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PubMed1999

Histidine placement in de novo-designed heme proteins.

The effects of histidine residue placement in a de novo-designed four-alpha-helix bundle are investigated by placement of histidine residues at coiled coil heptad a positions in two distinct heptads and at each position within a single heptad repeat of our prototype heme protein maquette, [H10H24]2 [[Ac-CGGGELWKL x HEELLKK x FEELLKL x HEERLKK x L-CONH2]2]2 composed of a generic (alpha-SS-alpha)2 peptide architecture. The heme to peptide stoichiometry of variants of [H10H24]2 with either or both histidines on each helix replaced with noncoordinating alanine residues ([H10A24]2, [A10H24]2, and [A10A24]2) demonstrates the obligate requirement of histidine for biologically significant heme affinity. Variants of [A10A24]2, [[Ac-CGGGELWKL x AEELLKK x FEELLKL x AEERLKK x L-CONH2]2]2, containing a single histidine per helix in positions 9 to 15 were evaluated to verify the design based on molecular modeling. The bis-histidine site formed between heptad positions a at 10 and 10' bound ferric hemes with the highest affinity, Kd1 and Kd2 values of 1.5 and 800 nM, respectively. Placement of histidine at position 11 (heptad position b) resulted in a protein that bound a single heme with moderate affinity, Kd1 of 9.5 microM, whereas the other peptides had no measurable apparent affinity for ferric heme with Kd1 values >200 microM. The bis-histidine ligation of heme to [H10A24]2 and [H11A24]2 was confirmed by electron paramagnetic resonance spectroscopy. The protein design rules derived from this study, together with the narrow tolerances revealed, are applicable for improving future heme protein designs, for analyzing the results of randomized heme protein combinatorial libraries, as well as for implementation in automated protein design.

Amino Acid Sequence↗
PubMed1992

DNA sequencing by primer walking with strings of contiguous hexamers.

When template DNA is saturated with a single-stranded DNA binding protein (SSB), strings of three or four contiguous hexanucleotides (hexamers) can cooperate through base-stacking interactions to prime DNA synthesis specifically from the 3' end of the string. Under the same conditions, priming by individual hexamers is suppressed. Strings of three of four hexamers representing more than 200 of the 4096 possible hexamers primed easily readable sequence ladders at more than 75 different sites in single-stranded or denatured double-stranded templates 6.4 kilobases to 40 kilobase pairs long, with a success rate of 60 to 90 percent. A synthesis of 1 micromole of hexamer supplies enough material for thousands of primings, so multiple libraries of all 4096 hexamers could be distributed at a reasonable cost. Such libraries would allow rapid and economical sequencing. Automating this strategy could increase the speed and efficiency of large-scale DNA sequencing by at least an order of magnitude.

Base Sequence↗
PubMed1999

Budding yeast as a screening tool for discovery of nucleoside analogs for use in HSV-1 TK suicide-gene therapy.

We present a fast, convenient and inexpensive method that allows the automated, large-scale screening of chemical libraries for compounds that are converted by the herpes simplex virus type 1 (HSV-1) thymidine kinase (TK) into inhibitors of cell growth. The method is based on the use of budding yeast (Saccharomyces cerevisiae) transformed with the HSV-1 TK gene on a multicopy plasmid. Eight nucleoside analogs (acyclovir, ganciclovir, penciclovir, lobucavir, brivudin, sorivudine, IVDU and ara-T), for which the cytostatic action against mammalian cells expressing the HSV-1 TK gene has been well documented, were studied for their inhibitory effect on the growth of yeast expressing the viral TK. These nucleoside analogs had little or no inhibitory effect on the growth of yeasts transformed with the empty vector, but inhibited to a significant extent the growth of yeast expressing the viral TK. Use of HSV-1 TK-expressing yeast allows quick screening in multi-well plate format for compounds with potential use in HSV-1 TK suicide gene therapy. The method may also be used as a tool to selectively suppress or arrest the growth of one population of yeast out of mixed yeast cell cultures.

Acyclovir↗
PubMed2004

Application of spectral libraries for characterization of oxidizers in post-blast residues by electrospray mass spectrometry.

The goal of this paper is to demonstrate that electrospray mass spectrometry when used with spectral libraries becomes a useful method for rapid identification of inorganic oxidizers commonly present in commercial and improvised explosives. Electrospray ionization mass spectra (ESI-MS) of oxidizers reveal a series of characteristic cluster ions. Such a set of cluster ions can be regarded as a "fingerprint" of a particular oxidizer. With the aid of a spectral library, tentative identification of inorganic oxidizer becomes automated and an easy-to-implement process. The oxidizer identity may be further confirmed by using tandem mass spectrometry (MS/MS). Because it is not necessary to separate the components before analysis, results become available in real time. Little sample consumption and the ease of sample preparation should also be noted. The methodology can be readily employed on various ESI-MS systems that are already in use in analytical laboratories. This is another important benefit as the ESI-MS instrumentation is becoming increasingly common in forensic laboratories.

Journal Article↗
PubMedDate not supplied

From telepathology to virtual pathology institution: the new world of digital pathology.

Telepathology has left its childhood. Its technical development is mature, and its use for primary (frozen section) and secondary (expert consultation) diagnosis has been expanded to a great amount. This is in contrast to a virtual pathology laboratory, which is still under technical constraints. Similar to telepathology, which can also be used for e-learning and e-training in pathology, as exemplarily is demonstrated on Digital Lung Pathology (Klaus.Kayser@charite.de) at least two kinds of virtual pathology laboratories will be implemented in the near future: a) those with distributed pathologists and distributed (> or = 1) laboratories associated to individual biopsy stations/surgical theatres, and b) distributed pathologists (usually situated in one institution) and a centralized laboratory, which digitizes complete histological slides. Both scenarios are under intensive technical investigations. The features of virtual pathology comprise a virtual pathology institution (mode a) that accepts a complete case with the patient's history, clinical findings, and (pre-selected) images for first diagnosis. The diagnostic responsibility is that of a conventional institution. The Internet serves as platform for information transfer, and an open server such as the iPATH (http://telepath.patho.unibas.ch) for coordination and performance of the diagnostic procedure. The size and number of transferred images have to be limited, and usual different magnifications have to be used. The sender needs to possess experiences in image sampling techniques, which present with the most significant information. A group of pathologists is "on duty", or selects one member for a predefined duty period. The diagnostic statement of the pathologist(s) on duty is retransmitted to the sender with full responsibility. The first experiences of a virtual pathology institution group working with the iPATH server working with a small hospital of the Salomon islands are promising. A centralized virtual pathology institution (mode b) depends upon the digitalization of a complete slide, and the transfer of large sized images to different pathologists working in one institution. The technical performance of complete slide digitalization is still under development. Virtual pathology can be combined with e-learning and e-training, that will serve for a powerful daily-work-integrated pathology system. At present, e-learning systems are "stand-alone" solutions distributed on CD or via Internet. A characteristic example is the Digital Lung Pathology CD, which includes about 60 different rare and common lung diseases with some features of electronic communication. These features include access to scientific library systems (PubMed), distant measurement servers (EuroQuant), automated immunohisto-chemistry measurements, or electronic journals (Elec J Pathol Histol, www.pathology-online.org). It combines e-learning and e-training with some acoustic support. A new and complete database based upon this CD will combine e-learning and e-teaching with the actual workflow in a virtual pathology institution (mode a). The technological problems are solved and do not depend upon technical constraints such as slide scanning systems. At present, telepathology serves as promoter for a complete new landscape in diagnostic pathology, the so-called virtual pathology institution. Industrial and scientific efforts will probably allow an implementation of this technique within the next two years with exciting diagnostic and scientific perspectives.

Computer Communication Networks↗
PubMed2006

Combined use of 16S ribosomal DNA and automated ribosomal intergenic spacer analysis to study the bacterial community in catfish ponds.

AIMS: To apply culture-independent techniques to explore the bacterial community composition in catfish pond water. METHODS AND RESULTS: 16S rDNA libraries were constructed and sequenced from 15 pond water samples. Automated ribosomal intergenic spacer analysis (ARISA) was used to fingerprint each bacterial community. A broad diversity in bacterial species composition was found by 16S rDNA analysis. Alphaproteobacteria was the most represented class in all ponds, followed by Gammaproteobacteria and Gram-positive high G + C content bacteria. Uniqueness of bacterial communities from each individual pond was confirmed by ARISA. Catfish pathogens were detected sporadically. CONCLUSIONS: Bacterial communities in a catfish aquaculture setting can vary from pond to pond at one given point. No correlation could be made between bacteria composition and fish strain or between bacterial profile and the presence of catfish pathogens in a particular pond. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report showing the composition of bacterial communities in catfish ponds. Fish health specialists and catfish aquaculture managers should be aware of the wide differences in bacterial communities between ponds and include this variable in fish husbandry practices.

Animals↗
PubMed2005

Automated microflow NMR: routine analysis of five-microliter samples.

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 microL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 microL of sample per well, as with vials, 5 microL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of approximately 11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in approximately 6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software.

Image Processing, Computer-Assisted↗
PubMedDate not supplied

High-throughput bioassay-guided fractionation: a technique for rapidly assigning observed activity to individual components of combinatorial libraries, screened in HTS bioassays.

In this paper, we describe an automated, high-throughput analytical tool for the unambiguous characterization of the active component(s) of a combinatorially derived reaction mixture. We call this technique high-throughput bioassay-guided fractionation (BGF). The novel aspects of this communication are the systematization of the BGF concept, the application of BGF to combinatorial chemistry, and the high-throughput nature of the identification technique. The identification of the active component in a well mixture is an essential step for subsequent resynthesis or isolation of the active component(s) or for removal of intractable wells from further consideration. We believe the technique described is also applicable to any mixture library, provided the expected component (or components) of each well is (are) known. Example mixture libraries would include collections of synthetic chemicals and collections of purified natural products. The mixture need not come from libraries produced using parallel synthesis. The BGF tool described herein allows full utilization of highly diverse combinatorial libraries, thereby obviating costly up-front purification or extensive prescreening characterization efforts.

Biological Assay↗
PubMed1993

Viral interleukin 10 is critical for the induction of B cell growth transformation by Epstein-Barr virus.

We have used an efficient cDNA subtraction library procedure to identify newly induced genes in human B lymphocytes infected for 6 h with Epstein-Barr virus (EBV). Among the genes identified by automated sequencing of a random subset of clones from this library, one coded the EBV BCRF1 open reading frame, which specifies the viral interleukin 10 gene (vIL-10). This molecule is highly homologous to human (h)IL-10 and was previously thought to represent a "late" viral gene expressed only during the lytic phase of virus replication. Using gene amplification by reverse transcriptase polymerase chain reaction of B cell RNA obtained at varying times after infection, we detected vIL-10 expression within a few hours of EBV infection, followed, 20-30 h later by expression of hIL-10. Expression of both genes continued beyond the initial transformation phase (5-10 d) and was present in all transformed cell lines tested. When added at the time of viral infection, antisense (but not sense) oligonucleotides for vIL-10 mRNA (cytosolic half-life, approximately 6 h) prevented subsequent B cell transformation. The antisense effect was highly specific, leaving the expression levels of other transformation-related genes intact. Addition of exogenous (h)IL-10 rescued the transformation process in antisense-treated cells. Our observations establish vIL-10 as a new latency gene with a directly transformation-prerequisite function.

B-Lymphocytes↗
PubMed1990

Automated evaluation of tryptic digest from recombinant human growth hormone using ultraviolet spectra and numeric peak information.

UV spectra were successfully employed in identifying peptide fragments from a tryptic digest of recombinant-DNA-derived human growth hormone (r-hGH). It was possible to distinguish very similar peptides utilizing a digital comparison of the UV spectra. An automated procedure was developed to generate a calibration library for the tryptic digest of a reference standard. The calibration library was then evaluated for reproducibility and selectivity and found to provide superior performance in correctly identifying ambiguous peaks as compared to the use of a conventional calibration table. Spectral match factors together with numerical information, derived from peak retention time, area and height, were used to arrive at a "peak score" descriptive of the similarity between standard and sample peaks. "Peak scores" could be combined to calculate a "sample score" indicative of overall similarity between an unknown and a standard. The scoring procedure was automated to generate a final report without operator intervention and successfully assigned appropriate scores to similar as well as dissimilar samples, e.g., native and oxidized r-hGH.

Algorithms↗
PubMed1995

Libraries of non-polymeric organic molecules.

New technology is emerging that permits the chemical synthesis of large numbers of different compounds simultaneously. Combinatorial chemistry is heavily dependent upon the adaptation of organic synthesis to solid supports and has necessitated the development of appropriate analytical and chemical approaches to both monitor solid-phase reactions and release finished compounds into solution. Considerable progress has recently been made in all of these areas. Small-molecule libraries of medicinally important chemical classes, such as 1,4-benzodiazepines, mercaptopropionyl amino acids, and peptidyl phosphonates, have recently been reported. Encoded combinatorial libraries of dihydrobenzopyran-based and acylpiperidine-based pharmacophores have yielded potent inhibitors of carbonic anhydrase. Automated instrumentation is growing in importance for the synthesis of small-molecule libraries.

Journal Article↗
PubMed1996

Mapping medical vocabularies to the Unified Medical Language System.

This paper presents our work in automated mapping of medical vocabularies to the National Library of Medicine's Unified Medical Language System (UMLS). We used the UMLS Knowledge Source (KS) tool to map terms from several sources to UMLS Metathesaurus concepts. We compared performance of the KS tools with our own Minimal Representable Units Method (MRUM). The KS tools were able to map terms from 13% to 54% of the time, depending on the term set and the KS options used. Our MRUM method mapped between 96% and 99% of the terms. Based on our experience, we believe that questions remain about the best method by which the UMLS can be used to achieve automated term translation.

Algorithms↗
PubMed1987

Primary structure of rat cardiac beta-adrenergic and muscarinic cholinergic receptors obtained by automated DNA sequence analysis: further evidence for a multigene family.

Two cDNA clones, lambda RHM-MF and lambda RHB-DAR, encoding the muscarinic cholinergic receptor and the beta-adrenergic receptor, respectively, have been isolated from a rat heart cDNA library. The cDNA clones were characterized by restriction mapping and automated DNA sequence analysis utilizing fluorescent dye primers. The rat heart muscarinic receptor consists of 466 amino acids and has a calculated molecular weight of 51,543. The rat heart beta-adrenergic receptor consists of 418 amino acids and has a calculated molecular weight of 46,890. The two cardiac receptors have substantial amino acid homology (27.2% identity, 50.6% with favored substitutions). The rat cardiac beta receptor has 88.0% homology (92.5% with favored substitutions) with the human brain beta receptor and the rat cardiac muscarinic receptor has 94.6% homology (97.6% with favored substitutions) with the porcine cardiac muscarinic receptor. The muscarinic cholinergic and beta-adrenergic receptors appear to be as conserved as hemoglobin and cytochrome c but less conserved than histones and are clearly members of a multigene family. These data support our hypothesis, based upon biochemical and immunological evidence, that suggests considerable structural homology and evolutionary conservation between adrenergic and muscarinic cholinergic receptors. To our knowledge, this is the first report utilizing automated DNA sequence analysis to determine the structure of a gene.

Amino Acid Sequence↗
PubMed2006

Engineering stability into Escherichia coli secreted Fabs leads to increased functional expression.

The recombinant expression of immunoglobulin domains, Fabs and scFvs in particular, in Escherichia coli can vary significantly from antibody to antibody. We hypothesized that poor Fab expression is often linked to poor intrinsic stability. To investigate this further, we applied a novel approach for stabilizing a poorly expressing anti-tetanus toxoid human Fab with a predisposition for being misfolded and non-functional. Forty-five residues within the Fab were chosen for saturation mutagenesis based on residue frequency analysis and positional entropy calculations. Using automated screening, we determined the approximate midpoint temperature of thermal denaturation (TM) for over 4000 library members with a maximum theoretical diversity of 855 unique mutations. This dataset led to the identification of 11 residue positions, primarily in the Fv region, which when mutated enhanced Fab stability. By combining these mutations, the TM of the Fab was increased to 92 degrees C. Increases in Fab stability correlated with higher expressed Fab yields and higher levels of properly folded and functional protein. The mutations were selected based on their ability to increase the apparent stability of the Fab and therefore the exact mechanism behind the enhanced expression in E.coli remains undefined. The wild-type and two optimized Fabs were converted to an IgG1 format and expressed in mammalian cells. The optimized IgG1 molecules demonstrated identical gains in thermostability compared to the Fabs; however, the expression levels were unaffected suggesting that the eukaryotic secretion system is capable of correcting potential folding issues prevalent in E.coli. Overall, the results have significant implications for the bacterial expression of functional antibody domains as well as for the production of stable, high affinity therapeutic antibodies in mammalian cells.

Escherichia coli↗
PubMed2003

Upscaling and automation of electrophysiology: toward high throughput screening in ion channel drug discovery.

Effective screening of large compound libraries in ion channel drug discovery requires the development of new electrophysiological techniques with substantially increased throughputs compared to the conventional patch clamp technique. Sophion Bioscience is aiming to meet this challenge by developing two lines of automated patch clamp products, a traditional pipette-based system called Apatchi-1, and a silicon chip-based system QPatch. The degree of automation spans from semi-automation (Apatchi-1) where a trained technician interacts with the system in a limited way, to a complete automation (QPatch 96) where the system works continuously and unattended until screening of a full compound library is completed. The performance of the systems range from medium to high throughputs.

Animals↗
PubMed2005

Automated renderer for visible human and volumetric scan segmentations.

Creating a library of binary segmentation mask sequences for the abdominal anatomy hierarchy of SNOMED and developing a quick, flexible automatic method for generating iso-surface models from these named structure masks has been a primary goal in our research. This paper describes our development of a clear path for computing visualizations of arbitrary groups of organs from these masks (typically generated from Visible Human data). One use of these methods is teaching the anatomy of various organ systems in the human body using virtual reality environments.

Computer Simulation↗
PubMed2004

Automated parallel, multi-step polymer-assisted solution phase (PASP) synthesis of substituted benzimidazole derivatives.

The automated polymer-assisted solution phase (PASP) synthesis of a 72 member library of 2-alkylthio-benzimidazoles 16 and benzimidazolin-2-ones 17 using commercially available robotic workstations is described. By incorporating both automated aqueous work-ups, in-line scavenging and 'catch and release' protocols the desired compounds were obtained directly in good yields and excellent purities without the need for conventional chromatographic purification. The synthesis described demonstrates how both manual and automated equipment may be utilised together to provide a versatile approach that facilitates parallel compound synthesis.

Automation↗