Home About us Contact
|
Home About us Contact | ||
|
|
||
High-throughput Analysis (high-throughput + analysis)
Selected AbstractsHigh-throughput analysis of in vitro cytochrome p450 inhibition samples using mass spectrometry coupled with an integrated liquid chromatography/autosampler systemRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2010Ann Brown First page of article [source] High-throughput analysis in drug discovery: application of liquid chromatography/ion-trap mass spectrometry for simultaneous cassette analysis of ,-1a antagonists and their metabolites in mouse plasmaRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2001Zongwei Cai The application of liquid chromatography/ion-trap mass spectrometry for simultaneous quantification of multiple drugs and detection of their metabolites for in vitro experiments was reported recently. In the current study, the use of these techniques was extended to in vivo pharmacokinetic (PK) studies of ,-1a antagonists. In combination with limited time-point PK, greatly increased throughput was demonstrated for the in vivo screening and investigation of in vivo,in vitro correlation. In addition to quantitative analyses, the technique allowed simultaneous detection of major in vivo metabolites without having to reanalyze the plasma samples. The drugs were individually dosed in mice intravenously via tail vein injection and the blood samples were collected 5,min and 2,h after dosing. After the plasma samples for the different drugs had been prepared separately, they were pooled for cassette analysis. The concentrations of five test compounds in the plasma samples at 2,h ranged from 36,1062,ng/mL, whereas their 5-min plasma levels were similar. From the same cassette analysis, major metabolites in the samples were also detected simultaneously through the interpretation of full-scan mass spectra. The metabolite identification confirmed the results from a previous report that the major sites of metabolism are hydroxylation of the phenyl ring not bearing the alkylsulfonamide substitutent, piperidine N-dealkylation, and N-demethylation of the alkylsulfonamide group. Copyright © 2001 John Wiley & Sons, Ltd. [source] Evaluation of CE methods for global metabolic profiling of urineELECTROPHORESIS, Issue 14 2010Rawi Ramautar Abstract In this study, the usefulness of noncovalently coated capillaries with layers of charged polymers is investigated to obtain global electrophoretic profiles of urinary metabolites covering a broad range of different compound classes in a highly repeatable way. Capillaries were coated with a bilayer of polybrene (PB) and poly(vinyl sulfonate) (PVS), or with a triple layer of PB, dextran sulfate (DS) and PB. The bilayer and triple layer coatings were evaluated at acidic (pH 2.0) and alkaline (pH 9.0) separation conditions, thereby providing separation conditions for basic and acidic compounds. A representative metabolite mixture and spiked urine samples were used for the evaluation of the four CE methods. Migration time repeatability (RSD<2%) and plate numbers (N, 100,000,400,000) were similar for the test compounds in all CE methods, except for some multivalent ions that may exhibit adsorption to oppositely charged coatings. The analysis of cationic compounds with the PB-DS-PB CE method at low pH (i.e. after the EOF time) provided a larger separation window and number of separated peaks in urine compared to the analysis with the PB-PVS CE method at low pH (i.e. before the EOF time). Approximately, 600 molecular features were detected in rat urine by the PB-DS-PB CE-MS method whereas about 300 features were found with the PB-PVS CE-MS method. This difference can be attributed to reduced comigration of compounds with the PB-DS-PB CE-MS method and a related decrease of ion suppression. With regard to the analysis of anionic compounds by CE-MS, in general analyte responses were significantly lower than that for cationic compounds, most probably due to less efficient ionization and to ion suppression effects caused by the background electrolyte. Hence, further optimization is required for the sensitive CE-MS analysis of anionic compounds in body fluids. It is concluded that the selection of a CE method for profiling of cationic metabolites in urine depends on the purpose of the study. For high-throughput analyses, the PB-PVS CE-MS method is favored whereas the PB-DS-PB CE-MS method provides a more information-rich metabolic profile, but at the cost of prolonged analysis time. [source] A novel ultra-sensitive method for the quantification of glycosaminoglycan disaccharides using an automated DNA sequencerELECTROPHORESIS, Issue 7 2006Kay Vogel Abstract Analysis of glycosaminoglycans (GAGs) is of increasing importance concerning alterations in extracellular matrix composition and selectivity of glomerular basement membrane. In this report we describe the analysis of chondroitin sulfate disaccharides as an example of GAG ,disaccharide analysis using standard DNA sequencing equipment (DNA sequencer-assisted GAG disaccharide separation, DSA-GAGS). The presented methodology allows nanomolar quantification of 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-derived GAG disaccharides. In comparison to RP-HPLC the established method is much more sensitive, showing detection limits of 38,fmol/,L. Variation coefficients were approximately 10%, enabling exact quantifications after run times of 17,min at 30°C and an electrophoresis voltage of 15,kV; using a capillary DNA sequencer, available in many molecular laboratories, presented advantages like automated sample injection, opportunity of high-throughput analyses, separation of even sulfated disaccharide epimers, and the possibility of using APTS-derived fucose as an internal standard. Furthermore, highly reproducible retention times rendered easy identification of specific signals (SD,0.02). With regard to these results, the described method is a useful tool for the quantification of GAG disaccharides in low amounts, indicating advantages of obverse RP-HPLC and slab gel polyacrylamide electrophoresis in sensitivity, error-proneness, automation, and handling. [source] On-line sample preconcentration with chemical derivatization of bacterial biomarkers by capillary electrophoresis: A dual strategy for integrating sample pretreatment with chemical analysisELECTROPHORESIS, Issue 21 2005Adam S. Ptolemy Abstract Simple, selective yet sensitive methods to quantify low-abundance bacterial biomarkers derived from complex samples are required in clinical, biological, and environmental applications. In this report, a new strategy to integrate sample pretreatment with chemical analysis is investigated using on-line preconcentration with chemical derivatization by CE and UV detection. Single-step enantioselective analysis of muramic acid (MA) and diaminopimelic acid (DAP) was achieved by CE via sample enrichment by dynamic pH junction with ortho -phthalaldehyde/N -acetyl- L -cysteine labeling directly in-capillary. The optimized method resulted in up to a 100-fold enhancement in concentration sensitivity compared to conventional off-line derivatization procedures. The method was also applied toward the detection of micromolar levels of MA and DAP excreted in the extracellular medium of Escherichia coli bacterial cell cultures. On-line preconcentration with chemical derivatization by CE represents a unique approach for conducting rapid, sensitive, and high-throughput analyses of other classes of amino acid and amino sugar metabolites with reduced sample handling, where the capillary functions simultaneously as a concentrator, microreactor, and chiral selector. [source] Microfabricated devices: A new sample introduction approach to mass spectrometryMASS SPECTROMETRY REVIEWS, Issue 4 2006Iulia M. Lazar Abstract Instrument miniaturization is one way of addressing the issues of sensitivity, speed, throughput, and cost of analysis in DNA diagnostics, proteomics, and related biotechnology areas. Microfluidics is of special interest for handling very small sample amounts, with minimal concerns related to sample loss and cross-contamination, problems typical for standard fluidic manipulations. Furthermore, the small footprint of these microfabricated structures leads to instrument designs suitable for high-density, parallel sample processing, and high-throughput analyses. In addition to miniaturized systems designed with optical or electrochemical detection, microfluidic devices interfaced to mass spectrometry have also been demonstrated. Instruments for automated sample infusion analysis are now commercially available, and microdevices utilizing chromatographic or capillary electrophoresis separation techniques are under development. This review aims at documenting the technologies and applications of microfluidic mass spectrometry for the analysis of proteomic samples. © 2006 Wiley Periodicals, Inc., Mass Spec Rev 25:573,594, 2006 [source] Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genesMOLECULAR ECOLOGY RESOURCES, Issue 5 2007RAFAEL G. SEVILLA Abstract This report describes a set of 21 polymerase chain reaction primers and amplification conditions developed to barcode practically any teleost fish species according to their mitochondrial cytochrome b and nuclear rhodopsin gene sequences. The method was successfully tested in more than 200 marine fish species comprising the main Actinopterygii family groups. When used in phylogenetic analyses, its combination of two genes with different evolutionary rates serves to identify fish at the species level. We provide a flow diagram indicating our validated polymerase chain reaction amplification conditions for barcoding and species identification applications as well as population structure or haplotyping analyses, adaptable to high-throughput analyses. [source] Automation of DNA marker analysis for molecular breeding in crops: practical experience of a plant breeding companyPLANT BREEDING, Issue 4 2007C. Dayteg Abstract In modern plant breeding, DNA marker analyses are of increasing importance and, as the methods become more widely adopted, the capacity for high-throughput analyses at low cost is crucial for its practical use. Automation of the analysis processes is a way to meet these requirements. In order to achieve this, while keeping adequate flexibility in the analysis processes, Svalöf Weibull AB (SW) has developed a fully automated polymerase chain reaction system. It has been evaluated on barley and canola lines and is capable of analysing up to 2200 samples per day at a cost of 0,24 , per analysis for marker-assisted selection and quality control of genetically modified organisms. A detailed description of this system is given, and improvements to the throughput and applications are discussed. [source] High-efficiency peptide analysis on monolithic multimode capillary columns: Pressure-assisted capillary electrochromatography/capillary electrophoresis coupled to UV and electrospray ionization-mass spectrometryELECTROPHORESIS, Issue 21 2003Alexander R. Ivanov Abstract High-efficiency peptide analysis using multimode pressure-assisted capillary electrochromatography/capillary electrophoresis (pCEC/pCE) monolithic polymeric columns and the separation of model peptide mixtures and protein digests by isocratic and gradient elution under an applied electric field with UV and electrospray ionization-mass spectrometry (ESI-MS) detection is demonstrated. Capillary multipurpose columns were prepared in silanized fused-silica capillaries of 50, 75, and 100 ,m inner diameters by thermally induced in situ copolymerization of methacrylic monomers in the presence of n -propanol and formamide as porogens and azobisisobutyronitrile as initiator. N -Ethylbutylamine was used to modify the chromatographic surface of the monolith from neutral to cationic. Monolithic columns were termed as multipurpose or multimode columns because they showed mixed modes of separation mechanisms under different conditions. Anion-exchange separation ability in the liquid chromatography (LC) mode can be determined by the cationic chromatographic surface of the monolith. At acidic pH and high voltage across the column, the monolithic stationary phase provided conditions for predominantly capillary electrophoretic migration of peptides. At basic pH and electric field across the column, enhanced chromatographic retention of peptides on monolithic capillary column made CEC mechanisms of migration responsible for separation. The role of pressure, ionic strength, pH, and organic content of the mobile phase on chromatographic performance was investigated. High efficiencies (exceeding 300,000 plates/m) of the monolithic columns for peptide separations are shown using volatile and nonvolatile, acidic and basic buffers. Good reproducibility and robustness of isocratic and gradient elution pressure-assisted CEC/CE separations were achieved for both UV and ESI-MS detection. Manipulation of the electric field and gradient conditions allowed high-throughput analysis of complex peptide mixtures. A simple design of sheathless electrospray emitter provided effective and robust low dead volume interfacing of monolithic multimode columns with ESI-MS. Gradient elution pressure-assisted mixed-mode separation CE/CEC-ESI-MS mass fingerprinting and data-dependent pCE/pCEC-ESI-MS/MS analysis of a bovine serum albumin (BSA) tryptic digest in less than 5 min yielding high sequence coverage (73%) demonstrated the potential of the method. [source] Chemoselective Reagents for Covalent Capture and Display of Glycans in Microarrays,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2010Emiliano Cló Abstract Glycobiology has made very significant progress in the past decades. However, further progress will significantly depend on the establishment of novel methods for miniaturized, high-throughput analysis of glycan,protein interactions. Robust solid-phase chemical tools and new, chemoselective reagents for biologically meaningful display of surface-immobilized glycans are likely to play a key role. Here we present four new bifunctional linkers that allow highly chemoselective capture of unprotected glycans in solution to form glycan-linker conjugates for direct construction of glycan microarrays (glycochips). The bifunctional linkers carry O -linked aminooxy moieties, some with N -substituents at one end and an amino group at the other. In addition, they contain a substituted benzene ring for UV traceability and improved purification of glycan-linker conjugates. NMR spectroscopic studies in solution proved that N -substituted aminooxy linkers provided model glycan-linker conjugates with the ,-glucopyranoside configuration, i.e. the ring-closed form required for biological recognition. Then an ensemble of glycan-linker conjugates were assembled from mannobiose, lactose, and N -acetyl-lactosamine and used for covalent printing of glycan microarrays. The stability of oximes were studied both in solution and on-chip. In solution, two of the linkers provided glycan-linker conjugates with a remarkable stability at pH 4 or higher, on-chip this relative stability was upheld. Two of the linkers, with different properties, are recommended for the glycobiology toolbox for the construction of glycan microarrays from unprotected glycans. [source] Development of a single-tube PCR-pyrosequencing method for the simultaneous and rapid detection of four variant alleles of CYP2C9 gene polymorphismJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 2 2008Y. Okada MS Summary Background and Objective:, CYP2C9 is a polymorphic enzyme that has been reported to metabolize several clinically useful drugs such as warfarin, phenytoin and non-steroidal anti-inflammatory drugs. We designed a rapid single-tube multiplex assay to detect four variant alleles of the CYP2C9 in a single polymerase chain reaction (PCR) and a single pyrosequencing reaction. Methods:, A multiplex PCR was designed to amplify two fragments simultaneously, one containing 430C>T (CYP2C9*2) polymorphism and other containing 1075A>C (CYP2C9*3), 1076T>C (CYP2C9*4) and 1080C>G (CYP2C9*5) polymorphisms. Results:, Four variants of the CYP2C9 gene could be simultaneously detected using only two varieties of pyrosequencing primers in a single-tube. The success rate for the four SNPs (*2, *3,*4 and *5) was high. Genotypes obtained by the multiplex reaction were 100% concordant with genotypes obtained using direct DNA sequencing (n = 96). The analysis time was halved, compared with existing simplex pyrosequencing. The system allowed high-throughput analysis of over 384 samples per hour. Discussion:, Our method reduces running cost and halves analysis time, compared to simplex pyrosequencing. Another advantage of this method is that it analyses and determines multiple bases around the polymorphic site thereby reducing the possibility of scoring a truncated PCR product. [source] Rapid Profiling of Swiss Cheese by Attenuated Total Reflectance (ATR) Infrared Spectroscopy and Descriptive Sensory AnalysisJOURNAL OF FOOD SCIENCE, Issue 6 2009N.A. Kocaoglu-Vurma ABSTRACT:, The acceptability of cheese depends largely on the flavor formed during ripening. The flavor profiles of cheeses are complex and region- or manufacturer-specific which have made it challenging to understand the chemistry of flavor development and its correlation with sensory properties. Infrared spectroscopy is an attractive technology for the rapid, sensitive, and high-throughput analysis of foods, providing information related to its composition and conformation of food components from the spectra. Our objectives were to establish infrared spectral profiles to discriminate Swiss cheeses produced by different manufacturers in the United States and to develop predictive models for determination of sensory attributes based on infrared spectra. Fifteen samples from 3 Swiss cheese manufacturers were received and analyzed using attenuated total reflectance infrared spectroscopy (ATR-IR). The spectra were analyzed using soft independent modeling of class analogy (SIMCA) to build a classification model. The cheeses were profiled by a trained sensory panel using descriptive sensory analysis. The relationship between the descriptive sensory scores and ATR-IR spectra was assessed using partial least square regression (PLSR) analysis. SIMCA discriminated the Swiss cheeses based on manufacturer and production region. PLSR analysis generated prediction models with correlation coefficients of validation (rVal) between 0.69 and 0.96 with standard error of cross-validation (SECV) ranging from 0.04 to 0.29. Implementation of rapid infrared analysis by the Swiss cheese industry would help to streamline quality assurance. [source] Optimization of multicomponent photopolymer formulations using high-throughput analysis and kinetic modelingAICHE JOURNAL, Issue 5 2010Peter M. Johnson Abstract While high throughput and combinatorial techniques have played an instrumental role in materials development and implementation, numerous problems in materials science and engineering are too complex and necessitate a prohibitive number of experiments, even when considering high throughput and combinatorial approaches, for a comprehensive approach to materials design. Here, we propose a unique combination of high throughput experiments focused on binary formulations that, in combination with advanced modeling, has the potential to facilitate true materials design and optimization in ternary and more complex systems for which experiments are never required. Extensive research on the development of photopolymerizable monomer formulations has produced a vast array of potential monomer/comonomer, initiator and additive combinations. This array dramatically expands the range of material properties that are achievable; however, the vast number of potential formulations has eliminated any possibility of comprehensive materials design or optimization. This limitation is addressed by maximizing the benefits and unique capabilities of high throughput experimentation coupled with predictive models for material behavior and properties. The high throughput experimentation-model combination is useful to collect a limited amount of data from as few as 11 experiments on binary combinations of 10 analyzed monomers, and then use this limited data set to predict and optimize formulation properties in ternary resins that would have necessitated at least 1000 high throughput experiments and several orders of magnitude greater numbers of traditional experiments. A data analysis approach is demonstrated, and the model development and implementation for one model application in which a range of material properties are prescribed, and an optimal formulation that meets those properties is predicted and evaluated. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] Quantification of urinary N -acetyl- S - (propionamide)cysteine using an on-line clean-up system coupled with liquid chromatography/tandem mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2005Chien-Ming Li Abstract Acrylamide has been reported to be present in high-temperature processed foods and normal processed food intake could lead to significant acrylamide exposure. Acrylamide in vivo can be conjugated with glutathione in the presence of glutathione transferase. This conjugation product is further metabolized and excreted as N -acetyl- S -(propionamide)cysteine (NASPC) in the urine. NASPC could be considered a biomarker for acrylamide exposure. The objective of this study was to develop a highly specific, rapid and sensitive method to quantify urinary NASPC, serving as a biomarker for acrylamide exposure assessment. Isotope-labeled [13C3]NASPC was successfully synthesized and used as an internal standard. This urine mixture was directly analyzed using a newly developed liquid chromatographic/tandem mass spectrometric method coupled with an on-line clean-up system. The detection limit for this method was estimated as <5 µg l,1(0.4 pmol) on-column. The method was applied to measure the urinary level of NASPC in 70 apparently health subjects. The results showed that the NASPC urinary level was highly associated with smoking. Smokers had a significantly higher urinary NASPC level (135 ± 88 µg g,1 creatinine) than non-smokers (76 ± 30 µg g,1 creatinine). A highly sensitive and selective LC/MS/MS isotope dilution method was successfully established. With an on-line clean-up system, this system is capable of routine high-throughput analysis and accurate quantitation of NASPC in urine. This could be a useful tool for health surveillance for acrylamide exposure in a population for future study. Copyright © 2005 John Wiley & Sons, Ltd. [source] Software utilities for the interpretation of mass spectrometric data of glycoconjugates: application to glycosphingolipids of human serumRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 7 2010Jamal Souady Glycosphingolipids (GSLs) are major components of the outer leaflet of the cell membrane. These lipids are involved in many cell surface events and show disease-related expression changes. GSLs could thus serve as useful targets for biomarker discovery. The GSL structure is characterized by two entities: a hydrophilic glycan and a hydrophobic ceramide moiety. Both components exhibit numerous structural variations, the combination of which results in a large diversity of GSL structures that can potentially exist. Mass spectrometry (MS) is a powerful tool for high-throughput analysis of GSL expression analysis and structural elucidation. Yet, the assignment of GSL structures using MS data is tedious and demands highly specialized expertise. SysBioWare, a software platform developed for MS data evaluation in glycomics, was here applied for the MS analysis of human serum GSLs. The program was tuned to provide automated compositional assignment, supporting a variety of glycan and ceramide structures. Upon in silico fragmentation, the masses of predicted ions arising from cleavages in the glycan as well as the ceramide moiety were calculated, thus enabling structural characterization of both entities. Validation of proposed structures was achieved by matching in silico calculated fragment ions with those of experimental MS/MS data. These results indicate that SysBioWare can facilitate data interpretation and, furthermore, help the user to deal with large sets of data by supporting management of MS and non-MS data. SysBioWare has the potential to be a powerful tool for high-throughput glycosphingolipidomics in clinical applications. Copyright © 2010 John Wiley & Sons, Ltd. [source] A collection of 11 800 single-copy Ds transposon insertion lines in ArabidopsisTHE PLANT JOURNAL, Issue 6 2004Takashi Kuromori Summary More than 10 000 transposon-tagged lines were constructed by using the Activator (Ac)/Dissociation (Ds) system in order to collect insertional mutants as a useful resource for functional genomics of Arabidopsis. The flanking sequences of the Ds element in the 11 800 independent lines were determined by high-throughput analysis using a semi-automated method. The sequence data allowed us to map the unique insertion site on the Arabidopsis genome in each line. The Ds element of 7566 lines is inserted in or close to coding regions, potentially affecting the function of 5031 of 25 000 Arabidopsis genes. Half of the lines have Ds insertions on chromosome 1 (Chr. 1), in which donor lines have a donor site. In the other half, the Ds insertions are distributed throughout the other four chromosomes. The intrachromosomal distribution of Ds insertions varies with the donor lines. We found that there are hot spots for Ds transposition near the ends of every chromosome, and we found some statistical preference for Ds insertion targets at the nucleotide level. On the basis of systematic analysis of the Ds insertion sites in the 11 800 lines, we propose the use of Ds -tagged lines with a single insertion in annotated genes for systematic analysis of phenotypes (phenome analysis) in functional genomics. We have opened a searchable database of the insertion-site sequences and mutated genes (http://rarge.gsc.riken.go.jp/) and are depositing these lines in the RIKEN BioResource Center as available resources (http://www.brc.riken.go.jp/Eng/). [source] High-throughput localization of organelle proteins by mass spectrometry: a quantum leap for cell biologyBIOESSAYS, Issue 8 2006Denise J.L. Tan Cells are the fundamental building blocks of organisms and their organization holds the key to our understanding of the processes that control Development and Physiology as well as the mechanisms that underlie disease. Traditional methods of analysis of subcellular structure have relied on the purification of organelles and the painstaking biochemical description of their components. The arrival of high-throughput genomic and, more significantly, proteomic technologies has opened hereto unforeseen possibilities for this task. Recently two reports(1,2) show how much can be gleaned from the combination of analytical centrifugation, mass spectrometry and advanced statistical techniques focused on a high-throughput analysis of the content and organization of plant and animal cells. The results reveal intriguing possibilities for the future and the possibility of mapping much of the known proteome onto our current map of the cell. BioEssays 28: 780,784, 2006. © 2006 Wiley Periodicals, Inc. [source] Rapid screening of polysaccharide-based plasma volume expanders dextran and hydroxyethyl starch in human urine by liquid chromatography,tandem mass spectrometryBIOMEDICAL CHROMATOGRAPHY, Issue 7 2008Sven Guddat Abstract The increasing number of samples and target substances in doping control requires continuously improved screening methods, combining high-throughput analysis, simplified sample preparation, robustness and reliability. Hence, a rapid screening procedure based on liquid chromatography,electrospray ionization,tandem mass spectrometry with in-source collision-induced dissociation was developed. The detection of the polysaccharide-based plasma volume expanders dextran and hydroxyethyl starch (HES) in human urine was established without further sample preparation. The in-source fragmentation strategy of the approach represented a valuable tool in the analysis of the polysaccharide-based compounds, allowing the use of tandem mass spectrometry. After direct injection of urine specimens, analytes were chromatographically separated on a monolithic reverse-phase column and detected via multiple reaction monitoring of diagnostic ions at detection limits of 10 µg/mL for HES and 30 µg/mL for dextran. Validation was performed regarding the parameters specificity, linearity, precision (8,18%) and accuracy (77,105%) and the method was applied to the investigation of approximately 400 doping control samples and seven dextran and two hydroxyethyl starch post-administration samples. The approach demonstrated its capability as a rapid screening tool for the detection of dextran and hydroxyethyl starch and represents an alternative to existing screening procedures since time consuming hydrolysis or derivatization steps were omitted. Copyright © 2008 John Wiley & Sons, Ltd. [source] The quest for the mechanisms of lifeBIOTECHNOLOGY & BIOENGINEERING, Issue 7 2003Maria I. Klapa Abstract The genomic revolution, manifested by the sequencing of the complete genome of many organisms, along with technological advances, such as DNA microarrays and developments in high-throughput analysis of proteins, metabolites, and isotopic tracer distribution patterns, challenged the conventional ways in which questions are approached in the biological sciences: (a) rather than examining a small number of genes and/or reactions at any one time;, we can now analyze gene expression and protein activity in the context of systems of interacting genes and gene products; (b) comprehensive analysis of biological systems requires the integration of all cellular fingerprints: genome sequence, maps of gene expression, protein expression, metabolic output, and in vivo enzymatic activity; and (c) collecting, managing, and analyzing comparable data from various cellular profiles requires expertise from several fields that transcend traditional discipline boundaries. While researchers in systems biology have still to address difficult challenges in both experimental and computational arenas, they possess, for the first time, the opportunity to unravel the mechanisms of life. The enormous impact of these discoveries in diverse areas, such as metabolic engineering, strain selection, drug screening and development, bioprocess development, disease prognosis and diagnosis, gene and other medical therapies, is an obvious motivation for pursuing integrated analyses of cellular systems. © 2003 Wiley Periodicals, Inc. [source] Microfluidic Tissue Model for Live Cell ScreeningBIOTECHNOLOGY PROGRESS, Issue 4 2007Philip J. Lee We have developed a microfluidic platform modeled after the physiologic microcirculation for multiplexed tissue-like culture and high-throughput analysis. Each microfabricated culture unit consisted of three functional components: a 50 ,m wide cell culture pocket, an artificial endothelial barrier with 2 ,m pores, and a nutrient transport channel. This configuration enabled a high density of cancer cells to be maintained for over 1 week in a solid tumor-like morphology when fed with continuous flow. The microfluidic chip contained 16 parallel units for "flow cell" based experiments where live cells were exposed to a soluble factor and analyzed via fluorescence microscopy or flow-through biochemistry. Each fluidically independent tissue unit contained ,500 cells fed with a continuous flow of 10 nL/min. As a demonstration, the toxicity profile of the anti-cancer drug paclitaxel was collected on HeLa cells cultured in the microfluidic format and compared with a 384-well dish for up to 5 days of continuous drug exposure. [source] Chemical Micropatterning of Polycarbonate for Site-Specific Peptide Immobilization and Biomolecular InteractionsCHEMBIOCHEM, Issue 3 2007Olivier Carion Dr. Abstract Polycarbonate (PC) is a useful substrate for the preparation of microfluidic devices. Recently, its utility in bioanalysis has attracted much attention owing to the possibility of using compact discs as platforms for the high-throughput analysis of biomolecular interactions. In this article we report a novel method for the chemical micropatterning of polycarbonate based on the printing of functionalized silica nanoparticles. The semicarbazide groups present on the surface of the nanoparticles were used for the site-specific semicarbazone ligation of unprotected peptides derivatized by an ,-oxoaldehyde group. The peptide micropatterns permitted the specific capture of antibodies. We report also the characterization of micropatterns on PC by using a wide-field optical imaging technique called Sarfus; this allows the detection of nm-thick films by using nonreflecting PC substrates and an optical microscope working with reflected differential interference contrast. The method described here is an easy way to modify polycarbonate surfaces for biomolecular interaction studies and should stimulate the use of PC for developing plastic biosensors. [source] Recent Advances and Future Prospects in Peptaibiotics, Hydrophobin, and Mycotoxin Research, and Their Importance for Chemotaxonomy of Trichoderma and HypocreaCHEMISTRY & BIODIVERSITY, Issue 5 2008Thomas Degenkolb Abstract Fungi of the genus Trichoderma with teleomorphs in Hypocrea are abundant producers of a group of amphiphilic, non-ribosomal peptide antibiotics, which are rich in the non-proteinogenic amino acid Aib (, -aminoisobutyric acid). They are referred to as peptaibiotics, or peptaibols, if a 1,2-amino alcohol is present at the C-terminus. Trichoderma/Hypocrea, like other ascomycetous fungi, also produce hydrophobins, a class of small, cysteine-rich proteins. Advanced soft ionization mass spectrometric techniques such as LC-CID-MS, LC-ESI-MSn, and IC-MALDI-TOF-MS enabled the high-throughput analysis, simultaneous detection and sequence determination of peptaibiotics and hydrophobins from minute quantities of fungal materials. Some Trichoderma species have been recognized to produce peptaibiotics as well as simple mycotoxins of the trichothecene group. The combination of sequence data of both groups of peptides with the pattern of low-molecular-weight secondary metabolites, including trichothecene-type mycotoxins, independently confirmed the results of morphological, molecular, and phylogenetic analyses. This approach established a new lineage in Trichoderma/Hypocrea, the Brevicompactum clade, comprising four new and one redescribed species. Notably, commercial preparations of single or mixed cultures of Trichoderma species, in particular T. harzianum, and T. koningii, are registered as biocontrol agents for soil and plant pathogens. In this context, it is emphasized that the four mycotoxin-producing species of the recently established Brevicompactum clade (T. brevicompactum, T. arundinaceum, T. turrialbense, and T. protrudens) are not closely related to any of the Trichoderma species currently used as biocontrol agents. Furthermore, possible health concerns about release of peptaibiotics in the biosphere are discussed with respect to their bioactivities and their use as drugs in human and veterinary medicine. Finally, future prospects regarding novel bioactivities and further research needs, including interdisciplinary taxonomic approaches, are outlined. [source] | |||||||||||||