Aggregation of slipped-cofacial phthalocyanine J-type dimers: Spectroscopic and AFM study.

Direct metallation of 2-hydroxyphthalocyanine J-type slipped-cofacial dimeric ligand by Mg, Zn, Cu, Ni and Co salts has been carried out to obtain corresponding metal complexes selectively without any noticeable dissociation or polymerization of the starting ligand. Integrated analysis of aggregation properties in the synthesized series has been conducted with the involvement of AFM microscopy, UV/Vis spectroscopy and theoretical assessment. As a result, a nonlinear relationship between absorption and concentration was found, with aggregation beginning to appear at concentrations above 3.3 × 10-5 mol L-1 with predominant formation of trimers from the dimeric molecules in THF solutions.

Light localization and SERS in tip-shaped silicon metasurface.

Optical properties of two dimensional periodic system of the silicon micro-cones are investigated. The metasurface, composed of the silicon tips, shows enhancement of the local optical field. Finite element computer simulations as well as real experiment reveal anomalous optical response of the dielectric metasurface due to excitation of the dielectric resonances. Various electromagnetic resonances are considered in the dielectric cone. The metal-dielectric resonances, which are excited between metal nanoparticles and dielectric cones, are also considered. The resonance local electric field can be much larger than the field in the usual surface plasmon resonances. To investigate local electric field the signal molecules are deposited on the metal nanoparticles. We demonstrate enhancement of the electromagnetic field and Raman signal from the complex of DTNB acid molecules and gold nanoparticles, which are distributed over the metasurface. The metasurfaces composed from the dielectric resonators can have quasi-continuous spectrum and serve as an efficient SERS substrates.

An integrated semiconductor device enabling non-optical genome sequencing.

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

DMET microarray technology for pharmacogenomics-based personalized medicine.

Human genome sequence variation in the form of single nucleotide polymorphisms (SNPs) as well as more complex structural variation such as insertions, duplications, and deletions underlies each individual's response to drugs and thus the likelihood of experiencing an adverse drug reaction. The ongoing challenge of the field of pharmacogenetics is to further understand the relationship between genetic variation and differential drug responses, with the overarching goal being that this will lead to improvements in both the safety and efficacy of drugs. The Affymetrix DMET Plus Premier Pack (DMET stands for Drug Metabolizing Enzymes and Transporters) enables highly multiplexed genotyping of known polymorphisms in Absorption, Distribution, Metabolism, and Elimination (ADME)-related genes on a single array. The DMET Plus Panel interrogates markers in 225 genes that have documented functional significance in phase I and phase II drug metabolism enzymes as well as drug transporters. The power of the DMET Assay has previously been demonstrated with regard to several different drugs including warfarin and clopidogrel. In a research study using an earlier four-color version of the assay, it was demonstrated that warfarin dosing can be influenced by a cytochrome P450 (CYP) 4F2 variant. Additionally, the assay has been used to demonstrate that CYP2C19 variants with decreased enzyme activity led to lower levels of the active clopidogrel metabolite, resulting in a decreased inhibition of platelets and a higher rate of cardiovascular events when compared to noncarriers of the DNA variant. Thus, highly multiplexed SNP genotyping focused on ADME-related polymorphisms should enable research into development of safer drugs with greater efficacy.

Application of quantum dots to multicolor microarray experiments: four-color genotyping.

Highly multiplexed genomics assays are challenged by the need for a sufficient signal-to-noise ratio for each marker scored on a microarray-detection platform. Typically, as the number of markers scored (or target complexity) increases, either more assay-target material must be applied to the array or the specific activity of each marker must be proportionately increased. However, hybridization of excessive amounts of target to the microarray can result in elevated nonspecific binding and consequent degradation of information. We have found that quantum dots provide a successful alternative to organic dyes for achieving highly multiplexed (>20,000-plex) and highly accurate, four-color genotyping and have the additional advantage of being excitable by a single wavelength of light despite their distinct emission wavelengths.

Integration of rapid cytosolic Ca2+ signals by mitochondria in cat ventricular myocytes.

Decoding of fast cytosolic Ca(2+) concentration ([Ca(2+)](i)) transients by mitochondria was studied in permeabilized cat ventricular myocytes. Mitochondrial [Ca(2+)] ([Ca(2+)](m)) was measured with fluo-3 trapped inside mitochondria after removal of cytosolic indicator by plasma membrane permeabilization with digitonin. Elevation of extramitochondrial [Ca(2+)] ([Ca(2+)](em)) to >0.5 microM resulted in a [Ca(2+)](em)-dependent increase in the rate of mitochondrial Ca(2+) accumulation ([Ca(2+)](em) resulting in half-maximal rate of Ca(2+) accumulation = 4.4 microM) via Ca(2+) uniporter. Ca(2+) uptake was sensitive to the Ca(2+) uniporter blocker ruthenium red and the protonophore carbonyl cyanide p-trifluoromethoxyphenylhydrazone and depended on inorganic phosphate concentration. The rates of [Ca(2+)](m) increase and recovery were dependent on the extramitochondrial [Na(+)] ([Na(+)](em)) due to Ca(2+) extrusion via mitochondrial Na(+)/Ca(2+) exchanger. The maximal rate of Ca(2+) extrusion was observed with [Na(+)](em) in the range of 20-40 mM. Rapid switching (0.25-1 Hz) of [Ca(2+)](em) between 0 and 100 microM simulated rapid beat-to-beat changes in [Ca(2+)](i) (with [Ca(2+)](i) transient duration of 100-500 ms). No [Ca(2+)](m) oscillations were observed, either under conditions of maximal rate of Ca(2+) uptake (100 microM [Ca(2+)](em), 0 [Na(+)](em)) or with maximal rate of Ca(2+) removal (0 [Ca(2+)](em), 40 mM [Na(+)](em)). The slow frequency-dependent increase of [Ca(2+)](m) argues against a rapid transmission of Ca(2+) signals between cytosol and mitochondria on a beat-to-beat basis in the heart. [Ca(2+)](m) changes elicited by continuous or pulsatile exposure to elevated [Ca(2+)](em) showed no difference in mitochondrial Ca(2+) uptake. Thus in cardiac myocytes fast [Ca(2+)](i) transients are integrated by mitochondrial Ca(2+) transport systems, resulting in a frequency-dependent net mitochondrial Ca(2+) accumulation.

Capacitative Calcium Entry.

Capacitative Ca(2+) entry is a recently discovered Ca(2+) entry pathway that is activated on depletion of intracellular Ca(2+) stores, providing an avenue for store refilling. Despite recent progress in elucidating the capacitative Ca(2+) entry pathway, the mysteries of its molecular identity, its biophysical properties, and the store depletion signal remain.