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High-throughput
Terms modified by High-throughput Selected AbstractsHigh-Throughput and Combinatorial Methods in Polymer Research: Their Time Has ComeMACROMOLECULAR RAPID COMMUNICATIONS, Issue 1 2003Ulrich S. Schubert No abstract is available for this article. [source] A Practical Oxone®-Mediated, High-Throughput, Solution-Phase Synthesis of Benzimidazoles from 1,2-Phenylenediamines and Aldehydes and Its Application to Preparative Scale Synthesis.CHEMINFORM, Issue 50 2003Pierre L. Beaulieu Abstract For Abstract see ChemInform Abstract in Full Text. [source] High-throughput multiplex microsatellite marker assay for detection and quantification of adulteration in Basmati rice (Oryza sativa)ELECTROPHORESIS, Issue 14 2007Sunil Archak Abstract Basmati rice is a very special type of aromatic rice known world-wide for its extra long grains and pleasant and distinct aroma. Traditional Basmati rice cultivars, confined to Indo-Gangetic regions of the Indian subcontinent, are often reported to be adulterated with crossbred Basmati varieties and long-grain non-Basmati varieties in the export market. At present, there is no commercial scale technology to reliably detect adulteration. We report here a CE-based multiplex microsatellite marker assay for detection as well as quantification of adulteration in Basmati rice samples. The single-tube assay multiplexes eight microsatellite loci to generate variety-specific allele profiles that can detect adulteration from 1% upwards. The protocol also incorporates a quantitative-competitive PCR-based analysis for quantification of adulteration. Accuracy of quantification has been shown to be ±1.5%. The experiments used to develop and validate the methodology are described. [source] Spatial near-infrared imaging of hydroxyl band coverage on ceria-based catalystsAICHE JOURNAL, Issue 4 2006Farid Aiouache Abstract High-throughput near-infrared imaging was used to distinguish catalyst activity for low-temperature methane steam-reforming. Geminal hydroxyls of reduced ceria were depicted during methane reforming at 673 K. The changes in absorbance maps under various water partial pressures showed evidence of formate intermediate formations without redox exchanges. Higher resolution was observed in absorbance change images than that of thermal images obtained from catalyst surface self-emissions. The experimental results illustrated higher activity of pure rhodium catalyst than that of bimetallic ones, likely because of the high dispersion of rhodium on the catalyst support. Moreover, the reaction was accelerated when high surface area silica was added because more reduced sites were exposed. Our filter bandwidths limited our interest in band-shift distribution of geminal hydroxyl band during the reduction process. © 2005 American Institute of Chemical Engineers AIChE J, 2006 [source] A multi-ontology framework to guide agriculture and food towards diet and healthJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 8 2007Matthew C Lange Abstract Global increases in metabolic diseases that can be influenced by diet have re-emphasized the importance of considering how different foods can improve human health. The entire agricultural enterprise has an unprecedented opportunity to increase its value by producing foods that improve the health of consumers. Research efforts in agriculture/food science/nutrition are endeavoring to do so, although little tangible success has been achieved. At the core of the problem is a failure to define the goal itself: health. Health, as a scientifically measurable concept, is poorly defined relative to disease, and yet consensus-based, curated vocabularies that describe the multiple variations in human health in useful terms are critical to unifying the scientific fields related to agriculture and nutrition. Each of the life-science disciplines relating to health has developed databases, thesauri, and/or ontologies to capture such knowledge. High-throughput and -omic technologies are expanding both the amount and heterogeneity of available information. Unfortunately, the language used to describe substantially similar (even logically equivalent) concepts is often different between information systems. Increasing the future value of agriculture, therefore, will depend on creating a process for generating common ontologies of the concept of health, and guiding the development of a common language. This paper illustrates a framework for integrating heterogeneous ontologies into interdisciplinary, foods-for-health knowledge systems. A common system of language that describes health and is shared by all the life-science disciplines will provide immediate benefits in terms of increased health-claim regulatory efficiencies and predictive functions for individualized diets. Ultimately, these vocabularies will guide agriculture to its next goal of producing health-enhancing foods. Copyright © 2007 Society of Chemical Industry [source] Noninvasive prenatal diagnosis of fetal blood group phenotypes: current practice and future prospectsPRENATAL DIAGNOSIS, Issue 2 2009Geoff Daniels Abstract Fetuses of women with alloantibodies to RhD (D) are at risk from hemolytic disease of the fetus and newborn, but only if the fetal red cells are D-positive. In such pregnancies, it is beneficial to determine fetal D type, as this will affect the management of the pregnancy. It is possible to predict, with a high level of accuracy, fetal blood group phenotypes from genotyping tests on fetal DNA. The best source is the small quantity of fetal DNA in the blood of pregnant women, as this avoids the requirement for invasive procedures of amniocentesis or chorionic villus sampling (CVS). Many laboratories worldwide now provide noninvasive fetal D genotyping as a routine service for alloimmunized women, and some also test for c, E, C and K. In many countries, anti-D immunoglobulin injections are offered to D-negative pregnant women, to reduce the chances of prenatal immunization, even though up to 40% of these women will have a D-negative fetus. High-throughput, noninvasive fetal D genotyping technologies are being developed so that unnecessary treatment of pregnant women can be avoided. Trials suggest that fetal D typing of all D-negative pregnant women is feasible and should become common practice in the near future. Copyright © 2008 John Wiley & Sons, Ltd. [source] Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2004Izabela Janda High-throughput (HT) protein crystallography is severely impeded by the relatively low success rate of protein crystallization. Proteins whose structures are not solved in the HT pipeline owing to attrition in any phase of the project are referred to as the high-hanging fruit, in contrast to those proteins that yielded good-quality crystals and crystal structures, which are referred to as low-hanging fruit. It has previously been shown that proteins that do not crystallize in the wild-type form can have their surfaces engineered by site-directed mutagenesis in order to create patches of low conformational entropy that are conducive to forming intermolecular interactions. The application of this method to selected proteins from the Bacillus subtilis genome which failed to crystallize in the HT mode is now reported. In this paper, the crystal structure of the product of the YdeN gene is reported. Of three prepared double mutants, i.e. E124A/K127A, E167A/E169A and K88A/Q89A, the latter gave high-quality crystals and the crystal structure was solved by SAD at 1.8,Å resolution. The protein is a canonical ,/, hydrolase, with an active site that is accessible to solvent. [source] Twenty-four-well plate miniature bioreactor high-throughput system: Assessment for microbial cultivationsBIOTECHNOLOGY & BIOENGINEERING, Issue 5 2007Kevin Isett Abstract High-throughput (HT) miniature bioreactor (MBR) systems are becoming increasingly important to rapidly perform clonal selection, strain improvement screening, and culture media and process optimization. This study documents the initial assessment of a 24-well plate MBR system, Micro (µ)-24, for Saccharomyces cerevisiae, Escherichia coli, and Pichia pastoris cultivations. MBR batch cultivations for S. cerevisiae demonstrated comparable growth to a 20-L stirred tank bioreactor fermentation by off-line metabolite and biomass analyses. High inter-well reproducibility was observed for process parameters such as on-line temperature, pH and dissolved oxygen. E. coli and P. pastoris strains were also tested in this MBR system under conditions of rapidly increasing oxygen uptake rates (OUR) and at high cell densities, thus requiring the utilization of gas blending for dissolved oxygen and pH control. The E. coli batch fermentations challenged the dissolved oxygen and pH control loop as demonstrated by process excursions below the control set-point during the exponential growth phase on dextrose. For P. pastoris fermentations, the µ-24 was capable of controlling dissolved oxygen, pH, and temperature under batch and fed-batch conditions with subsequent substrate shot feeds and supported biomass levels of 278 g/L wet cell weight (wcw). The average oxygen mass transfer coefficient per non-sparged well were measured at 32.6,±,2.4, 46.5,±,4.6, 51.6,±,3.7, and 56.1,±,1.6 h,1 at the operating conditions of 500, 600, 700, and 800 rpm shaking speed, respectively. The mixing times measured for the agitation settings 500 and 800 rpm were below 5 and 1 s, respectively. Biotechnol. Bioeng. 2007;98: 1017,1028. © 2007 Wiley Periodicals, Inc. [source] Hochdurchsatz-Methoden in der Festkörperchemie.CHEMIE IN UNSERER ZEIT (CHIUZ), Issue 5 2007Schneller zum Ziel Abstract Hochdurchsatz-Methoden zeichnen sich gegenüber konventionellen Methoden durch eine größere Effizienz aus. Mittlerweile steht im Bereich der Anorganischen Festkörperchemie und der Materialwissenschaften eine Vielzahl von Werkzeugen zur Verfügung, um die Entdeckung und Optimierung von Materialien durch Verwendung von HD-Methoden schneller voranzutreiben. Für alle Arbeitstechniken gilt: Das Ausmaß der Automatisierung, Parallelisierung und Miniaturisierung sowie die Integration aller Einzelschritte in einen Gesamtprozess bestimmt die Effizienz einer HD-Methodik. Durch eine systematische Untersuchung des Parameterraumes und durch sorgfältige Datenevaluierung (möglichst Software-gestützt) können Trends gefunden werden, die zu einem besseren Verständnis der untersuchten Systeme beitragen. Der vorgestellte Ansatz zur HD-Untersuchung von Solvothermalreaktionen erlaubt die automatisierte Synthese und Charakterisierung von bis zu 48 Produkten ohne die Proben einzeln manipulieren zu müssen. Der geringe Reagenzienverbrauch zusammen mit der Möglichkeit, die Reaktionen unter identischen Prozessparametern (Temperatur, Zeit, Druck, usw.) durchführen zu können, ermöglichen die systematische Untersuchung eines größeren Parameterraumes. An Hand zahlreicher Beispiele haben wir das Potential von Hochdurchsatz- Methoden bei der Entdeckung neuer Verbindungen, der Optimierung von Reaktionen, beim Auffinden von Reaktionstrends sowie der Untersuchung des Einflusses von Prozessparametern gezeigt. High-throughput (HT) methods applied to materials discovery have attracted much attention over the last few years because they permit a fast and efficient investigation of parameter space while consuming only small amounts of starting materials. Nowadays, many different HT techniques in solid state science are employed in order to accelerate the discovery and optimization of materials. The degree of parallelisation, automation, and miniaturization determines the efficiency of a HT methodology. Systematic investigation of parameter space and careful data analysis allow the identification of reaction trends and may give important guidance in better understanding of reaction systems. The described HT methodology for solvothermal reactions allows the systematic investigation of 48 different hydrothermal reactions at a time. The methodology includes automatic dispensing of solids and liquids, followed by homogenization, pH measurement, synthesis, isolation, washing as well as automated phase analysis by X-ray diffraction without the manipulation of individual samples. The focus of this article is on the application of HT methods in the investigation of the parameter space in solid state sciences. Based on selected examples, the power of HT methods in the discovery of new compounds, the optimization of reactions, the identification of reaction trends, as well as the investigation of the influence of process parameters is described. The large amount of data obtained in a short time leads to an improvement towards the understanding of the role that synthesis and process parameters play in the formation of compounds and materials. [source] GridBLAST: a Globus-based high-throughput implementation of BLAST in a Grid computing frameworkCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 13 2005Arun KrishnanArticle first published online: 24 JUN 200 Abstract Improvements in the performance of processors and networks have made it feasible to treat collections of workstations, servers, clusters and supercomputers as integrated computing resources or Grids. However, the very heterogeneity that is the strength of computational and data Grids can also make application development for such an environment extremely difficult. Application development in a Grid computing environment faces significant challenges in the form of problem granularity, latency and bandwidth issues as well as job scheduling. Currently existing Grid technologies limit the development of Grid applications to certain classes, namely, embarrassingly parallel, hierarchical parallelism, work flow and database applications. Of all these classes, embarrassingly parallel applications are the easiest to develop in a Grid computing framework. The work presented here deals with creating a Grid-enabled, high-throughput, standalone version of a bioinformatics application, BLAST, using Globus as the Grid middleware. BLAST is a sequence alignment and search technique that is embarrassingly parallel in nature and thus amenable to adaptation to a Grid environment. A detailed methodology for creating the Grid-enabled application is presented, which can be used as a template for the development of similar applications. The application has been tested on a ,mini-Grid' testbed and the results presented here show that for large problem sizes, a distributed, Grid-enabled version can help in significantly reducing execution times. Copyright © 2005 John Wiley & Sons, Ltd. [source] Genetic Identification of Pelagic Shark Body Parts for Conservation and Trade MonitoringCONSERVATION BIOLOGY, Issue 4 2002Mahmood Shivji Difficulties with the identification of many commonly fished sharks and their body parts has resulted in a global dearth of catch and trade information, making reliable assessment of exploitation effects and conservation needs for individual species nearly impossible. We developed and tested a highly streamlined molecular genetic approach based on species-specific, polymerase-chain-reaction primers in an eight-primer multiplex format to discriminate simultaneously between body parts from six shark species common in worldwide pelagic fisheries. The species-specific primers are based on DNA sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus. The primers and multiplex format accurately and sensitively distinguished samples from each of three lamnid ( Isurus oxyrinchus, Isurus paucus, and Lamna nasus) and three carcharhinid ( Prionace glauca, Carcharhinus obscurus, and Carcharhinus falciformis) species from all but one other shark species encountered in the North Atlantic fishery. Furthermore, the three lamnid primers were robust enough in their discriminatory power to be useful for species diagnosis on a global scale. Preliminary testing of dried fins from Asian and Mediterranean commercial markets suggests that our genetic approach will be useful for determining the species of origin of detached fins, thus allowing the monitoring of trade in shark fins for conservation assessment. Our approach will also facilitate detection of products from protected and other at-risk shark species and may prove useful as a model for development of the high-throughput, genetic, species-diagnosis methods typically required in conservation and management contexts. Resumen: La conservación y manejo de tiburones fundamentado a nivel de especie es una necesidad imperativa debido a la creciente demanda de aletas de tiburón y el reconocimiento de que las especies individuales de tiburones responden de manera distinta a la explotación. Las dificultades para la identificación de muchos tiburones capturados comúnmente, así como de partes de su cuerpo, han resultado en una escasez global de información sobre capturas y comercialización, haciendo casi imposible el poder realizar evaluaciones de los efectos de la explotación y de las necesidades de conservación. Desarrollamos y evaluamos un método altamente estilizado de genética molecular basado en detonadores de la reacción en cadena de la polimerasa, especie-específicos, en un formato múltiple de ocho detonadores para discriminar simultáneamente entre las partes del cuerpo de seis especies de tiburones provenientes de pesquerías pelágicas mundiales comunes. Los detonadores especie-específicos están basados en diferencias en las secuencias de ADN entre especies del locus espaciador 2 nuclear, ribosomal, transcrito. Los detonadores y el formato múltiple distinguen muestras con precisión y sensitividad de cada uno de los tres lámnidos ( Isurus oxyrinchus, Isurus paucus y Lamna nasus) y tres especies de carcarínidos ( Prionace glauca, Carcharhinus obscurus y Carcharhinus falciformis) especies todas encontradas en las pesquerías de Norteamérica, excepto una. Mas aún, los detonadores de los tres lamnidos fueron lo suficientemente robustos en su poder discriminante como para ser usados para el diagnóstico de especies a escala mundial. Las pruebas preliminares de aletas secas de los mercados comerciales de Asia y el Mediterráneo sugieren que nuestro método genético puede ser útil para determinar la especie de origen de las aletas separadas, permitiendo así usar el monitoreo de las aletas de tiburón para evaluaciones de conservación. Nuestro método también podría facilitar la detección de productos provenientes de especies protegidas o en riesgo y podría resultar útil como un modelo para el desarrollo de métodos genéticos de alto rendimiento para el diagnóstico de especies, métodos típicamente requeridos en los contextos de conservación y manejo. [source] Genetics of type 2 diabetes mellitus: status and perspectivesDIABETES OBESITY & METABOLISM, Issue 2 2005Lars Hansen Throughout the last decade, molecular genetic studies of non-autoimmune diabetes mellitus have contributed significantly to our present understanding of this disease's complex aetiopathogenesis. Monogenic forms of diabetes (maturity-onset diabetes of the young, MODY) have been identified and classified into MODY1,6 according to the mutated genes that by being expressed in the pancreatic ,-cells confirm at the molecular level the clinical presentation of MODY as a predominantly insulin secretory deficient form of diabetes mellitus. Genomewide linkage studies of presumed polygenic type 2 diabetic populations indicate that loci on chromosomes 1q, 5q, 8p, 10q, 12q and 20q contain susceptibility genes. Yet, so far, the only susceptibility gene, calpain-10 (CAPN10), which has been identified using genomewide linkage studies, is located on chromosome 2q37. Mutation analyses of selected ,candidate' susceptibility genes in various populations have also identified the widespread Pro12Ala variant of the peroxisome proliferator-activated receptor-, and the common Glu23Lys variant of the ATP-sensitive potassium channel, Kir6.2 (KCNJ11). These variants may contribute significantly to the risk type 2 diabetes conferring insulin resistance of liver, muscle and fat (Pro12Ala) and a relative insulin secretory deficiency (Glu23Lys). It is likely that, in the near future, the recent more detailed knowledge of the human genome and insights into its haploblocks together with the developments of high-throughput and cheap genotyping will facilitate the discovery of many more type 2 diabetes gene variants in study materials, which are statistically powered and phenotypically well characterized. The results of these efforts are likely to be the platform for major progress in the development of personalized antidiabetic drugs with higher efficacy and few side effects. [source] Application of flow cytometry for biomarker-based cervical cancer cells detectionDIAGNOSTIC CYTOPATHOLOGY, Issue 2 2008Jian Ling Ph.D. Abstract The Pap test used for cervical cancer screening is subjective, labor-intensive, and has relatively low sensitivity and specificity for the detection of underlying clinically significant lesions. The objective of this study is to develop a biomarker/flow cytometry-based approach for cervical cancer screening. Immunofluorescence technology to quantify cervical cell expression of two biomarkers p16INK4A and Mcm5 was developed and evaluated by both microcopy and flow cytometry. The capability of using biomarker/flow cytometry approach to detect rare-event dysplastic cells in a large background of benign epithelial and inflammatory cells was evaluated. The results indicate that flow cytometry could detect 0.01% dysplastic cells in a background of normal cervical epithelial cells with the combination of the two biomarkers. Thirty-two clinical specimens were used to test the biomarker/flow cytometry-based approach and the results were compared with the liquid-based cervical cytology. The experiment yielded 100% sensitivity and 93% specificity with reference to the liquid-based cervical cytology. This study indicates the promise of using multi-color fluorescence flow cytometry for biomarker-based cervical cancer screening. This molecular-based, potentially high-throughput and automated method is expected to provide an alternative/auxiliary means of cervical cancer screening. Diagn. Cytopathol. 2008;36:76,84. © 2008 Wiley-Liss, Inc. [source] Monoclonal antibody proteomics: Discovery and prevalidation of chronic obstructive pulmonary disease biomarkers in a single stepELECTROPHORESIS, Issue 23 2007Eszter Csanky Abstract We define mAb proteomics as the global generation of disease specific antibodies that permit mass screening of biomarkers. An integrated, high-throughput, disease-specific mAb-based biomarker discovery platform has been developed. The approach readily provided new biomarker leads with the focus on large-scale discovery and production of mAb-based, disease-specific clinical assay candidates. The outcome of the biomarker discovery process was a highly specific and sensitive assay, applicable for testing of clinical validation paradigms, like response to treatment or correlation with other clinical parameters. In contrast to MS-based or systems biology-based strategies, our process produced prevalidated clinical assays as the outcome of the discovery process. By re-engineering the biomarker discovery paradigm, the encouraging results presented in this paper clearly demonstrate the efficiency of the mAb proteomics approach, and set the grounds for the next steps of studies, namely, the hunt for candidate biomarkers that respond to drug treatment. [source] Construction of an antibody microarray based on agarose-coated slidesELECTROPHORESIS, Issue 3 2007Lin-Li Lv Abstract The antibody microarray, a high-throughput multiplex immunoassay method, has become a significant tool for quantitative proteomics studies. We describe here the strategies for optimizing the condition of antibody microarray building based on agarose-coated slides. In this study, modified glass slides were robotically printed with capture antibodies against monocyte chemoattractant protein 1 (MCP-1), then dilutions of the cytokine were applied to the arrays, and the protein was detected with biotin-labeled antibody coupled with Cy3-conjugated streptavidin. Thus a protein profiling microarray based on sandwich immunoassay has been established. Various factors in the production of antibody microarrays were analyzed: the capture antibody concentrations, shelf life of the postprinting slides, blocking buffers, and reproducibility of the system. A calibration curve with a correlation coefficient of 0.9995 was established which suggested that the matrix can retain arrayed proteins in near-quantitative fashion. The results revealed high signal uniformity and reproducibility with regard to intra-array (1.3%) and the interarray (8.7%) variation at the capture antibody concentration of 125,µg/mL. Besides, the printed arrays could be stored for at least two months without any apparent change of the performance parameters. [source] Measurement of specific radioactivity in proteins separated by two-dimensional gel electrophoresisELECTROPHORESIS, Issue 5-6 2006Shaobo Zhou Abstract We report a method to quantify the specific radioactivity of proteins that have been separated by 2-DE. Gels are stained with SyproRuby, and protein spots are excised. The SyproRuby dye is extracted from each spot using DMSO, and the fluorescence is quantified automatically using a plate reader. The extracted gel piece is then dissolved in hydrogen peroxide and radioactivity is quantified by liquid scintillation counting. Gentle agitation with DMSO for 24,h was found to extract all the SyproRuby dye from gel fragments. The fluorescence of the extract was linearly related to the amount of BSA loaded onto a series of 1-D gels. When rat muscle samples were run on 2-DE gels, the fluorescence extracted from 54,protein spots showed a good correlation (r = 0.79, p < 0.001) with the corresponding spot intensity measured by conventional scanning and image analysis. DMSO extraction was found not to affect the amount of radioactive protein left in the gel. When a series of BSA solutions of known specific radioactivity were run on 2-DE gels, the specific radioactivity measured by the new method showed a good correlation (r = 0.98, p < 0.01, n = 5) with the specific radioactivity measured directly before loading. Reproducibility of the method was measured in a series of 2-DE gels containing proteins from the livers of rats and mice that had been injected with [35S]methionine. Variability tended to increase when the amount of radioactivity in the protein spot was low, but for samples containing at least 10,dpm above background the CV was around 30%, which is comparable to that obtained when measuring protein expression by conventional image analysis of SyproRuby-stained 2-DE gels. Similar results were obtained whether spots were excised manually or using a spot excision robot. This method offers a high-throughput, cost-effective and reliable method of quantifying the specific radioactivity of proteins from metabolic labelling experiments carried out in,vivo, so long as sufficient quantities of radioactive tracer are used. [source] Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Xavier Mayali Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source] Direct toxicity assessment of wastewater: Baroxymeter, a portable rapid toxicity device and the industry perspectiveENVIRONMENTAL TOXICOLOGY, Issue 3 2002Achilles Tzoris Abstract Direct toxicity assessment of wastewater is becoming necessary, and new legislation may render it compulsory for the water industry. At present such assessment is performed at a laboratory away from a site, at considerable cost, and results often come too late, after a toxic event has occurred and the toxin has been released into the environment. Some of the rapid toxicity tests available today require certain conditions to function properly, or their results do not always correlate with other methods. The objective of this study was to assess a portable device, the Baroxymeter, for its suitability as an instrument to test wastewater toxicity. The way the device works is based on monitoring respiration of a bacterial culture by pressure measurements and using respiration inhibition as a toxicity alert. It has been shown that it is possible to detect toxic substances such as 3,5-dichlorophenol and bronopol within 5 min from a 1-mL sample. The benefits and future applications of the Baroxymeter as a high-throughput, cost-effective alternative for toxicity screening are discussed in this article. © 2002 Wiley Periodicals, Inc. Environ Toxicol 17: 284,290, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/tox.10059 [source] Systematic Hydrothermal Investigation of Metal Phosphonatobenzenesulfonates by High-Throughput MethodsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 24 2010Palanikumar Maniam Abstract A high-throughput (HT) investigation using the rigid bifunctional ligand 4-phosphonobenzenesulfonic acid, H2O3P-C6H4 -SO3H (H3L), generated five new phosphonatobenzenesulfonates with copper(II) or lead(II) ions. A comprehensive HT study comprising the screenings of different metal ions, metal salt types and the synthesis optimization were conducted whereby the influence of pH and molar ratios M2+/H3L were investigated. The HT-study led to five new compounds Pb2[(O3P-C6H4 -SO3)(OH)] (1), Cu1.5[(O3P-C6H4 -SO3)(H2O)] (2), NaCu(O3P-C6H4 -SO3)(H2O)3 (3), Cu2[(O3P-C6H4 -SO3)(OH)(H2O)] (4) and Cu3[(O3P-C6H4 -SO3)2(H2O)2] (5). Metal ion screening showed lead(II) and copper(II) to be suitable metal ions. The utilization of discovery and focused arrays allowed to determine the optimal formation fields of the respective compounds. The crystal structures were determined from single-crystal X-ray diffraction and revealed the presence of various MOx polyhedra that form clusters, chains or layers which are connected through the organic linker. IR spectra, thermogravimetric studies, magnetic susceptibility measurements and elemental analyses were conducted to further characterize the compounds 1, 3, 4 and 5. [source] Synthesis and Structure Characterization of Copper Terephthalate Metal,Organic FrameworksEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2009Cantwell G. Carson Abstract In this paper, we report on a high-throughput (gram quantities) solvothermal method for the synthesis of copper terephthalate metal,organic frameworks in dmf. While the structure of MOF-2 and some of the associated polymorphs are well known, we know of no equivalent structural studies for the isostructural copper terephthalate (Cu,tpa). The material we have made crystallizes in the C2/m space group. Cu,tpa also exhibits reversible solvent-exchange properties. These properties make this material useful for potential applications in gas storage and catalysis applications. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Reliable high-throughput screening with Pichia pastoris by limiting yeast cell death phenomenaFEMS YEAST RESEARCH, Issue 2 2004Roland Weis Abstract Comparative screening of gene expression libraries employing the potent industrial host Pichia pastoris for improving recombinant eukaryotic enzymes by protein engineering was an unsolved task. We simplified the protocol for protein expression by P. pastoris and scaled it down to 0.5-ml cultures. Optimising standard growth conditions and procedures, programmed cell death and necrosis of P. pastoris in microscale cultures were diminished. Uniform cell growth in 96-deep-well plates now allows for high-throughput protein expression and screening for improved enzyme variants. Furthermore, the change from one host for protein engineering to another host for enzyme production becomes dispensable, and this accelerates the protein breeding cycles and makes predictions for large-scale production more accurate. [source] Fabrication of Flexible Binary Amplitude Masks for Patterning on Highly Curved SurfacesADVANCED FUNCTIONAL MATERIALS, Issue 20 2009Audrey M. Bowen Abstract This paper describes soft lithography methods that expand current fabrication capabilities by enabling high-throughput patterning on nonplanar substrates. These techniques exploit optically dense elastomeric mask elements embedded in a transparent poly(dimethylsiloxane) (PDMS) matrix by vacuum-assisted microfluidic patterning, UV,ozone-mediated irreversible sealing, and chemical etching. These protocols provide highly flexible photomasks exhibiting either positive- or negative-image contrasts, which serve as amplitude masks for large-area photolithographic patterning on a variety of curved (and planar) surfaces. When patterning on cylindrical surfaces, the developed masks do not experience significant pattern distortions. For substrates with 3D curvatures/geometries, however, the PDMS mask must undergo relatively large strains in order to make conformal contact. The new methods described in this report provide planar masks that can be patterned to compliantly compensate for both the displacements and distortions of features that result from stretching the mask to span the 3D geometry. To demonstrate this, a distortion-corrected grid pattern mask was fabricated and used in conjunction with a homemade inflation device to pattern an electrode mesh on a glass hemisphere with predictable registration and distortion compensation. The showcased mask fabrication processes are compatible with a broad range of substrates, illustrating the potential for development of complex lithographic patterns for a variety of applications in the realm of curved electronics (i.e., synthetic retinal implants and curved LED arrays) and wide field-of-view optics. [source] A review of current large-scale mouse knockout effortsGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 2 2010Chunmei Guan Abstract After the successful completion of the human genome project (HGP), biological research in the postgenome era urgently needs an efficient approach for functional analysis of genes. Utilization of knockout mouse models has been powerful for elucidating the function of genes as well as finding new therapeutic interventions for human diseases. Gene trapping and gene targeting are two independent techniques for making knockout mice from embryonic stem (ES) cells. Gene trapping is high-throughput, random, and sequence-tagged while gene targeting enables the knockout of specific genes. It has been about 20 years since the first gene targeting and gene trapping mice were generated. In recent years, new tools have emerged for both gene targeting and gene trapping, and organizations have been formed to knock out genes in the mouse genome using either of the two methods. The knockout mouse project (KOMP) and the international gene trap consortium (IGTC) were initiated to create convenient resources for scientific research worldwide and knock out all the mouse genes. Organizers of KOMP regard it as important as the HGP. Gene targeting methods have changed from conventional gene targeting to high-throughput conditional gene targeting. The combined advantages of trapping and targeting elements are improving the gene trapping spectrum and gene targeting efficiency. As a newly-developed insertional mutation system, transposons have some advantages over retrovirus in trapping genes. Emergence of the international knockout mouse consortium (IKMP) is the beginning of a global collaboration to systematically knock out all the genes in the mouse genome for functional genomic research. genesis 48:73,85, 2010. © 2010 Wiley-Liss, Inc. [source] Force transducer-based movement detection in fear conditioning in mice: A comparative analysisHIPPOCAMPUS, Issue 1 2002Thomas Fitch Abstract Fear conditioning (FC) allows the dissociation of hippocampal and nonhippocampal behavioral function in rodents, and has become a diagnostic tool in transgenic mouse research employed to investigate mutation-induced changes in brain function. Although the procedural details of the paradigm have been established, quantification of the behavioral output, freezing, remains problematic in mice. Observation-based techniques are time-consuming and may be subject to bias, while movement detection with photocells is imprecise. Here we describe an alternative method for movement detection, based on an electronic force transducer system that allows the quantification of acceleration forces generated by a moving subject. We compare the behavior of two inbred strains of mice (C57BL/6 and DBA/2) whose performance is known to differ in hippocampal tasks, including FC. The comparison is made using multiple techniques: the force transducer approach, and three observation-based methods, a computer-aided event-recording approach, a traditional time-sampling paper/pencil method, and a subjective impression-based scoring system. In addition, we investigate the correlation structures of behavioral elements quantified by event recording, using principal component analyses; we conclude that fear may manifest in multiple forms and in a stimulus- and genotype-dependent manner. We suggest that the force transducer system provides precise quantification of movements in an automated manner and will allow high-throughput screening for mutation and drug effects in mice. However, we also argue that fear responses can be complex, and freezing behavior may not be the only measure of fear or fear-associated memory. Hippocampus 2002;12:4,17. © 2002 Wiley-Liss, Inc. [source] Array-MLPA: comprehensive detection of deletions and duplications and its application to DMD patients,HUMAN MUTATION, Issue 1 2008Fanyi Zeng Abstract Multiplex ligation-dependent probe amplification (MLPA) is widely used to screen genes of interest for deletions and duplications. Since MLPA is usually based on size-separation of the amplification products, the maximum number of target sequences that can be screened in parallel is usually limited to ,40. We report the design of a robust array-based MLPA format that uses amplification products of essentially uniform size (100,120,bp) and distinguishes between them by virtue of incorporated tag sequences. We were thus able to increase probe complexity to 124, with very uniform product yields and signals that have a low coefficient of variance. The assay designed was used to screen the largest set studied so far (249 patients) of unrelated Duchenne muscular dystrophy (DMD) cases from the Chinese population. In a blind study we correctly assigned 98% of the genotypes and detected rearrangements in 181 cases (73%); i.e., 163 deletions (65%), 13 duplications (5%), and five complex rearrangements (2%). Although this value is significantly higher for Chinese patients than previously reported, it is similar to that found for other populations. The location of the rearrangements (76% in the major deletion hotspot) is also in agreement with other findings. The 96-well flow-through microarray system used in this research provides high-throughput and speed; hybridization can be completed in 5 to 30,minutes. Since array processing and data analysis are fully automated, array-MLPA should be easy to implement in a standard diagnostic laboratory. The universal array can be used to analyze any tag-modified MLPA probe set. Hum Mutat 29(1), 190,197, 2008. © 2007 Wiley-Liss, Inc. [source] Novel PlexorÔ SNP genotyping technology: comparisons with TaqMan® and homogenous MassEXTENDÔ MALDI-TOF mass spectrometry,HUMAN MUTATION, Issue 9 2007E.A. Tindall Abstract Analysis of SNPs for association, linkage, haplotype, and pharmacogenetic studies has led to a dramatic increase in the number and evolution of medium- to high-throughput genotyping technologies. This study introduces PlexorÔ as a new method for medium-throughput (single SNP) genotyping. We compare this fluorescent-based chemistry for call rate, accuracy, affordability, throughput, and overall efficiency against two commonly used technologies. These include fluorescent-based TaqMan® allelic discrimination for single SNP analysis (medium-throughput) and the homogenous MassEXTENDÔ (hMEÔ) chemistry using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for multiple SNP analysis (high-throughput). Analysis of 11 SNPs, including all six possible nucleotide substitutions, showed PlexorÔ to be highly comparable for both call rate (94.7%) and accuracy (99.2%) to the TaqMan® (94.6% and 99.8%, respectively) and hMEÔ (91.9% and 98.1%, respectively) chemistries. We demonstrate that this novel method is an efficient, cost-effective alternative to TaqMan® genotyping commonly used in diagnostic settings. Hum Mutat 28(9), 922,927, 2007. © 2007 Wiley-Liss, Inc. [source] Exploring Optical Properties of Liquid Crystals for Developing Label-Free and High-Throughput Microfluidic Immunoassays,ADVANCED MATERIALS, Issue 2 2009Chang-Ying Xue The orientational transition of liquid crystals (LCs) is used as a label-free detection mechanism for immunoassays developed in microfluidic systems. LCs only show bright optical textures (visible to the naked eye) in the line-line intersections in which label-free antibodies bind to their surface-immobilized antigens, suggesting the feasibility of using LCs to detect specific antigen-antibody binding events in a high-throughput and multiplexed manner. [source] Management of metadata and automation for mail-in measurements with the APS 11-BM high-throughput, high-resolution synchrotron powder diffractometerJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2009Brian H. Toby A high-resolution and high-throughput synchrotron powder diffractometer has been automated for use with samples that are mailed in by Advanced Photon Source users. Implementation of a relational database with web interfaces for both outside users and beamline staff, which is integrated into the facility-wide proposal and safety system, allows all aspects of beamline management to be integrated. This system permits users to request kits for mounting samples, to provide sample safety information, to obtain their collected data and to provide usage information upon project completion in a quick and simple manner. Beamline staff use a separate interface to note receipt of samples, schedule and collect diffraction data, post-process and quality-check data, and dispose of samples. The design of the software and database are discussed in detail. [source] Review: Microscale methods for high-throughput chromatography development in the pharmaceutical industryJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 7 2009Sunil Chhatre Abstract Demands within the pharmaceutical sector to cut costs and improve process efficiencies have grown considerably in recent years. Major challenges exist for companies trying to establish financially viable and robust manufacturing processes for increasingly complex therapeutics. These issues have driven the investigation of miniaturised process-design techniques by which to identify suitable operating conditions using small volumes of feed material typical of that available in the early stages of bioprocess development. Such techniques are especially valuable for the optimisation of chromatographic separations, which often represent a significant percentage of manufacturing costs and hence for which there is a pressing need to determine the best operating policies. Several methods employing microlitre volumes of sample and resin have been explored recently, which are aimed at the high-throughput and cost-effective exploration of the design space for chromatographic separations. This methodology paper reviews these microscale approaches and describes how they work, gives examples of their application, discusses their advantages and disadvantages and provides a comparative assessment of the different methods, along with a summary of the challenges that remain to be overcome in relation to these techniques. Copyright © 2009 Society of Chemical Industry [source] Advances in membrane receptor screening and analysisJOURNAL OF MOLECULAR RECOGNITION, Issue 4 2004Matthew A. Cooper Abstract During the last decade there has been significant progress in the development of analytical techniques for the screening of ligand binding to membranes and membrane receptors. This review focuses on developments using label-free assays that facilitate ligand,membrane,receptor screening without the need for chemical-, biological- or radiological-labelled reagents. These assays include acoustic, optical surface plasmon resonance biosensing, sedimentation (analytical ultracentrifugation), chromatographic assays, isothermal titration calorimetry and differential scanning calorimetry. The merits and applications of cell-based screening systems and of different model membrane systems, including planar supported lipid layers, bead-supported membranes and lipid micro-arrays, are discussed. Recent advances involving more established techniques including intrinsic fluorescence, FRET spectroscopy, scintillation proximity assays and automated patch clamping are presented along with applications to peripheral membrane proteins, ion channels and G protein-coupled receptors. Novel high-throughput assays for determination of drug- and protein-partitioning in membranes are also highlighted. To aid the experimenter, a brief synopsis of the techniques commonly employed to purify and reconstitute membranes and membrane receptors is included. 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