Single-cell recording and stimulation with a 16k micro-nail electrode array integrated on a 0.18 μm CMOS chip

To cope with the growing needs in research towards the understanding of cellular function and network dynamics, advanced micro-electrode arrays (MEAs) based on integrated complementary metal oxide semiconductor (CMOS) circuits have been increasingly reported. Although such arrays contain a large number of sensors for recording and/or stimulation, the size of the electrodes on these chips are often larger than a typical mammalian cell. Therefore, true single-cell recording and stimulation remains challenging. Single-cell resolution can be obtained by decreasing the size of the electrodes, which inherently increases the characteristic impedance and noise. Here, we present an array of 16,384 active sensors monolithically integrated on chip, realized in 0.18 μm CMOS technology for recording and stimulation of individual cells. Successful recording of electrical activity of cardiac cells with the chip, validated with intracellular whole-cell patch clamp recordings are presented, illustrating single-cell readout capability. Further, by applying a single-electrode stimulation protocol, we could pace individual cardiac cells, demonstrating single-cell addressability. This novel electrode array could help pave the way towards solving complex interactions of mammalian cellular networks.     

Noncontrast dynamic MRA in intracranial arteriovenous malformation (AVM), comparison with time of flight (TOF) and digital subtraction angiography (DSA)

Digital subtraction angiography (DSA) remains the gold standard to diagnose intracranial arteriovenous malformations (AVMs) but is invasive. Existing magnetic resonance angiography (MRA) is suboptimal for assessing the hemodynamics of AVMs. The objective of this study was to evaluate the clinical utility of a novel noncontrast four-dimensional (4D) dynamic MRA (dMRA) in the evaluation of intracranial AVMs through comparison with DSA and time-of-flight (TOF) MRA. Nineteen patients (12 women, mean age 26.2±10.7 years) with intracranial AVMs were examined with 4D dMRA, TOF and DSA. Spetzler-Martin grading scale was evaluated using each of the above three methods independently by two raters. Diagnostic confidence scores for three components of AVMs (feeding artery, nidus and draining vein) were also rated. Kendall's coefficient of concordance was calculated to evaluate the reliability between two raters within each modality (dMRA, TOF, TOF plus dMRA). The Wilcoxon signed-rank test was applied to compare the diagnostic confidence scores between each pair of the three modalities. dMRA was able to detect 16 out of 19 AVMs, and the ratings of AVM size and location matched those of DSA. The diagnostic confidence scores by dMRA were adequate for nidus (3.5/5), moderate for feeding arteries (2.5/5) and poor for draining veins (1.5/5). The hemodynamic information provided by dMRA improved diagnostic confidence scores by TOF MRA. As a completely noninvasive method, 4D dMRA offers hemodynamic information with a temporal resolution of 50-100 ms for the evaluation of AVMs and can complement existing methods such as DSA and TOF MRA.     

Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures

Verification by imaging of the structure of 3D DNA constructs, both bare and conjugated to metal nanoparticles, is challenging. We demonstrate here two transmission electron microscopy (TEM) based methods to distinguish between fully formed tetrahedra, synthesized from DNA conjugated with gold nanoparticles (GNPs) at their vertices, and structures which are only partially formed. When deposited on a surface, fully formed tetrahedra are expected to retain their 3D pyramidal structure, while partially formed structures are expected to form a 2D structure. The first method by which 3D and 2D structures were distinguished was imaging them at different defocusing values. While for 2D structures all the four GNPs acquire Fresnel fringes at the same defocusing value, for 3D structures at least one particle is at a different plane with respect to the others, and so it acquires Fresnel fringes at a different defocusing value. The second method we show is imaging of the structures at different angles. While a single TEM image gives only a 2D projection of the structure, by combining information achieved from imaging at several tilting angles one may verify the structural construct.     

HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.     

An Operations Research Approach to the Problem of the Sugarcane Selection

Selection for superior clones is the most important aspect of sugar cane improvement programs, and is a long and expensive process. While studies have investigated different components of selection independently, there has not been a whole system approach to improve the process. This study observes the problem as an integrated system, where if one parameter changes the state of the whole system changes. A computer based stochastic simulation model that accurately represents the selection was developed. This paper describes the simulation model, showing its accuracy as well as how a combination of dynamic programming and branch and bound can be applied to the model to optimise the selection system, giving a new application of these techniques. The model can be directly applied to any region targeted by sugarcane breeding programs or to other clonally propagated crops.     

Improving the Sensitivity of a Quartz Crystal Microbalance for Biosensing by Using Porous Gold

 A quartz crystal microbalance can be used as a biosensor if biological receptor molecules (ligands) are attached to the crystal. To improve the sensitivity, the surface area of the gold electrodes on the crystal was increased by rendering the electrodes porous. This increased the response up to a factor of 3. A protein model system with human anti-myoglobin as ligand and sheep skeletal myoglobin at different concentrations as analyte was used. The quartz crystal was mounted in a flow-cell, where immobilisation, binding and regeneration of the surface were carried out. The kinetics of the model system was monitored under various experimental conditions. Received February 2, 2000. Revision June 30, 2000.     

Determination of deoxynivalenol in cereals and cereal products by immunoaffinity column cleanup with liquid chromatography: interlaboratory study

An interlaboratory study was performed on behalf of the UK Food Standards Agency to evaluate the effectiveness of an immunoaffinity column cleanup liquid chromatographic (LC) method for the determination of deoxynivalenol in a variety of cereals and cereal products at proposed European regulatory limits. The test portion was extracted with water. The sample extract was filtered a applied to an immunoaffinity column. After being washed with water, the deoxynivalenol was eluted with acetonitrile or methanol. Deoxynivalenol was quantitated by reversed-phase LC with UV determination. Samples of artificially contaminated wheat-flour, rice flour, oat flour, polenta, and wheat based breakfast cereal, naturally contaminated wheat flour, and blank (very low level) samples of each matrix were sent to 13 collaborators in 7 European countries. Participants were asked to spike test portions of all samples at a range of deoxynivalenol concentrations equivalent to 200-2000 ng/g deoxynivalenol. Average recoveries ranged from 78 to 87%. Based on results for 6 artificially contaminated samples (blind duplicates), the relative standard deviation for repeatability (RSDr) ranged from 3.1 to 14.1%, and the relative standard deviation for reproducibility (RSDR) ranged from 11.5 to 26.3%. The method showed acceptable within-laboratory and between-laboratory precision for all 5 matrixes, as evidenced by HorRat values < 1.3.     

Probing the interaction of solvents with the stationary phase of C18 high-performance liquid chromatographic column material by variable-temperature dependent 129Xe nuclear magnetic resonance spectroscopy

VT (129)Xe NMR was applied to probe the interactions of solvents having different polarity indices with the stationary phase of a RP-C18 HPLC column material. It was observed that the highly polar ethylene glycol molecules do not mix with the alkyl chains of the RP-C18 stationary phase and the solvent is unable to enter the pores and the spaces between the particles. Three phases in this sample are defined as stationary/xenon phase, xenon gas phase (in the pores and the spaces between the particles) and ethylene glycol/xenon phase. In contrast to ethylene glycol, the nonpolar solvent cyclohexane was observed to be well mixed with the RP-C18 stationary phase. The capillary rise effect allows the solvent to enter the pores and the spaces between the particles. Two phases in this sample are defined as stationary/cyclohexane/xenon phase and cyclohexane/xenon phases. The properties of ethyl acetate are between those of ethylene glycol and cyclohexane. The (129)Xe NMR results show that the rational reversed phases should be conditioned from highly solvating to more polar solvents to remove the trapped air. The (129)Xe NMR results also show that pure stationary phase exists only when a highly polar solvent is used in reversed-phase chromatography. For a solvent with lower polarity, a stationary/solvent phase actually forms. This, together with the mobile phase, determines the selective factor for separating mixtures.     

Total synthesis of (-)-reveromycin a

The asymmetric total synthesis of (-)-reveromycin A is described. The key steps involved a Lewis acid catalyzed inverse electron demand hetero-Diels-Alder reaction followed by hydroboration/oxidation to afford the spiroketal core 4 in a highly stereoselective manner and introduction of the C18 hemisuccinate by high-pressure acylation.     

Determination of molar absorptivity coefficients for major type-B trichothecenes and certification of calibrators for deoxynivalenol and nivalenol

This paper presents results from the European Commission-funded project Doncalibrant, the objective of which was to produce calibrators with certified mass fractions of the Fusarium toxins deoxynivalenol (DON), 3-acetyldeoxynivalenol (3-Ac-DON), 15-acetyldeoxynivalenol (15-Ac-DON), and nivalenol (NIV), in acetonitrile. The calibrators, available in ampoules, were sufficiently homogeneous, with between-bottle variations (s _bb) of less than 2%. Long-term stability studies performed at four different temperatures between −18 and 40 °C revealed no significant negative trends (at a confidence level of 95%). Molar absorptivity coefficients (in L mol⁻¹ cm⁻¹) were determined for all four toxins (DON: 6805 ± 126, NIV: 6955 ± 205, 3-Ac-DON: 6983 ± 141, 15-Ac-DON: 6935 ± 142) on the basis of a mini-interlaboratory exercise. The overall uncertainty of the calibrators’ target values for DON and NIV were evaluated on the basis of gravimetric preparation data and include uncertainty contributions from possible heterogeneity, storage, and transport. The Doncalibrant project resulted in the production of calibrators for DON (IRMM-315) and NIV (IRMM-316) in acetonitrile with certified mass fractions of 25.1 ± 1.2 μg g⁻¹ and 24.0 ± 1.1 μg g⁻¹, respectively. Both CRMs became commercially available from the Institute for Reference Materials and Measurements (IRMM, Geel, Belgium) at the beginning of 2007.