A novel combinatorial approach to high-density peptide arrays

Combinatorial synthesis of peptides on solid supports (1), either as spots on cellulose membranes (2) or with split-pool-libraries on polymer beads (3), substantially forwarded research in the field of peptide-protein interactions. Admittedly, these concepts have specific limitations, on one hand the number of synthesizable peptide sequences per area, on the other hand elaborate decoding/encoding strategies, false-positive results and sequence limitations. We recently established a method to produce high-density peptide arrays on microelectronic chips (4). Solid amino acid microparticles were charged by friction and transferred to defined pixel electrodes onto the chip's surface, where they couple to a functional polymer coating simply upon melting (Fig. 16.1 A-D,F). By applying standard Fmoc chemistry according to Merrifield, peptide array densities of up to 40,000 spots per square centimetre were achieved (Fig. 16.1G). The term "Merrifield synthesis" describes the consecutive linear coupling and deprotecting of L-amino acids modified with base-labile fluorenylmethoxy (Fmoc) groups at the N-terminus and different acid-sensitive protecting groups at their side chains. Removing side chain protecting groups takes place only once at the very end of each synthesis and generates the natural peptide sequence thereby.

A multicenter assessment of the analytical performance of the routine thyroid panel on the Olympus AU3000i immunoassay system

BACKGROUND

The AU3000i thyroid assay panel (TSH, fT4, T4, fT3, T3) was evaluated at four sites in a European multicenter study. The study was designed to assess the basic analytical performance characteristics of the Olympus thyroid assays. In addition, a comprehensive assessment of the TSH functional sensitivity was undertaken to challenge the manufacturer's claim of 4th generation assay performance.

RESULTS

Repeatability (within-run precision) of TSH, ff4 and T4 was better than 3% across the measurable range, T3 and fT3 repeatability was better than 6%. Within-laboratory (total) precision was better than 10% for all assays, for fT4, it was better than 3%. Method comparisons were undertaken against the Roche Elecsys 2010, the Siemens Advia Centaur and the Abbott Architect. Overall, good to excellent correlations were seen, however in some cases there were systematic differences which can be attributed to the lack of an appropriate standard or reference method and/or heterogeneity of the analyte. The functional sensitivity of the Olympus TSH assay was confirmed to be 4th generation, giving a mean functional sensitivity (at 20% CV) of 0.0011 mIU/L with no sites exceeding 0.002 mIU/L. Plasma (Li-heparinate) was shown to be an acceptable sample type for use in these assays.

CONCLUSION

The results generated in this study indicate that the assays of the Olympus AU3000i routine thyroid panel are precise, correlate well with other established assays, and are suitable for use in the routine clinical laboratory.

Fully automated two-dimensional electrophoresis system for high-throughput protein analysis

A fully automated two-dimensional electrophoresis (2DE) system for rapid and reproducible protein analysis is described. 2DE that is a combination of isoelectric focusing (IEF) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) is widely used for protein expression analysis. Here, all the operations are achieved in a shorter time and all the transferring procedures are performed automatically. The system completed the entire process within 1.5 h. A device configuration, operational procedure, and data analysis are described using this system.

Multicenter evaluation of workflow performances of the new Olympus AU3000i

BACKGROUND

A new immunoanalyzer (AU3000i) has been developed by Olympus (Rungis, France) with the intention of offering a consolidated workcell. The aim of this experiment was to assess, in a multi-centre study (two French sites, one German site), the practicability of the Olympus AU3000i in terms of throughput (test/h), rerun capabilities, emergency sample handling and reflex test capabilities.

RESULTS

The workload study showed that the AU3000i was capable of running both one- and two-step assay protocols with a throughput of 240 tests per hour which corresponds to 209.3 tests per hour including the initialization time. Emergency samples were correctly treated as a priority in less than 30 minutes for ten samples. Furthermore the analyzer could be programmed to generate automatic dilution, rerun and reflex tests, reducing the hands-on labour time for technicians.

CONCLUSION

Workflow studies showed that Olympus AU3000i and AU Clinical Chemistry can cover the combined workload of various routine analyzers in a variety of laboratory environments.

High-throughput construction of ORF clones for production of the recombinant proteins

Expression-ready cDNA clones, where the open reading frame (ORF) of the gene of interest is placed under the control of an appropriate promoter, are critical for functional characterization of the gene products. To create a resource of human gene products, we attempted to systematically convert original cDNA clones to expression-ready forms for recombinant proteins. For this purpose, we adopted a rare-cutting restriction enzyme-based system, the Flexi cloning system, to construct ORF clones. Taking advantage of the fully sequenced cDNA clones we accumulated to date, a number of sets of Flexi ORF clones in a 96-well format have been prepared. In this section, two methods for the preparation of Flexi ORF clones in a 96-well format are described. A protocol for transferring ORFs between Flexi vectors in a 96-well format is also described. We believe that the resultant clone set could be successfully used as a versatile reagent for functional characterization of human proteins.

A new classification system for the actions of IRS chemicals traditionally used for malaria control

Knowledge of how mosquitoes respond to insecticides is of paramount importance in understanding how an insecticide functions to prevent disease transmission. A suite of laboratory assays was used to quantitatively characterize mosquito responses to toxic, contact irritant, and non-contact spatial repellent actions of standard insecticides. Highly replicated tests of these compounds over a range of concentrations proved that all were toxic, some were contact irritants, and even fewer were non-contact repellents. Of many chemicals tested, three were selected for testing in experimental huts to confirm that chemical actions documented in laboratory tests are also expressed in the field. The laboratory tests showed the primary action of DDT is repellent, alphacypermethrin is irritant, and dieldrin is only toxic. These tests were followed with hut studies in Thailand against marked-released populations. DDT exhibited a highly protective level of repellency that kept mosquitoes outside of huts. Alphacypermethrin did not keep mosquitoes out, but its strong irritant action caused them to prematurely exit the treated house. Dieldrin was highly toxic but showed no irritant or repellent action. Based on the combination of laboratory and confirmatory field data, we propose a new paradigm for classifying chemicals used for vector control according to how the chemicals actually function to prevent disease transmission inside houses. The new classification scheme will characterize chemicals on the basis of spatial repellent, contact irritant and toxic actions.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

Background

The invention of the Genome Sequence 20™ DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.

Methodology

We use conventional PCR with 5′-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20™ DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5′tag-analysis.

Conclusions

We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5′ nucleotide of the tag. In particular, primers 5′ labelled with a cytosine are heavily overrepresented among the final sequences, while those 5′ labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5′primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.

Toxicity assays in nanodrops combining bioassay and morphometric endpoints

Background

Improved chemical hazard management such as REACH policy objective as well as drug ADMETOX prediction, while limiting the extent of animal testing, requires the development of increasingly high throughput as well as highly pertinent in vitro toxicity assays.

Methodology

This report describes a new in vitro method for toxicity testing, combining cell-based assays in nanodrop Cell-on-Chip format with the use of a genetically engineered stress sensitive hepatic cell line. We tested the behavior of a stress inducible fluorescent HepG2 model in which Heat Shock Protein promoters controlled Enhanced-Green Fluorescent Protein expression upon exposure to Cadmium Chloride (CdCl₂), Sodium Arsenate (NaAsO₂) and Paraquat. In agreement with previous studies based on a micro-well format, we could observe a chemical-specific response, identified through differences in dynamics and amplitude. We especially determined IC50 values for CdCl₂ and NaAsO₂, in agreement with published data. Individual cell identification via image-based screening allowed us to perform multiparametric analyses.

Conclusions

Using pre/sub lethal cell stress instead of cell mortality, we highlighted the high significance and the superior sensitivity of both stress promoter activation reporting and cell morphology parameters in measuring the cell response to a toxicant. These results demonstrate the first generation of high-throughput and high-content assays, capable of assessing chemical hazards in vitro within the REACH policy framework.

Quantification of the proliferation index of human dermal fibroblast cultures with the ArrayScan high-content screening reader

High-throughput cell-based assays are becoming a powerful approach in the drug discovery process. The ArrayScan high-content screening (HCS) reader is a cytometer based on a fully automated fluorescence microscope that is able to obtain quantitative information on the intensity and localization of fluorescence signals within single cells over a wide cell population. The aim of this work was to set up an automated HCS multiparameter analysis for the quantification of the in vitro proliferation index of normal human dermal fibroblast (NHDF) cultures. The authors stimulated starved NHDF with insulin-like growth factor-1, platelet-derived growth factor, epidermal growth factor, fibroblast growth factor, or serum, and they quantified the proliferation index by measuring the expression of Ki-67 antigen, the incorporation of bromodeoxyuridine (BrdU), and the phosphorylation of the retinoblastoma protein (pRb). This approach also allowed quantification of the mitotic index by phospho-histone H3 staining and the percentage of cells in the S-phase by BrdU incorporation. The proliferation data from the ArrayScan assays were validated by comparison with a reference enzyme-linked immunosorbent assay (ELISA) and by flow cytometry. The measured proliferation indices were highly reproducible in repeated measures and independent experiments. The authors therefore propose that the ArrayScan HCS system could be used for high-throughput multiparameter analysis and quantification of the proliferation of cellular cultures.