acids in their FA compositions, particularly when sections (e.g., Cembroides vs. Pinus sections) or subsections (e.g., Flexiles and Cembrae subsections from the section Strobus) are compared, although they show qualitatively the same FA patterns characteristic of Pinoids. Multicomponent analysis of Abietoid seed FA allowed grouping of individual species into genera that coincide with the same genera otherwise characterized by more classical botanical criteria. Our studies exemplify how seed FA compositions, particularly owing to the presence of Δ5-olefinic acids, may be useful in sustaining and adding some precision to existing taxonomy of the major family of gymnosperms, Pinaceae.     

From a theoretical model to a predictive simulation model of operator interaction with support systems: designing experiments to build the numerical simulation

In this paper, we will discuss a methodology developed and applied in the European ITERATE project with the objective of designing experiments that will provide data to seed the numerical model of operator behaviour in different surface transport modes: road vehicles, rail transport and ships. The experiments aim to investigate how new technologies support different types of operators in different contexts. A structured approach was adopted. Firstly, an initial selection of the systems to be investigated was made, describing the support they provide for operators. Hypotheses were formulated on the effects of operator parameters on the interaction with the systems. A final selection of systems for the experiments was made, focusing on systems providing support for collision avoidance and speed management. The operator parameters (culture, attitude and personality, experience, driver state (such as fatigue) and the demands of the task) were operationalised and piloted. The next step was the development of scenarios to be implemented in a driving simulator. In the last step, the final experiments were designed and detailed.     

Bench-scale continuous hydrogenation of Australian coals — study of iron catalysts and recycle solvent composition

The inter-relations between iron catalysts, recycle solvent composition and product yield and composition have been investigated in bench-scale (1–2 kg h^?1) continuous hydrogenation of Australian coals at process severity of 21–22 MPa at 400–430°C. Products and recycle solvent are recovered in batch distillation (atmospheric and vacuum) and the distillate solvent is returned to slurry feed without further treatment. Successive samples of recycle solvent are analysed by g.c.-m.s., i.r. and titrimetry. The effect of adding iron catalysts in the form of red mud - sulphur mixtures or compounds after a short period of continuous operation without catalyst is demonstrated. Distillate yields from black coals increase from 24–34 wt% daf under non-catalytic conditions to 35–53 wt% daf by adding iron catalysts. The composition of the almost equilibrated recycle solvent also changes and a new equilibrium is approached after the iron catalyst is added. The effect of solvent composition on distillate yield can not be determined from these data. The ratio of hydroaromatic components to hydroaromatic plus aromatic components in the solvent increases from ≈0.2 at non-catalytic equilibrium to ≈0.5–0.6 at catalysed equilibrium after adding iron. Other compositional parameters in the recycle solvent do not show any clear responses to the addition of iron. Equilibrium solvent composition under constant operating conditions is attained at ≈10 passes at 1 kg ^h?1 throughput with total system holdup of ≈20 kg. Paraffins for the Queensland subbituminous coal equilibrated at 18–24% in the solvent, phenolics at 16–21%, basic nitrogen at ≈0.4% (as N), and the balance a mixture of aromatics and hydroaromatics. The total aromatics neglecting phenolics in the equilibrium recycle solvent consists of ≈40–50% each of two-and three-ring and 5–10% four-ring members.     

Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection

Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.     

Are hormones from the neuropeptide Y family recognized by their receptors from the membrane-bound state?

Hormones and many other neurotransmitters, growth factors, odorant molecules, and light all present stimuli for a class of membrane-anchored receptors called G protein-coupled receptors (GPCRs). The GPCRs are the largest family of cell-surface receptors involved in signal transduction. About 1% of all known genes of Drosophila and more than 5% of the genes of Caenorhabditis elegans encode GPCRs. In addition, more than 50% of current therapeutic agents on the market target these receptors. When the enormous biological and pharmaceutical importance of these receptors is considered, it is surprising how little is known about the mechanism with which these receptors recognize their natural ligands. In this review we present a structural approach, utilizing techniques of high-resolution NMR spectroscopy, to address the question of whether peptides from the neuropeptide Y family of neurohormones are recognized directly from solution or from the membrane-bound state. In our studies we discovered that the structures of the membrane-bound species are better correlated to the pharmacological properties of these peptides than the solution structures are. These findings are supported by the observation that many biophysical properties of these peptides seem to be optimized for membrane binding. We finally present a scenario of possible events during receptor recognition.     

Einfluss der Wechselwirkung von Reaktion und Fluiddynamik auf das Verhalten von Strahlschlaufenreaktoren

Jet loop reactors are used as apparatus to facilitate chemical or biological reactions. This type of apparatus is characterized by an internal circulation flow, essentially driven by the injection of liquid. The nozzle can also be used to inject and disperse gas. The internal fluid dynamics and thus the reactor behavior is significantly determined by the introduced momentum and by the internal gas distribution. To describe the mutual influence of a gas-consuming reaction and the internal fluid dynamics, a simplified model based on a momentum balance and a material balance was used. From the exemplary calculations, a critical range for non-selective reactions and for fluid dynamic stability is given.     

Segmentation of the fascia lata and reproducible quantification of intermuscular adipose tissue (IMAT) of the thigh

Magnetic Resonance Materials in Physics, Biology and Medicine - To develop a precise semi-automated segmentation of the fascia lata (FL) of the thigh to quantify IMAT volume in T1w MR images and...