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At least 1,603 records · Page 89Linked to original sources
PubMed2002

Rapid prototyping for injection moulded integrated microfluidic devices and diffractive element arrays.

This paper describes two fabrication procedures that makes it possible to design, fabricate and injection mold a microfluidic system with an on board coupling element or an optical array platform in less than four hours. Epoxy masters for the array and a single diffractive element were produced using conventional soft lithography techniques and a commercially available UV curable epoxy. The fabrication of the master for the integrated microfluidic device utilized the surface chemistry of polyester and its interaction with the anionic surfactant sodium dodecyl sulfate (SDS), to selectively inhibit the adhesion between the epoxy and the polyester film during the curing reaction. The transfer of a microfluidic design and the required coupling element (632 nm holographic grating) along the base of the channel was completed in a single step. The turnaround time from design to injection molded device whether a microchannel or array was 3.5 h.

Journal Article↗
PubMed2003

A prototype solid phase synthesis of pteridines and related heterocyclic compounds.

The development of a versatile solid phase synthesis of bicyclic polyaza heterocycles including pteridines, purines, and deazapurines is described. The strategy comprises the linking of a pre-formed pyrimidine through a thioether at the 2 or 4 position to a polystyrene resin, the cyclisation of the second ring, and the direct or oxidative cleavage of the product from the resin by nucleophilic substitution. This provides not only for substituent variation in the second ring, but also for variation at the site of cleavage. Limitations in the scope of the methodology are set by the intrinsic reactivity of pyrimidinyl 2- or 4-thioethers which, whilst undergoing ready nitration at C5, are surprisingly difficult to alkylate and acylate.

Cyclization↗
PubMed2003

An integrated optical oxygen sensor fabricated using rapid-prototyping techniques.

This paper details the design and fabrication of an integrated optical biochemical sensor using a select oxygen-sensitive fluorescent dye, tris(2,2'-bipyridyl) dichlororuthenium(ii) hexahydrate, combined with polymeric waveguides that are fabricated on a glass substrate. The sensor uses evanescent interaction of light confined within the waveguide with the dye that is immobilized on an SU-8 waveguide surface. Adhesion of the dye to the integrated waveguide surface is accomplished using a unique process of spin-coating/electrostatic layer-by-layer formation. The SU-8 waveguide was chemically modified to allow the deposition process. Exposure of the dye molecules to the analyte and subsequent chemical interaction is achieved by directly coupling the fluid channel to the integrated waveguide. The completed sensor was linear in the dissolved oxygen across a wide range of interest and had a sensitivity of 0.6 ppm. A unique fabrication aspect of this sensor is the inherent simplicity of the design, and the resulting rapidity of fabrication, while maintaining a high degree of functionality and flexibility.

Journal Article↗
PubMed2004

High affinity DNAzyme-based ligands for transition metal cations - a prototype sensor for Hg2+.

Inspired by recent interest in DNAzymes as transition metal ion sensors, a survey of the effects of various transition metals on the intramolecular cleavage rate of an imidazole modified, M(2+)-independent, self-cleaving "9(25)-11" DNA is reported. In particular, 9(25)-11 activity was strongly inhibited by Hg(2+)(K(d)(APP)= 110 +/- 9 nM). It is postulated that the affinity and selectivity of 9(25)-11 for Hg(2+) stems from the fact that this synthetically modified DNAzyme contains imidazoles. This study demonstrates the utility of modified nucleotides in developing DNAzyme sensors for metals ions, especially those for which unmodified nucleic acids might not serve as inherently good ligands.

Base Pairing↗
PubMed2004

Microfluidic channel fabrication in dry film resist for production and prototyping of hybrid chips.

Microfluidic networks are patterned in a dry film resist (Ordyl SY300/550) that is sandwiched in between two substrates. The technique enables fabrication of complex biochips with active elements both in the bottom and the top substrate (hybrid chips). The resist can be double bonded at relatively low temperatures without the use of extra adhesives. A postbake transfers the resist into a rigid structure. The resist is qualified in terms of resolution, biocompatibility and fluidic sealing. Fabrication in both a fully equipped cleanroom setting as well as a minimally equipped laboratory is described. The technique is applied for dielectrophoresis-based cell separation systems and a fuel cell reaction chamber with micropillars. The dry film resist can be considered a cheap and fast alternative to SU-8.

Journal Article↗
PubMed2005

Transition metal-complexed catenanes and rotaxanes as molecular machine prototypes.

Transition metal-containing catenanes and rotaxanes are ideally suited to build molecular machines and motors; in the present review article, three examples from our group are discussed which consist of (i) a fast-moving electrochemically-driven pirouetting machine, (ii) a linear rotaxane dimer whose behaviour is reminiscent of muscles, in the sense that it can be stretched or contracted and (iii) a light-driven machine consisting of a catenane constructed around a ruthenium(II) centre.

Journal Article↗
PubMed2005

The effect of solvent polarity on the photophysical properties of 4-cyano-(4'-methylthio)diphenylacetylene: a prototypic donor-acceptor system.

The photophysical properties of the target compound are extremely sensitive to changes in solvent polarity since the lowest-energy excited states possess considerable charge-transfer character. Excitation results in a greatly increased dipole moment, with the resultant excited singlet state retaining a lifetime of ca. 1 ns in all solvents. Radiative decay involves coupling between the lowest-energy excited singlet state and both the ground state and an upper excited singlet state. The level of coupling to the upper singlet decreases in non-polar solvents, presumably due to symmetry factors. The radiative rate constant decreases smoothly with increasing solvent polarity function as the molecule acquires an ever increasing dipolar character. Non-radiative decay includes both intersystem crossing and internal conversion, but the former process dominates in polar solvents. The excited singlet state lifetime is very weakly dependent upon temperature in the solid state. However, in polar solutions where the Stokes' shift decreases with decreasing temperature, there is clear evidence for an activated process. This is believed to involve coupling to the upper-lying singlet excited state.

Acetylene↗
PubMed2001

Structural, signalling and regulatory properties of the group I metabotropic glutamate receptors: prototypic family C G-protein-coupled receptors.

In 1991 a new type of G-protein-coupled receptor (GPCR) was cloned, the type 1a metabotropic glutamate (mGlu) receptor, which, despite possessing the defining seven-transmembrane topology of the GPCR superfamily, bore little resemblance to the growing number of other cloned GPCRs. Subsequent studies have shown that there are eight mammalian mGlu receptors that, together with the calcium-sensing receptor, the GABA(B) receptor (where GABA is gamma-aminobutyric acid) and a subset of pheromone, olfactory and taste receptors, make up GPCR family C. Currently available data suggest that family C GPCRs share a number of structural, biochemical and regulatory characteristics, which differ markedly from those of the other GPCR families, most notably the rhodopsin/family A GPCRs that have been most widely studied to date. This review will focus on the group I mGlu receptors (mGlu1 and mGlu5). This subgroup of receptors is widely and differentially expressed in neuronal and glial cells within the brain, and receptor activation has been implicated in the control of an array of key signalling events, including roles in the adaptative changes needed for long-term depression or potentiation of neuronal synaptic connectivity. In addition to playing critical physiological roles within the brain, the mGlu receptors are also currently the focus of considerable attention because of their potential as drug targets for the treatment of a variety of neurological and psychiatric disorders.

Animals↗
PubMed1981

The complete amino acid sequence of a prototype immunoglobulin-lambda light-chain-type amyloid-fibril protein AR.

The amino acid sequence of an amyloid-fibril protein of immunoglobulin light-chain type (AL) was elucidated. The sequence determination involved digesting the protein with trypsin, thermolysin and pepsin. The protein was found to consist of 154 amino acid residues and is thus missing about half of the constant region of a light chain. A certain heterogeneity in the length of the polypeptide was observed in the C-terminal region. The amino acid sequence from CDR (complementary-determining region) 1 and FR (framework region) 3 indicated an oligoclonal origin of the protein. By comparing the primary structure of protein AR with other lambda- and even kappa-chains, it was revealed that protein AR had an insertion of two residues of aspartic acid, namely residues 68 and 69, which has not been reported previously in light chains. The overall sequence homology in the variable region showed that protein AR is more similar to V lambda V than to the other subgroups [Kabat, Wu & Bilofsky (1979) Variable regions of Immunoglobulin Chains, Medical Computer Systems, Bolt, Beranek and Newman, Cambridge, MA].

Amino Acid Sequence↗
PubMed2002

Identification of two domains and distal histidine ligands to the four haems in the bacterial c-type cytochrome NapC; the prototype connector between quinol/quinone and periplasmic oxido-reductases.

NapC is a tetra-haem member of a family of bacterial membrane-anchored multi-haem c -type cytochromes implicated in electron transfer between membrane quinols and periplasmic enzymes. The water-soluble tetra-haem fragment of Paracoccus pantotrophus NapC has been expressed as a periplasmic protein (NapC(sol)) in Paracoccus denitrificans, P. pantotrophus and Escherichia coli. Site-specific mutagenesis of NapC(sol), combined with spectroscopic studies, suggests that each haem iron centre has bis -histidinyl co-ordination. Four proximal ligands arise from each of four Cys-Xaa-Xaa-Cys-His haem-binding motifs; candidates for the four distal ligands are His(81), His(99), His(174) and His(194). NapC(H81A), NapC(H99A), NapC(H174A) and NapC(H194A) mutants (with alanine substituted for each of the four candidate residues) have all been purified from E. coli. In each case, one of the haems has become high-spin, as judged by the presence of a broad absorption band between 620 nm and 650 nm for the oxidized cytochrome; this feature is absent for wild-type protein and presumably arises because of the absence of the distal histidine ligand from one of the haems. NapC(H81A) and NapC(H174A) are less well expressed in E. coli than NapC(H99A) and NapC(H194A) and cannot be detected when expressed in P. denitrificans or P. pantotrophus. In vitro and in vivo complementation studies demonstrate that the soluble periplasmic NapC can mediate electron transfer from quinols to the periplasmic nitrate reductase. This capacity was retained in vitro with the NapC(H99A) and NapC(H194A) mutants but was lost in vivo. A model for the structural organization of NapC(sol) into two domains, each containing a di-haem pair, is proposed. In this model, each haem pair obtains one distal haem ligand from its own domain and a second from the other domain. The suggestion of two domains is supported by observations that the 24 kDa NapC(sol) cleaves to yield a 12 kDa haem-staining band. Determination of the cleavage site showed it was between two equally sized di-haem domains predicted from sequence analysis.

Amino Acid Sequence↗
PubMed2005

Crystal structure of DMGO provides a prototype for a new tetrahydrofolate-binding fold.

The crystal structure of DMGO (dimethylglycine oxidase) from Arthrobacter globiformis in complex with folate compounds has revealed a novel THF (tetrahydrofolate)-binding fold [Leys, Basran and Scrutton (2003) EMBO J. 22, 4038-4048]. This fold is widespread among folate-binding proteins. The crystal structures of aminomethyltransferase (T-protein), YgfZ and TrmE all reveal similar THF-binding folds despite little similarity in sequence or function. The THF-binding site is highly specific for reduced folate compounds and most members of this fold family enhance the nucleophilic character of the THF N10 position.

Binding Sites↗
PubMed2003

Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function.

Signal transduction by a traditional two-component system involves a sensor protein that recognizes a physiological signal, autophosphorylates and transfers its phosphate, and a response regulator protein that receives the phosphate, alters its affinity toward specific target proteins or DNA sequences and causes change in metabolic activity or gene expression. In some cases the sensor protein, when unphosphorylated, has a positive effect upon the rate of dephosphorylation of the regulator protein (bifunctional sensor), whereas in other cases it has no such effect (monofunctional sensor). In this work we identify structural and functional differences between these two designs. In the first part of the paper we use sequence data for two-component systems from several organisms and homology modelling techniques to determine structural features for response regulators and for sensors. Our results indicate that each type of reference sensor (bifunctional and monofunctional) has a distinctive structural feature, which we use to make predictions regarding the functionality of other sensors. In the second part of the paper we use mathematical models to analyse and compare the physiological function of systems that differ in the type of sensor and are otherwise equivalent. Our results show that a bifunctional sensor is better than a monofunctional sensor both at amplifying changes in the phosphorylation level of the regulator caused by signals from the sensor and at attenuating changes caused by signals from small phosphodonors. Cross-talk to or from other two-component systems is better suppressed if the transmitting sensor is monofunctional, which is the more appropriate design when such cross-talk represents pathological noise. Cross-talk to or from other two-component systems is better amplified if the transmitting sensor is bifunctional, which is the more appropriate design when such cross-talk represents a physiological signal. These results provide a functional rationale for the selection of each design that is consistent with available experimental evidence for several two-component systems.

Bacterial Proteins↗
PubMed2002

The structure of the O-chain of the lipopolysaccharide of a prototypal diarrheagenic strain of Hafnia alvei that has characteristics of a new species under the genus Escherichia.

The structure of the O-polysaccharide of the lipopolysaccharide from a diarrheal strain isolated in Bangladesh was studied with sugar, and methylation analysis, NMR spectroscopy, mass spectrometry and partial acid hydrolysis. The strain was first designated as Hafnia alvei, but later found to be a possible new species in the genus Escherichia. Two different polysaccharides were detected, a major and a minor one. The structure of the major polysaccharide is given below, while the structure of the minor one was not investigated. The structure of the repeating unit was established as The structure does not resemble any of the previously investigated lipopolysaccharide O-chains from Escherichia coli or H. alvei, but could fit in either group based on types of sugar residues and acidity. Phenotypic microbiological studies cannot definitely assign it to either species of the two genera. Genetic hybridization studies indicate that the Bangladeshi isolates may require a new species designation under the genus Escherichia.

Carbohydrate Conformation↗
PubMed2002

A prototype HeartQuest ventricular assist device for particle image velocimetry measurements.

The objective of this study is to fully characterize the flow within the HeartQuest ventricular assist device (VAD), a magnetically levitated centrifugal VAD, using particle image velocimetry (PIV) to identify regions of potential high shear or stagnation and validate and refine computational models of the flow. An acrylic model of the pump was designed and constructed to allow optical access into all interior regions of the pump. The geometry of the exterior housing and the use of a novel working fluid make quantitative measurements of velocity within the exit volute, blade passage, cut-water, blade tip clearance, and pump inlet possible. Highly accurate velocity measurements using particle PIV have been made in one region (the inlet elbow), and measurements in the other critical regions of the pump will be made. These measurements are used for investigation of regions with potential for hemolysis resulting from high shear stress or with potential for thrombosis caused by recirculation or stagnation. Quantitative velocity data are also needed for comparison with computational fluid dynamics (CFD) models of the VAD. In this study, experiments have again proven to be an essential complement to CFD for thorough investigations of the flow inside the pump.

Blood Flow Velocity↗