Photoaffinity labeling with cholesterol analogues precisely maps a cholesterol-binding site in voltage-dependent anion channel-1

Voltage-dependent anion channel-1 (VDAC1) is a highly regulated β-barrel membrane protein that mediates transport of ions and metabolites between the mitochondria and cytosol of the cell. VDAC1 co-purifies with cholesterol and is functionally regulated by cholesterol, among other endogenous lipids. Molecular modeling studies based on NMR observations have suggested five cholesterol-binding sites in VDAC1, but direct experimental evidence for these sites is lacking. Here, to determine the sites of cholesterol binding, we photolabeled purified mouse VDAC1 (mVDAC1) with photoactivatable cholesterol analogues and analyzed the photolabeled sites with both top-down mass spectrometry (MS), and bottom-up MS paired with a clickable, stable isotope-labeled tag, FLI-tag. Using cholesterol analogues with a diazirine in either the 7 position of the steroid ring (LKM38) or the aliphatic tail (KK174), we mapped a binding pocket in mVDAC1 localized to Thr83 and Glu73, respectively. When Glu73 was mutated to a glutamine, KK174 no longer photolabeled this residue, but instead labeled the nearby Tyr62 within this same binding pocket. The combination of analytical strategies employed in this work permits detailed molecular mapping of a cholesterol-binding site in a protein, including an orientation of the sterol within the site. Our work raises the interesting possibility that cholesterol-mediated regulation of VDAC1 may be facilitated through a specific binding site at the functionally important Glu73 residue

Small world effect in an epidemiological model

A model for the spread of an infection is analyzed for different population structures. The interactions within the population are described by small world networks, ranging from ordered lattices to random graphs. For the more ordered systems, there is a fluctuating endemic state of low infection. At a finite value of the disorder of the network, we find a transition to self-sustained oscillations in the size of the infected subpopulation

Isomorphs in model molecular liquids

Isomorphs are curves in the phase diagram along which a number of static and dynamic quantities are invariant in reduced units. A liquid has good isomorphs if and only if it is strongly correlating, i.e., the equilibrium virial/potential energy fluctuations are more than 90% correlated in the NVT ensemble. This paper generalizes isomorphs to liquids composed of rigid molecules and study the isomorphs of two systems of small rigid molecules, the asymmetric dumbbell model and the Lewis-Wahnstrom OTP model. In particular, for both systems we find that the isochoric heat capacity, the excess entropy, the reduced molecular center-of-mass self part of the intermediate scattering function, the reduced molecular center-of-mass radial distribution function to a good approximation are invariant along an isomorph. In agreement with theory, we also find that an instantaneous change of temperature and density from an equilibrated state point to another isomorphic state point leads to no relaxation. The isomorphs of the Lewis-Wahnstrom OTP model were found to be more approximative than those of the asymmetric dumbbell model, which is consistent with the OTP model being less strongly correlating. For both models we find "master isomorphs", i.e., isomorphs have identical shape in the virial/potential energy phase diagram.Comment: 20 page

Penicillium verrucosum occurrence and Ochratoxin A contents in organically cultivated grain with special reference to ancient wheat types and drying practice

This study addresses the relationship between the ochratoxigenic strains of Penicillium verrucosum and ochratoxin A (OTA) contents in organically cultivated grain. It included 37 combined, non-dried grain samples from farmers with no drying facilities as well as 19 non-dried and 22 dried samples from six farms with on-farm drying facilities (Case studies 1-6). The study focused on the ancient wheat type spelt but also included samples of wheat, rye, barley, oats, triticale, emmer, and einkorn. All 78 samples were analysed for moisture content (MC) and occurrence of P. verrucosum. The latter was assessed by plating non-disinfected kernels on DYSG agar and counting those contaminated by the fungus. Fiftyfive samples were analysed for OTA. Most of the combine harvested samples (82%) were contaminated with P. verrucosum prior to drying. This was ascribed to difficult harvest conditions and many samples of spelt, which was significantly more contaminated by P. verrucosum than oats, wheat and barley. Though not statistically significant, the results also indicated that spelt was more contaminated than rye, which is usually regarded the most sensitive small grain cereal. No correlation was found between number of kernels contaminated by P. verrucosum and OTA content. Despite many non-dried samples being contaminated by P. verrucosum, only two exceeded the EU maximum limit for grain (5 ng OTA g-1), both being spring spelt with 18 and 92 ng g-1, respectively. The problems were most likely correlated to a late harvest and high MC of the grain. The case studies showed exceedings of the maximum limit in a batch of dried oats and spring wheat, respectively, probably to be explained by insufficient drying of late harvested grain with high MC. Furthermore, our results clearly indicate that OTA is not produced in significant amounts in samples with MCs below 17%. All dried samples with MCs above 18% exceeded the 5 ng OTA g-1 limit in grain. However, no correlation between MC and the amount of OTA produced was found

Extremal dynamics model on evolving networks

We investigate an extremal dynamics model of evolution with a variable number of units. Due to addition and removal of the units, the topology of the network evolves and the network splits into several clusters. The activity is mostly concentrated in the largest cluster. The time dependence of the number of units exhibits intermittent structure. The self-organized criticality is manifested by a power-law distribution of forward avalanches, but two regimes with distinct exponents tau = 1.98 +- 0.04 and tau^prime = 1.65 +- 0.05 are found. The distribution of extinction sizes obeys a power law with exponent 2.32 +- 0.05.Comment: 4 pages, 5 figure

Perception of nonnative tonal contrasts by Mandarin-English and English-Mandarin sequential bilinguals

This study examined the role of acquisition order and crosslinguistic similarity in influencing transfer at the initial stage of perceptually acquiring a tonal third language (L3). Perception of tones in Yoruba and Thai was tested in adult sequential bilinguals representing three different first (L1) and second language (L2) backgrounds: L1 Mandarin-L2 English (MEBs), L1 English-L2 Mandarin (EMBs), and L1 English-L2 intonational/non-tonal (EIBs). MEBs outperformed EMBs and EIBs in discriminating L3 tonal contrasts in both languages, while EMBs showed a small advantage over EIBs on Yoruba. All groups showed better overall discrimination in Thai than Yoruba, but group differences were more robust in Yoruba. MEBs’ and EMBs’ poor discrimination of certain L3 contrasts was further reflected in the L3 tones being perceived as similar to the same Mandarin tone; however, EIBs, with no knowledge of Mandarin, showed many of the same similarity judgments. These findings thus suggest that L1 tonal experience has a particularly facilitative effect in L3 tone perception, but there is also a facilitative effect of L2 tonal experience. Further, crosslinguistic perceptual similarity between L1/L2 and L3 tones, as well as acoustic similarity between different L3 tones, play a significant role at this early stage of L3 tone acquisition.Published versio

An intervention framework for collaboration

This paper provides an intervention framework for collaboration to improve services. When collaboration is an intervention, its development and effectiveness depend on intervention logic. Intervention logic requires a precise conceptualization of collaboration. This conceptualization emphasizes its vital and unique components. It includes a developmental progression in which collaboration is contrasted with companion concepts. It also includes progress benchmarks, outcome measures, and logic models. These models depict relations among the benchmarks and outcomes, and they identify the mediating and moderating variables that account for collaboration's development and effectiveness. These models are designed to improve planning, evaluation, and their relations. This intervention framework for collaboration contrasts sharply with other conceptualizations and strategies. Although its aim is to unify and improve collaboration policy and practice, its inherent selectivity is an obvious limitation. [PUBLICATION ABSTRACT

Collective oscillations of excitable elements: order parameters, bistability and the role of stochasticity

We study the effects of a probabilistic refractory period in the collective behavior of coupled discrete-time excitable cells (SIRS-like cellular automata). Using mean-field analysis and simulations, we show that a synchronized phase with stable collective oscillations exists even with non-deterministic refractory periods. Moreover, further increasing the coupling strength leads to a reentrant transition, where the synchronized phase loses stability. In an intermediate regime, we also observe bistability (and consequently hysteresis) between a synchronized phase and an active but incoherent phase without oscillations. The onset of the oscillations appears in the mean-field equations as a Neimark-Sacker bifurcation, the nature of which (i.e. super- or subcritical) is determined by the first Lyapunov coefficient. This allows us to determine the borders of the oscillating and of the bistable regions. The mean-field prediction thus obtained agrees quantitatively with simulations of complete graphs and, for random graphs, qualitatively predicts the overall structure of the phase diagram. The latter can be obtained from simulations by defining an order parameter q suited for detecting collective oscillations of excitable elements. We briefly review other commonly used order parameters and show (via data collapse) that q satisfies the expected finite size scaling relations.Comment: 19 pages, 7 figure

Ion Transport across Biological Membranes by Carborane-Capped Gold Nanoparticles

Carborane-capped gold nanoparticles (Au/carborane NPs, 2-3 nm) can act as artificial ion transporters across biological membranes. The particles themselves are large hydrophobic anions that have the ability to disperse in aqueous media and to partition over both sides of a phospholipid bilayer membrane. Their presence therefore causes a membrane potential that is determined by the relative concentrations of particles on each side of the membrane according to the Nernst equation. The particles tend to adsorb to both sides of the membrane and can flip across if changes in membrane potential require their repartitioning. Such changes can be made either with a potentiostat in an electrochemical cell or by competition with another partitioning ion, for example, potassium in the presence of its specific transporter valinomycin. Carborane-capped gold nanoparticles have a ligand shell full of voids, which stem from the packing of near spherical ligands on a near spherical metal core. These voids are normally filled with sodium or potassium ions, and the charge is overcompensated by excess electrons in the metal core. The anionic particles are therefore able to take up and release a certain payload of cations and to adjust their net charge accordingly. It is demonstrated by potential-dependent fluorescence spectroscopy that polarized phospholipid membranes of vesicles can be depolarized by ion transport mediated by the particles. It is also shown that the particles act as alkali-ion-specific transporters across free-standing membranes under potentiostatic control. Magnesium ions are not transported