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PubMed2006

Automated analysis of behavior: a computer-controlled system for drug screening and the investigation of learning.

Efforts to understand cognition will be greatly facilitated by computerized systems that enable the automated analysis of animal behavior. A number of controversies in the invertebrate learning field have resulted from difficulties inherent in manual experiments. Driven by the necessity to overcome these problems during investigation of neural function in planarian flatworms and frog larvae, we designed and developed a prototype for an inexpensive, flexible system that enables automated control and analysis of behavior and learning. Applicable to a variety of small animals such as flatworms and zebrafish, this system allows automated analysis of innate behavior, as well as of learning and memory in a plethora of conditioning paradigms. We present here the schematics of a basic prototype, which overcomes experimenter effects and operator tedium, enabling a large number of animals to be analyzed with transparent on-line access to primary data. A scaled-up version of this technology represents an efficient methodology to screen pharmacological and genetic libraries for novel neuroactive reagents of basic and biomedical relevance.

Animals↗
PubMed2002

Novel ceftazidime-resistance beta-lactamases generated by a codon-based mutagenesis method and selection.

Four known and nine new ceftazidime-resistance beta-lactamases were generated by a novel, contaminating codon-based mutagenesis approach. In this method, wild-type codons are spiked with a set of mutant codons during oligonucleotide synthesis, generating random combinatorial libraries of primers that contain few codon replacements per variant. Mutant codons are assembled by tandem addition of a diluted mixture of five Fmoc-dimer amidites to the growing oligo and a mixture of four DMTr-monomer amidites to generate 20 trinucleotides that encode a set of 18 amino acids. Wild-type codons are assembled with conventional chemistry and the whole process takes place in only one synthesis column, making its automation feasible. The random and binomial behavior of this approach was tested in the polylinker region of plasmid pUC19 by the synthesis of three oligonucleotide libraries mutagenized at different rates and cloned as mutagenic cassettes. Additionally, the method was biologically assessed by mutating six contiguous codons that encode amino acids 237-243 (ABL numbering) of the TEM(pUC19) beta-lactamase, which is functionally equivalent to the clinically important TEM-1 beta-lactamase. The best ceftazidime-recognizing variant was a triple mutant, R164H:E240K: R241A, displaying a 333-fold higher resistance than the wild-type enzyme.

Amino Acid Substitution↗
PubMed1999

Deconvolution gas chromatography/mass spectrometry of urinary organic acids--potential for pattern recognition and automated identification of metabolic disorders.

The National Institute of Standards and Technology (NIST) Automated Mass Spectral Deconvolution and Identification System (AMDIS) is applied to a selection of data files obtained from the gas chromatography/mass spectrometry (GC/MS) analysis of urinary organic acids. Mass spectra obtained after deconvolution are compared with a special user library containing both the mass spectra and retention indices of ethoxime-trimethylsilyl (EO-TMS) derivatives of a set of organic acids. Efficient identification of components is achieved and the potential of the procedure for automated diagnosis of inborn errors of metabolism and for related research is demonstrated.

Acyl-CoA Dehydrogenase↗
PubMed1988

Automated profiling of urinary organic acids by dual-column gas chromatography and gas chromatography/mass spectrometry.

A multi-stage screening and identification scheme for the diagnosis of inborn errors in amino acid, fatty acid, carbohydrate and intermediary metabolism is described. The method is based on a computerized analysis of data obtained with dual-column gas chromatography/FID (GC/FID) and gas chromatography/mass spectrometry (GC/MS) profiling of urinary organic acids. It involves: (1) isolation of the compounds by solvent or solid-phase extraction; (2) conversion into trimethylsilyl (TMS) or TMS-oxime derivatives; (3) GC/FID analysis on SE-52 and OV-1701 capillary columns; (4) tentative identification by comparing the methylene unit (MU) values on both columns with a user-built library of reference compounds; (5) quantitative evaluation of the excretion profile; and (6) analysis by GC/MS of samples with an abnormal profile using an automated peak identification programme.

Acids↗
PubMed2002

Automated high throughput screening for serine kinase inhibitors using a LEADseeker scintillation proximity assay in the 1536-well format.

High-throughput screening in the 1536-well format has been largely restricted to solution-based and cell-based screens. In this article, we show the feasibility of a completely automated, robust scintillation proximity assay in the 1536-well format that is suitable to identify inhibitors for a serine/threonine kinase from a compound library. The introduction of [(33)P]phosphate into a biotinylated peptide substrate mirrors the activity of the kinase. The peptide is immobilized on streptavidin-coated LEADseeker imaging beads and [(33)P]phosphate incorporation is detected with the LEADseeker imaging system of Amersham Pharmacia Biotech. To improve the liquid handling procedures for imaging bead suspensions in the low microliter range, we developed a novel trough with an integrated stirring function. A comparison of the 1536-well assay to a 384-well assay revealed a comparable assay quality with Z' factors of about 0.7 for the 384-well format and 0.6 for the 1536-well format. In an automated screen of a random compound collection, 94.4% of the inhibitory compounds could be identified with both assay formats. Dose-response curves were performed for a selection of identified kinase inhibitors and revealed similar IC(50) values for both assay formats.

Automation↗
PubMed1990

Proposal for sequencing DNA using ligation of hexamers to generate sequential elongation primers (SPEL-6).

The efficiency of the directed-priming proposal of Studier [Proc. Natl. Acad. Sci. USA 86 (1989) 6917-1921] can be improved upon by employing a library of less than 4094 hexamers, allowing for the easy construction of all required primers using template-directed automated ligation. This 'top-down' sequencing procedure should be several times more efficient than the present 'bottom-up' procedures [see Watson, Science 248 (1990) 44-49].

Base Sequence↗
PubMed2006

Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes.

Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic DNA isolation, restriction endonuclease treatment, subsequent religation, transformation of religated DNA into an Escherichia coli host, and re-isolation as a plasmid, which is then used as a template in sequencing reactions with primers that read from the plasposon ends into the flanking DNA regions. We describe here a method that produces flanking DNA sequences directly from genomic DNA that is isolated from plasposon mutants. By eliminating the need for rescue cloning, our protocol dramatically reduces time and effort, typically by 2 to 3 working days, as well as costs associated with digestion, ligation, transformation, and plasmid isolation. Furthermore, it allows for a high-throughput automated approach to analysis of the plasposome, i.e. the collective set of plasposon insertion sites in a plasposon mutant library. We have tested the utility of genomic flank-sequencing on three plasposon mutants of the soil bacterium Collimonas fungivorans with abolished ability to degrade chitin.

3' Flanking Region↗
PubMed2003

Two novel Bv8-like peptides from skin secretions of the toad Bombina maxima.

Two novel bioactive peptides were purified from skin secretions of the toad Bombina maxima. The partial N-terminal sequences of these two peptides were determined by automated Edman degradation. This allowed the cloning of full-length cDNAs encoding these two peptides from a cDNA library prepared from the toad skin. The deduced complete amino acid sequences indicate that both peptides are composed of 77 amino acids. A FASTA search in the databanks revealed that they exhibit 86-91% sequence identity with Bv8, a peptide originally isolated from skin secretions of Bombina variegata. They were thus named as Bv8-like peptide 1 (Bv8-LP1) and Bv8-like peptide 2 (Bv8-LP2), respectively. Sequence differences between Bv8-LP1 and 2 were due to six amino acid substitutions at positions 6, 11, 23, 24, 62 and 63. Bv8-LP1 and 2 differed from Bv8 with eleven and seven amino acid substitutions, respectively. Like Bv8, Bv8-LP1 and 2 possessed contractile activity on isolated guinea pig ileum. Additionally, they stimulated contraction of rabbit aortic rings in a dose-dependent manner at nanomolar concentrations.

Amino Acid Sequence↗
PubMedDate not supplied

Comparing the performance of FLUFF-BALL to SEAL-CoMFA with a large diverse estrogen data set: from relevant superpositions to solid predictions.

In this work a template-based molecular mechanistic superposition algorithm FLUFF (Flexible Ligand Unified Force Field) and an accompanying local coordinate QSAR method BALL (Boundless Adaptive Localized Ligand) are validated against the benchmark techniques SEAL (Steric and Electrostatic Alignment) and CoMFA (Comparative Molecular Field Analysis) using a large diverse set of 245 xenoestrogens extracted from the EDKB (Endocrine Disruptor Knowledge Base) maintained by NCTR (National Centre for Toxicological Research). The results indicate that FLUFF is capable of generating relevant superpositions not only for BALL but also for CoMFA, as both techniques give predictive QSAR models. When the BALL and CoMFA methods are compared, it is clear that the BALL algorithm met or even exceeded the results of the standard 3D-QSAR method CoMFA using alignments either from the tailor-made superposition technique FLUFF or the reference method SEAL. The FLUFF-BALL method can be easily automated, and it is computationally light, providing thus a good computational "sieve" capable of fast screening of large molecule libraries.

Algorithms↗
PubMed2002

The role of quantitative structure--activity relationships (QSAR) in biomolecular discovery.

Empirical methods for building predictive models of the relationships between molecular structure and useful properties are becoming increasingly important. This has arisen because drug discovery and development have become more complex. A large amount of biological target information is becoming available through molecular biology. Automation of chemical synthesis and pharmacological screening has also provided a vast amount of experimental data. Tools for designing libraries and extracting information from molecular databases and high-throughput screening experiments robustly and quickly enable leads to be discovered more effectively. As drug leads progress down the development pipeline, the ability to predict physicochemical, pharmacokinetic and toxicological properties of these leads is becoming increasingly important in reducing the number of expensive, late development failures. Quantitative structure-activity relationship (QSAR) methods have much to offer in these areas. However, QSAR analysis has many traps for unwary practitioners. This review introduces the concepts behind QSAR, points out problems that may be encountered, suggests ways of avoiding the pitfalls and introduces several exciting, new QSAR methods discovered during the last decade.

Models, Molecular↗
PubMed2004

Neural networks as robust tools in drug lead discovery and development.

Empirical methods for building predictive models of the relationships between molecular structure and useful properties are becoming increasingly important. This has arisen because drug discovery and development have become more complex. A large amount of biological target information is becoming available though molecular biology. Automation of chemical synthesis and pharmacological screening has also provided a vast amount of experimental data. Tools for designing libraries and extracting information from molecular databases and high-throughput screening (HTS) experiments robustly and quickly enable leads to be discovered more effectively. As drug leads progress down the development pipeline, the ability to predict physicochemical, pharmacokinetic, and toxicological properties of these leads is becoming increasingly important in reducing the number of expensive, late-development failures. Neural network methods have much to offer in these areas. This review introduces the concepts behind neural networks applied to quantitative structure-activity relationships (QSARs), points out problems that may be encountered, suggests ways of avoiding the pitfalls, and introduces several exciting new neural network methods discovered during the last decade.

Animals↗
PubMed2004

A multiple-ontology customizable search interface for retrieval of clinical guidelines.

A major problem in the effective use of clinical guidelines is fast and accurate access at the point of care. Thus, we are developing a digital electronic guideline library (DeGeL) and a set of tools for incremental conversion of free-text guidelines into increasingly machine-comprehensible representations, which support automated application. Even if guidelines are represented in electronic fashion, care providers need to be able to quickly retrieve the guidelines that best fit the clinical situation at hand. We describe Vaidurya, a search and retrieval engine that exploits the hybrid nature of guideline representation in the DeGeL architecture. Vaidurya can use not only free-text keywords, but also multiple semantic indices along which the guidelines are classified, and the mark up of guidelines in DeGeL, using the semantic roles of one or more guideline-representation languages (ontologies). Vaidurya offers a wide variety of querying options, in order to enable different types of users to query the guideline library in a manner that is both efficient and user friendly. We describe the customizable query interface, in which each user can create their own personal query interface.

Expert Systems↗
PubMed2000

Pesticide residue analysis in foodstuffs applying capillary gas chromatography with mass spectrometric detection. State-of-the-art use of modified DFG-multimethod S19 and automated data evaluation.

This paper focuses on recent developments in the author's laboratory and reports on the "ultimate" analysis scheme which has evolved over the last 20 years in our laboratory. This demonstrates the feasibility of screening analyses for pesticide residue identification, mainly by full scan GC-MS, down to the 0.01 ppm concentration level in plant foodstuffs. It is based on a miniaturized DFG S19 extraction applying acetone for extraction followed by liquid-liquid extraction with ethyl acetate-cyclohexane followed by gel permeation chromatography. The final chromatographic determination is carried out with a battery of three parallel operating gas chromatographic systems using effluent splitting to electron-capture and nitrogen-phosphorus detection, one with a SE-54 the other with a OV-17 capillary column and the third one with a SE-54 capillary column and mass selective detection for identification and quantitation. The method is established for monitoring more than 400 pesticides amenable to gas chromatography. These pesticide residues are identified in screening analyses by means of the dedicated mass spectral library PEST.L containing reference mass spectra and retention times of more than 400 active ingredients and also metabolites applying the macro program AuPest (Automated residue analysis on Pesticides) for automated evaluation which runs with Windows based HP ChemStation software. The two gas chromatographic systems with effluent splitting to electron-capture and nitrogen-phosphorus detection are used to check the results obtained with the automated GC-MS screening and also to detect those few pesticides which exhibit better response to electron-capture and nitrogen-phosphorus detection than to mass spectrometry in full scan.

Automation↗
PubMed1996

Automation of toxicological screenings on a Hewlett Packard Chemstation GC-MS system.

OBJECTIVES: To optimize the interpretation of GC-MS toxicological screenings (i.e., to facilitate ion specific queries, create custom reports specifically adapted to each confirmation procedure, and eliminate redundant and/or inaccurate data on library search reports). DESIGN AND METHODS: The MS Chemstation software of the Hewlett Packard 5972 is constructed in a modular way. We made extensive modifications to two modules, the data analysis and the report modules, using the built-in MS Chemstation macro language. RESULTS: Ion specific queries were automated for over 60 commonly encountered analytes. Custom reports were created for the confirmation of positive drugs-of-abuse immunoassay results. With the incorporation of decision support rules into the data processing and the reporting phases, we obtained sensitive, accurate, and concise reports. CONCLUSIONS: The MS Chemstation software can be tailored to the needs of each individual application. The incorporation of a rule-based decision support system enhances the quality of the GC-MS toxicological screenings and results in faster, easier, and more reliable processing.

Gas Chromatography-Mass Spectrometry↗
PubMed2006

Informatics solutions for high-throughput proteomics.

The success of mass-spectrometry-based proteomics as a method for analyzing proteins in biological samples is accompanied by challenges owning to demands for increased throughput. These challenges arise from the vast volume of data generated by proteomics experiments combined with the heterogeneity in data formats, processing methods, software tools and databases that are involved in the translation of spectral data into relevant and actionable information for scientists. Informatics aims to provide answers to these challenges by transferring existing solutions from information management to proteomics and/or by generating novel computational methods for automation of proteomics data processing.

Databases, Protein↗
PubMed2001

Modification of an automated liquid-handling system for reagent-jet, nanoliter-level dispensing.

Reducing the scale of biochemical reactions is becoming commonplace. Examples include the screening of large libraries of chemical compounds or gene sequences. These applications demand the ability to transfer sub-microliter volumes of fluid. To this end, we have modified a Hamilton MICROLAB 2200 with high-speed solenoids and a liquid pressurization system to modulate volume delivery down to the nanoliter level. Additional modifications include the use of sapphire-tipped dispensing nozzles and a high-resolution substage to assist in the construction of DNA microarrays. Techniques for characterizing the dispensed volume are presented.

Aluminum Oxide↗
PubMed2002

Profiling patterned transcripts in Drosophila embryos.

Here we describe a high-throughput screen to isolate transcripts with spatially restricted patterns of expression in early embryos. Our approach utilizes robotic automation for rapid analysis of sequence-selected cDNAs in a whole-mount in situ hybridization assay. We determined the spatial distribution of a random collection of 778 different genes from an embryonic cDNA library and show that a significant fraction of these exhibit patterned profiles of expression. In addition, gene ontology studies revealed groups of gene products exhibiting shared expression patterns, providing new insights into the largely overlooked effector molecules that function in development. As described in this paper, automated hybridization to whole-mount embryos in situ proved to be straightforward and provided us with a very powerful method for the global survey of gene expression in early embryos. From the perspective of biological significance, our finding that many spatially restricted transcripts correspond to loci encoding novel transcripts that have not been previously identified in nearly saturating genetic screens for maternal effect and zygotic lethals is particularly notable.

Animals↗
PubMed2001

Luminescent proteins from Aequorea victoria: applications in drug discovery and in high throughput analysis.

Recent progress in generating a vast number of drug targets through genomics and large compound libraries through combinatorial chemistry have stimulated advancements in drug discovery through the development of new high throughput screening (HTS) methods. Automation and HTS techniques are also highly desired in fields such as clinical diagnostics. Luminescence-based assays have emerged as an alternative to radiolabel-based assays in HTS as they approach the sensitivity of radioactive detection along with ease of operation, which makes them amenable to miniaturization. Luminescent proteins provide the advantage of reduced reagent and operating costs because they can be produced in unlimited amounts through the use of genetic engineering tools. In that regard, the use of two naturally occurring and recombinantly produced luminescent proteins from the jellyfish Aequorea victoria, namely, aequorin and the green fluorescent protein (GFP), has attracted attention in a number of analytical applications in diverse research areas. Aequorin is naturally bioluminescent and has therefore, virtually no associated background signal, which allows its detection down to attomole levels. GFP has become the reporter of choice in a variety of applications given that it is an autofluorescent protein that does not require addition of any co-factors for fluorescence emission. Furthermore, the generation of various mutants of GFP with differing luminescent and spectral properties has spurred additional interest in this protein. In this review, we focus on the use of aequorin and GFP in the development of highly sensitive assays that find applications in drug discovery and in high throughput analysis.

Aequorin↗