Microfluidic capture and release of bacteria in a conical nanopore array

We present a simple and inexpensive method for the capture and release of bacteria contained in an array of conical nanopores on a membrane inside a microfluidic device. As an example, we demonstrate that cyanobacteria can be captured, one bacterium per pore, in a defined orientation with over 500 bacteria per membrane with viabilities as high as 100%. The device can also specifically capture cyanobacteria from a mixed suspension of cyanobacteria and chlamydomonas with a selectivity as high as 90%.     

Potential and limitations of ensemble docking

A major problem in structure-based virtual screening applications is the appropriate selection of a single or even multiple protein structures to be used in the virtual screening process. A priori it is unknown which protein structure(s) will perform best in a virtual screening experiment. We investigated the performance of ensemble docking, as a function of ensemble size, for eight targets of pharmaceutical interest. Starting from single protein structure docking results, for each ensemble size up to 500,000 combinations of protein structures were generated, and, for each ensemble, pose prediction and virtual screening results were derived. Comparison of single to multiple protein structure results suggests improvements when looking at the performance of the worst and the average over all single protein structures to the performance of the worst and average over all protein ensembles of size two or greater, respectively. We identified several key factors affecting ensemble docking performance, including the sampling accuracy of the docking algorithm, the choice of the scoring function, and the similarity of database ligands to the cocrystallized ligands of ligand-bound protein structures in an ensemble. Due to these factors, the prospective selection of optimum ensembles is a challenging task, shown by a reassessment of published ensemble selection protocols.     

An investigation of a genomewide supported psychosis variant in ZNF804A and white matter integrity in the human brain

ZNF804A, a genomewide supported susceptibility gene for schizophrenia and bipolar disorder, has been associated with task-independent functional connectivity between the left and right dorsolateral prefrontal cortices. Several lines of evidence have converged on the hypothesis that this effect may be mediated by structural connectivity. We tested this hypothesis using diffusion tensor magnetic resonance imaging in three samples: one German sample of 50 healthy individuals, one Scottish sample of 83 healthy individuals and one Scottish sample of 84 unaffected relatives of bipolar patients. Voxel-based analysis and tract-based spatial statistics did not detect any fractional anisotropy (FA) differences between minor allele carriers and individuals homozygous for the major allele at rs1344706. Similarly, region-of-interest analyses and quantitative tractography of the genu of the corpus callosum revealed no significant FA differences between the genotype groups. Examination of effect sizes and confidence intervals indicated that this negative finding is very unlikely to be due to a lack of statistical power. In summary, despite using various analysis techniques in three different samples, our results were strikingly and consistently negative. These data therefore suggest that it is unlikely that the effects of genetic variation at rs1344706 on functional connectivity are mediated by structural integrity differences in large, long-range white matter fiber connections.     

Polarized Raman spectroscopy of oligothiophene crystals to determine unit cell orientation

Raman spectra were recorded experimentally and calculated theoretically for bithiophene, terthiophene, and quaterthiophene samples as a function of excitation polarization. Distinct spectral signatures were assigned and correlated to the molecular/unit cell orientation as determined by X-ray diffraction. The ability to predict molecular/unit cell orientation within organic crystals using polarized Raman spectroscopy was evaluated by predicting the unit cell orientation in a simulated terthiophene crystal given a random set of simulated polarized Raman spectra. Polarized Raman spectroscopy offers a promising tool to quickly and economically determine the unit cell orientation in known organic crystals and crystalline thin films. Implications of our methodologies for studying individual molecule conformations are discussed.     

Computational studies on ethylene addition to nickel bis(dithiolene)

The density functionals B3LYP, B3PW91, BMK, HSE06, LC-ωPBE, M05, M06, O3LYP, TPSS, ω-B97X, and ω-B97XD are used to optimize key transition states and intermediates for ethylene addition to Ni(edt)(2) (edt = S(2)C(2)H(2)). The efficacy of the basis sets 6-31G**, 6-31++G**, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ is also examined. The geometric parameters optimized with different basis sets and density functionals are similar and agree well with experimental values. The ω-B97XD functional gives relative energies closest to those from CCSD, while M06 and HSE06 yield results close to those from CCSD(T). CASSCF and CASSCF-PT2 calculation results are also given. Variation of the relative energies from different density functionals appears to arise, in part, from the multireference character of this system, as confirmed by the T1 diagnostic and CASSCF calculations.     

Maximising the efficiency of continuous photo-oxidation with singlet oxygen in supercritical CO2 by use of fluorous biphasic catalysis

Using a continuous fluorous biphasic separation, a photo-oxidation catalyst can be recycled, with increased productivity and a ×20 fold decrease in the amount of catalyst required.     

Selective guest recognition by a self-assembled paramagnetic cage complex

A cubic cage complex assembled from twelve bis-bidentate ligands and eight Co(II) ions provides a cavity that selectively recognises and binds coumarin in MeCN solution. The cage portals are large enough to allow guest exchange, but small enough to provide a kinetic trap; the cage paramagnetism facilitates detailed NMR analysis.     

The three-channel model of sound localization mechanisms: interaural level differences

The current understanding of mammalian sound localization is that azimuthal (horizontal) position assignments are dependent upon the relative activation of two populations of broadly-tuned hemifield neurons with overlapping medial borders. Recent psychophysical work has provided evidence for a third channel of low-frequency interaural time difference (ITD)-sensitive neurons tuned to the azimuthal midline. However, the neurophysiological data on free-field azimuth receptive fields, especially of cortical neurons, has primarily studied high-frequency cells whose receptive fields are more likely to have been shaped by interaural level differences (ILDs) than ITDs. In four experiments, a selective adaptation paradigm was used to probe for the existence of a midline channel in the domain of ILDs. If no midline channel exists, symmetrical adaptation of the lateral channels should not result in a shift in the perceived intracranial location of subsequent test tones away from the adaptors because the relative activation of the two channels will remain unchanged. Instead, results indicate a shift in perceived test tone location away from the adaptors, which supports the existence of a midline channel in the domain of ILDs. Interestingly, this shift occurs not only at high frequencies, traditionally associated with ILDs in natural settings, but at low frequencies as well.     

Distribution of coexisting solid and fluid phases alters the kinetics of collapse from phospholipid monolayers

To determine how coexistence of liquid-expanded (LE) and tilted-condensed (TC) phases in phospholipid monolayers affects collapse from the air/water interface, we studied binary films containing dioleoyl phosphatidylcholine-dipalmitoyl phosphatidylcholine (DPPC) mixtures between 10 and 100% DPPC. Previously published results established that this range of compositions represents the LE-TC coexistence region at the equilibrium spreading pressure of 47 mN/m. When held at 49.5 mN/m on a captive bubble, the extent of total collapse fit with the LE area predicted by the phase diagram. The kinetics of collapse, however, when normalized for changes in the LE area, slowed with increasing mole fraction of DPPC. Surface area expressed as stretched exponential functions of time yielded an Avrami exponent that decreased from 1 for the homogeneously LE film to 0.3 for DPPC > or = 70%. Microscopic studies showed that the largest changes in kinetics occurred when either alterations of the initial composition or the process of collapse induced the films to cross the percolation threshold, so that the LE phase became divided into isolated domains. Our results show that although coexisting solid and fluid phases collapse to extents that are independent, the kinetics of collapse, corrected for differences in LE area, depend on the distribution of the two phases.