L<Subscript>2</Subscript>-norm multiple kernel learning and its application to biomedical data fusion

Background  

This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L _∞, L ₁, and L ₂ MKL. In particular, L ₂ MKL is a novel method that leads to non-sparse optimal kernel coefficients, which is different from the sparse kernel coefficients optimized by the existing L _∞ MKL method. In real biomedical applications, L ₂ MKL may have more advantages over sparse integration method for thoroughly combining complementary information in heterogeneous data sources.     

Inhibition of rabbit beta-globin synthesis by complementary oligonucleotides: identification of mRNA sites sensitive to inhibition

We tested the effects of a series of synthetic oligonucleotides (hybridons) complementary to the 5' noncoding and coding regions of rabbit beta-globin mRNA on endogenous protein synthesis in a rabbit reticulocyte cell-free translation system. With highly purified hybridons inhibition was completely specific for beta-globin. The sites most sensitive to inhibition are the beginning of the 5' noncoding region and a sequence including the initiation codon and several upstream bases. The region between these was relatively insensitive to inhibition. The sites of maximum sensitivity coincide with known protein binding sites, suggesting that hybridons exert their effects in part by blocking the binding of proteins required for translation. Their effectiveness seems related to the ease with which they are displaced by ribosomes.     

Transmembrane extension and oligomerization of the CLIC1 chloride intracellular channel protein upon membrane interaction

Chloride intracellular channel proteins (CLICs) differ from most ion channels as they can exist in both soluble and integral membrane forms. The CLICs are expressed as soluble proteins but can reversibly autoinsert into the membrane to form active ion channels. For CLIC1, the interaction with the lipid bilayer is enhanced under oxidative conditions. At present, little evidence is available characterizing the structure of the putative oligomeric CLIC integral membrane form. Previously, fluorescence resonance energy transfer (FRET) was used to monitor and model the conformational transition within CLIC1 as it interacts with the membrane bilayer. These results revealed a large-scale unfolding between the C- and N-domains of CLIC1 as it interacts with the membrane. In the present study, FRET was used to probe lipid-induced structural changes arising in the vicinity of the putative transmembrane region of CLIC1 (residues 24-46) under oxidative conditions. Intramolecular FRET distances are consistent with the model in which the N-terminal domain inserts into the bilayer as an extended α-helix. Further, intermolecular FRET was performed between fluorescently labeled CLIC1 monomers within membranes. The intermolecular FRET shows that CLIC1 forms oligomers upon oxidation in the presence of the membranes. Fitting the data to symmetric oligomer models of the CLIC1 transmembrane form indicates that the structure is large and most consistent with a model comprising approximately six to eight subunits.     

The spread of topically-applied pyrethrin I from the cuticle to the central nervous system of the cockroach Periplaneta americana

Penetration of topically-applied pyrethrin I into adult male American cockroaches (Periplaneta americana L.) and its subsequent distribution within the insects was studied microchemically and biologically. After applying an LD95 (0.5 g per insect), pyrethrin I was lost from the surface of the insects at a rate diminishing with time; 20% of the dose applied penetrated during the first hour, but elimination limited the amount found inside the insects to a maximum of 13%. The amount inside the insects increased for an hour after dosing, when symptoms of poisoning had become severe, but then remained steady until the end of the test, 48 hrs after dosing.Pyrethrin I sorbs strongly but reversibly on insect solids from aqueous solution, and at equilibrium is distributed between solids and solution in the ratio 3 × 10⁴: 1. This ratio would give a concentration of only 4 × 10^–11 M of pyrethrin I in the haemolymph of insects poisoned with an LD95 of the insecticide, but solids in the haemolymph would increase its pyrethrin I content and speed the spread of the insecticide from cuticle to nervous system. Chemical tests able to detect pyrethrin I at concentrations of 2×10^–8 M failed to show its presence in the haemolymph of poisoned cockroaches, but the haemolymph caused symptoms resembling those of pyrethroid poisoning when applied to nerve preparations from normal cockroaches.Although pyrethrin I at 4 × 10^–11 M in the haemolymph of cockroaches treated topically with LD95s of the insecticide seems too dilute to have produced the symptoms observed in their nervous systems, the results of additional tests did not support the alternative suggestion that the insecticide reached the nervous system by spreading over the cuticle and through the tracheal system. Larger concentrations of pyrethrin I occurring locally in the haemolymph near the nervous system during the early stages of poisoning may explain the anomaly.

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Résumé La pénétration d'une application topique de pyrethrine I chez le mâle adulte de Periplaneta americana et sa distribution ultérieure dans l'organisme est étudiée microchimiquement et biologiquement. Après application d'une dose égale à la DL 95 (0,5 g par insecte), la pyrethrine I est absorbée à la surface de l'insecte à un taux décroissant avec le temps; 20% de la dose appliquée pénètre durant la 1ère heure, mais l'élimination limite la quantité trouvée dans l'organisme à un maximum de 13%. La quantité trouvée dans l'organisme s'accroît pendant la 1ère heure après l'intoxication, quand les symptômes de l'intoxication deviennent importants, puis reste stationnaire jusqu'à la fin du test, soit 48 heures après l'intoxication.La pyrethrine I s'absorbe fortement mais réversiblement sur la phase solide de l'insecte, à partir de la solution aqueuse et le coefficient de partition est de 3×10⁴: 1. Ce coefficient donnarait une concentration de pyrethrine I de seulement 4 × 10^–11 M dans l'hémolymphe des insectes intoxiqués à la DL 95, mais la phase solide de l'hémolymphe augmenterait sa teneur en pyrethrine I et accélérerait la vitesse de pénétration de l'insecticide, de la cuticule vers le système nerveux. Des tests chimiques capables de déceler la pyrethrine I à la concentration de 2×10^–8 M n'ont pu établir sa présence dans l'hémolymphe des blattes intoxiquées, mais cette hémolymphe provoque des symptômes analogues à ceux de l'intoxication par les pyrethrines, quand elle est appliquée à des préparations nerveuses de blattes nonintoxiquées.Quoique la pyrethrine I à la concentration de 4 × 10^–11 M dans l'hémolymphe de blattes traitées localement à la DL 95 de cet insecticide, semble trop diluée pour produire les symptômes observés dans le système nerveux, des résultats supplémentaires n'ont pas autorisé une autre hypothèse, à savoir que l'insecticide atteindrait le système nerveux via la cuticule et le système trachéen. Des concentrations plus fortes de pyrethrine I, localisées près du système nerveux pendant les premiers stades de l'intoxication pourraient expliquer cette anomalie.

     

Basis for allosteric open-state stabilization of voltage-gated potassium channels by intracellular cations

The open state of voltage-gated potassium (Kv) channels is associated with an increased stability relative to the pre-open closed states and is reflected by a slowing of OFF gating currents after channel opening. The basis for this stabilization is usually assigned to intrinsic structural features of the open pore. We have studied the gating currents of Kv1.2 channels and found that the stabilization of the open state is instead conferred largely by the presence of cations occupying the inner cavity of the channel. Large impermeant intracellular cations such as N-methyl-d-glucamine (NMG⁺) and tetraethylammonium cause severe slowing of channel closure and gating currents, whereas the smaller cation, Cs⁺, displays a more moderate effect on voltage sensor return. A nonconducting mutant also displays significant open state stabilization in the presence of intracellular K⁺, suggesting that K⁺ ions in the intracellular cavity also slow pore closure. A mutation in the S6 segment used previously to enlarge the inner cavity (Kv1.2-I402C) relieves the slowing of OFF gating currents in the presence of the large NMG⁺ ion, suggesting that the interaction site for stabilizing ions resides within the inner cavity and creates an energetic barrier to pore closure. The physiological significance of ionic occupation of the inner cavity is underscored by the threefold slowing of ionic current deactivation in the wild-type channel compared with Kv1.2-I402C. The data suggest that internal ions, including physiological concentrations of K⁺, allosterically regulate the deactivation kinetics of the Kv1.2 channel by impairing pore closure and limiting the return of voltage sensors. This may represent a primary mechanism by which Kv channel deactivation kinetics is linked to ion permeation and reveals a novel role for channel inner cavity residues to indirectly regulate voltage sensor dynamics.     

Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity

Cannabidiol (CBD) is the primary nonpsychotropic phytocannabinoid found in Cannabis sativa, which has been proposed to be therapeutic against many conditions, including muscle spasms. Among its putative targets are voltage-gated sodium channels (Navs), which have been implicated in many conditions. We investigated the effects of CBD on Nav1.4, the skeletal muscle Nav subtype. We explored direct effects, involving physical block of the Nav pore, as well as indirect effects, involving modulation of membrane elasticity that contributes to Nav inhibition. MD simulations revealed CBD’s localization inside the membrane and effects on bilayer properties. Nuclear magnetic resonance (NMR) confirmed these results, showing CBD localizing below membrane headgroups. To determine the functional implications of these findings, we used a gramicidin-based fluorescence assay to show that CBD alters membrane elasticity or thickness, which could alter Nav function through bilayer-mediated regulation. Site-directed mutagenesis in the vicinity of the Nav1.4 pore revealed that removing the local anesthetic binding site with F1586A reduces the block of I_Na by CBD. Altering the fenestrations in the bilayer-spanning domain with Nav1.4-WWWW blocked CBD access from the membrane into the Nav1.4 pore (as judged by MD). The stabilization of inactivation, however, persisted in WWWW, which we ascribe to CBD-induced changes in membrane elasticity. To investigate the potential therapeutic value of CBD against Nav1.4 channelopathies, we used a pathogenic Nav1.4 variant, P1158S, which causes myotonia and periodic paralysis. CBD reduces excitability in both wild-type and the P1158S variant. Our in vitro and in silico results suggest that CBD may have therapeutic value against Nav1.4 hyperexcitability.