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High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis.

We have developed an automated, high-throughput fingerprinting technique for large genomic DNA fragments suitable for the construction of physical maps of large genomes. In the technique described here, BAC DNA is isolated in a 96-well plate format and simultaneously digested with four 6-bp-recognizing restriction endonucleases that generate 3' recessed ends and one 4-bp-recognizing restriction endonuclease that generates a blunt end. Each of the four recessed 3' ends is labeled with a different fluorescent dye, and restriction fragments are sized on a capillary DNA analyzer. The resulting fingerprints are edited with a fingerprint-editing computer program and contigs are assembled with the FPC computer program. The technique was evaluated by repeated fingerprinting of several BACs included as controls in plates during routine fingerprinting of a BAC library and by reconstruction of contigs of rice BAC clones with known positions on rice chromosome 10.

Chromosome Mapping↗

High-throughput microfluidic mixing and multiparametric cell sorting for bioactive compound screening.

HyperCyt, an automated sample handling system for flow cytometry that uses air bubbles to separate samples sequentially introduced from multiwell plates by an autosampler. In a previously documented HyperCyt configuration, air bubble separated compounds in one sample line and a continuous stream of cells in another are mixed in-line for serial flow cytometric cell response analysis. To expand capabilities for high-throughput bioactive compound screening, the authors investigated using this system configuration in combination with automated cell sorting. Peptide ligands were sampled from a 96-well plate, mixed in-line with fluo-4-loaded, formyl peptide receptor-transfected U937 cells, and screened at a rate of 3 peptide reactions per minute with approximately 10,000 cells analyzed per reaction. Cell Ca(2+) responses were detected to as little as 10(-11) M peptide with no detectable carryover between samples at up to 10(-7) M peptide. After expansion in culture, cells sort-purified from the 10% highest responders exhibited enhanced sensitivity and more sustained responses to peptide. Thus, a highly responsive cell subset was isolated under high-throughput mixing and sorting conditions in which response detection capability spanned a 1000-fold range of peptide concentration. With single-cell readout systems for protein expression libraries, this technology offers the promise of screening millions of discrete compound interactions per day.

Calcium↗

The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments.

SBASE 3.0 is the third release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins as defined by their publishing authors. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], and BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513] which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. The present release contains 41,749 entries provided with standardized names and cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalogue of protein sequence patterns. The entries are clustered into 2285 groups using the BLAST algorithm for computing similarity measures. SBASE 3.0 is freely available on request to the authors or by anonymous 'ftp' file transfer from < ftp.icgeb.trieste.it >. Individual records can be retrieved with the gopher server at < icgeb.trieste.it > and with a www-server at < http:@www.icgeb.trieste.it >. Automated searching of SBASE by BLAST can be carried out with the electronic mail server < sbase@icgeb.trieste.it >. Another mail server < domain@hubi.abc.hu > assigns SBASE domain homologies on the basis of SWISS-PROT searches. A comparison of pertinent search strategies is presented.

Amino Acid Sequence↗

The difficulty of identifying genes in anonymous vertebrate sequences.

The identification of genes in newly determined vertebrate genomic sequences can range from a trivial to an impossible task. In a statistical preamble, we show how "insignificant" are the individual features on which gene identification can be rigorously based: promoter signals, splice sites, open reading frames, etc. The practical identification of genes is thus ultimately a tributary of their resemblance to those already present in sequence databases, or incorporated into training sets. The inherent conservatism of the currently popular methods (database similarity search, GRAIL) will greatly limit our capacity for making unexpected biological discoveries from increasingly abundant genomic data. Beyond a very limited subset of trivial cases, the automated interpretation (i.e. without experimental validation) of genomic data, is still a myth. On the other hand, characterizing the 60,000 to 100,000 genes thought to be hidden in the human genome by the mean of individual experiments is not feasible. Thus, it appears that our only hope of turning genome data into genome information must rely on drastic progresses in the way we identify and analyse genes in silico.

Amino Acid Sequence↗

Molecular cloning of the cDNA which encodes beta-N-acetylhexosaminidase A from Dictyostelium discoideum. Complete amino acid sequence and homology with the human enzyme.

beta-N-Acetylhexosaminidase A (EC 3.2.1.52), the product of the nag A gene, is a lysosomal enzyme which is developmentally regulated in Dictyostelium discoideum. The enzyme plays a role during the slug stage of development in the maintenance of pseudoplasmodia of normal size. We used a homogeneous preparation of deglycosylated enzyme subunits to generate antibody. The antibody was suitable for screening a lambda gt11 cDNA expression library derived from the mRNA of late log stage axenic cells. We isolated seven positive clones. One of these contains the complete coding sequence of the protein. We also isolated a genomic clone which contains 800 base pairs of 5'-flanking sequence and 728 base pairs of coding sequence. Analysis of the sequences and of primer extension studies indicates an inferred transcript size of 1665 bases which closely matches the 1.8-kilobase mRNA size estimated by Northern blot analysis of poly(A+) mRNA from the organism. The sequence contains an open reading frame which encodes a protein of 59,787 kDa. This equals the apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gels of in vitro translated enzyme. The amino terminus of the purified enzyme appeared to be blocked, but internal peptide sequences were obtained by automated Edman degradation of gel-purified peptides generated by treatment of protein subunits with staphylococcal V-8 protease. These sequences are included in the inferred sequence. In addition to a typical signal sequence, the open reading frame encodes a second candidate transmembrane region, a serine-rich region, and four potential N-glycosylation sites. These are discussed with regard to the localization and processing of the enzyme during its biogenesis. Beginning at amino acid 100 of the Dictyostelium enzyme sequence, 36% of its amino acids are identical to the corresponding sequence of the beta chain, and 33% are identical with those of the alpha chain of human beta-N-acetylhexosaminidase. This is strong evidence that the Dictyostelium enzyme is homologous to the alpha and beta chains of the human enzyme.

Amino Acid Sequence↗

Automated information retrieval in science and technology.

The rapid advances in computer and communication technology in the 1970's have enabled large interactive scientific and technical information retrieval systems to be implemented. Major search services today offer on-line access to millions of bibliographic citations and an increasing number of "electronic handbooks." In addition, development of knowledge bases is well under way. Despite the impressive speed and flexibility of interactive retrieval systems, their impact has been lessened by limited awareness of their existence, uneven quality of retrieval, inadequate linkages among data bases, and reliance on specially trained intermediaries.

Computers↗

ESTminer: a Web interface for mining EST contig and cluster databases.

UNLABELLED: ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster datasets. The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or a threshold number of members. The results are displayed as color-coded tree nodes, where the color indicates the fractional size of each cDNA library component. The nodes are expandable, revealing library statistics as well as EST or contig members, with links to sequence data, GenBank records or user configurable links. Also, the interface allows 'queries within queries' where the result set of a query is further filtered by the subsequent query. AVAILABILITY: ESTminer is implemented in Java/JSP and the package, including MySQL and Oracle schema creation scripts, is available from http://cggc.agtec.uga.edu/Data/download.asp CONTACT: agingle@uga.edu.

Algorithms↗

Primary structure of the major beta-chain of rat haemoglobins.

The amino acid sequence of the major beta-chain, (II)beta, from rat haemoglobins was established with an automated sequencer. Amino acid heterogeneities were found that appear to result from allelic variation at particular residues. We applied several new or unusual techniques in determining the sequence: (1) reaction of the polypeptide with dansylaziridine for detection of cysteine; (2) blockage of the N-terminal residue and the epsilon-amino group of lysine residues with 1-fluoro-2-nitro-4-trimethylammoniobenzene iodide and subsequent identification of the modified lysine phenylthiohydantoin by absorbance at 420nm; (3) identification of histidine phenylthiohydantoin by its blue fluorescence under long-wave u.v. light; (4) cleavage of the chain into two or three fragments and subsequent sequencing without purification [a detailed statement giving the major phenylthiohydantoins assigned at each step for each sequence run before their alignment in individual sequences has been deposited as Supplementary Publication SUP 50084 (10 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1978) 169, 5]; (5) separation of fragments produced by CNBr cleavage by cation-exchange chromatography; (6) peptide sequencing after attachment of the peptide to cytochrome c. The amino acid sequence was confirmed by amino acid compositions of the complete chain, of CNBr fragments 1 and 3, and of 11 purified tryptic peptides.

Amino Acid Sequence↗

Emerging techniques for the discovery and validation of therapeutic targets for skeletal diseases.

Advances in genomics and proteomics have revolutionised the drug discovery process and target validation. Identification of novel therapeutic targets for chronic skeletal diseases is an extremely challenging process based on the difficulty of obtaining high-quality human diseased versus normal tissue samples. The quality of tissue and genomic information obtained from the sample is critical to identifying disease-related genes. Using a genomics-based approach, novel genes or genes with similar homology to existing genes can be identified from cDNA libraries generated from normal versus diseased tissue. High-quality cDNA libraries are prepared from uncontaminated homogeneous cell populations harvested from tissue sections of interest. Localised gene expression analysis and confirmation are obtained through in situ hybridisation or immunohistochemical studies. Cells overexpressing the recombinant protein are subsequently designed for primary cell-based high-throughput assays that are capable of screening large compound banks for potential hits. Afterwards, secondary functional assays are used to test promising compounds. The same overexpressing cells are used in the secondary assay to test protein activity and functionality as well as screen for small-molecule agonists or antagonists. Once a hit is generated, a structure-activity relationship of the compound is optimised for better oral bioavailability and pharmacokinetics allowing the compound to progress into development. Parallel efforts from proteomics, as well as genetics/transgenics, bioinformatics and combinatorial chemistry, and improvements in high-throughput automation technologies, allow the drug discovery process to meet the demands of the medicinal market. This review discusses and illustrates how different approaches are incorporated into the discovery and validation of novel targets and, consequently, the development of potentially therapeutic agents in the areas of osteoporosis and osteoarthritis. While current treatments exist in the form of hormone replacement therapy, antiresorptive and anabolic agents for osteoporosis, there are no disease-modifying therapies for the treatment of the most common human joint disease, osteoarthritis. A massive market potential for improved options with better safety and efficacy still remains. Therefore, the application of genomics and proteomics for both diseases should provide much needed novel therapeutic approaches to treating these major world health problems.

Animals↗

Retrieval of crystallographically-derived molecular geometry information.

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

Journal Article↗

Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.

Plant genomes are filled with retrotransposons and their derivatives, constantly undergoing sequence diversification and structural rearrangement. Among them, short, non-autonomous retrotransposons lack full coding capacity and often form subfamilies. As a result, non-autonomous retrotransposons are incompletely identified in most to all genome assemblies.Here, we capitalize on our comprehensive understanding of the transposable element (TE) landscape in sugar beet (Beta vulgaris) to assess the extent of the blind spot for non-autonomous long terminal repeat (LTR) retrotransposons. This use case serves to answer if all of these sequences are derivatives of easier-to-identify full-length elements or if there is more variability that is currently overlooked.For this we applied a semi-automated structural discovery workflow followed by in-depth manual verification to characterize non-autonomous LTR retrotransposons in sugar beet. We retrieve more than 100 non-autonomous LTR retrotransposon families that lack complete autonomous coding capacity, including canonical terminal-repeat retrotransposons in miniature (TRIMs), elongated non-coding derivatives and families retaining fragmented coding remnants. The identified families span a broad range, including elements exceeding 15,000&#xa0;bp in length and display evidence for reshuffling and modular evolution. Only a subset of families could be confidently linked to autonomous retrotransposons, showing sequence diversification within the non-autonomous LTR retrotransposon fraction beyond the autonomous genomic templates.We highlight that a large fraction of non-autonomous LTR retrotransposons is incompletely recovered with the current TE identification workflows, even if the output is well-curated and condensed into TE libraries and suggest procedures to remedy this gap. This study gives a genome-wide view into the non-autonomous LTR retrotransposon landscape of a single plant genome and highlights the importance of structure-based approaches for their identification and classification.

LTR retrotransposons↗

Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra.

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is the pre-eminent technique for mass mapping of glycans. In order to make this technique practical for high-throughput screening, reliable automatic methods of annotating peaks must be devised. We describe an algorithm called Cartoonist that labels peaks in MALDI spectra of permethylated N-glycans with cartoons which represent the most plausible glycans consistent with the peak masses and the types of glycans being analyzed. There are three main parts to Cartoonist. (i) It selects annotations from a library of biosynthetically plausible cartoons. The library we currently use has about 2800 cartoons, but was constructed using only about 300 archetype cartoons entered by hand. (ii) It determines the precision and calibration of the machine used to generate the spectrum. It does this automatically based on the spectrum itself. (iii) It assigns a confidence score to each annotation. In particular, rather than making a binary yes/no decision when annotating a peak, it makes all plausible annotations and associates them with scores indicating the probability that they are correct.

Algorithms↗

The NLM Indexing Initiative.

The objective of NLM's Indexing Initiative (IND) is to investigate methods whereby automated indexing methods partially or completely substitute for current indexing practices. The project will be considered a success if methods can be designed and implemented that result in retrieval performance that is equal to or better than the retrieval performance of systems based principally on humanly assigned index terms. We describe the current state of the project and discuss our plans for the future.

Abstracting and Indexing↗

The performance of three visual coding procedures and three computer programs in classification of electrocardiograms according to the Minnesota Code.

A test library composed of the ECG's of 228 patients with clinically proven myocardial infarction and 294 subjects without clinical evidence of infarction was used to assess the performance of three visual coding procedures and three computer programs designed to classify ECGs according to the Minnesota Code. The results showed that visual coding performed by one experienced senior coder tended to be more consistent than visual coding relying on two less experienced coders and arbitration of disagreements by a supervisor. There was no significant difference in coding results when only one preprocessed complex was coded in comparison with the more elaborate coding of the whole source ECG using majority rule. The coding performance of the three computer programs was similar to that of the visual coding procedures. It is concluded that computer coding of ECGs according to the Minnesota Code is feasible. Combined optimal use of automated coding and visual verification of selected items may still further improve coding precision. However, when judged against an ECG independent standard, the accuracy of all coding procedures in discriminating infarcts from non-infarcts according to the Minnesota code criteria is rather limited. 'Soft' criteria give a reasonable sensitivity with low specificity whereas the use of 'hard' criteria with adequate specificity results in a substantial drop in sensitivity.

Computers↗

Characterization and quantitative analysis with GC/TOFMS comparing enhanced separation with tandem-column stop-flow GC and spectral deconvolution of overlapping peaks.

Time-of-flight mass spectrometry is unique in that ion abundance ratios are constant over the chromatographic peak profile provided that the peak contains only one component. This provides the means for the automated finding and spectral deconvolution of overlapping chromatographic peaks from completely unknown mixtures if the mass spectra for the overlapping components are sufficiently unique. This can greatly reduce the chromatographic resolution requirements, which allows for very rapid quantitative analysis as well as for high-speed mixture characterization. High-speed GC with stop-flow operation of a series-coupled column ensemble can be used to completely separate some component pairs that coelute from the column ensemble, thus eliminating the need for spectral deconvolution of those mixture components. This provides two options for high-speed qualitative and quantitative analysis, using either the mass spectra from deconvoluted overlapping peaks or the mass spectra from the completely separated peaks obtained with stop-flow operation of the tandem column ensemble. These options are compared with respect to the similarity for spectral matching with a library and to peak area linearity with concentration, calibration plot correlation coefficients, and shot-to-shot reproducibility.

Journal Article↗

Genetic expression by fetal chorionic villi during the first trimester of human gestation.

OBJECTIVE: The growth and differentiation of the embryo and the contiguous placental structures are fundamental to human reproduction and survival. Little is known, however, about the genetic control of these processes during early human development. Normal placentation is the result of a well-orchestrated sequence of events that consists of cellular adhesion and limited invasion controlled by relatively unknown genetic processes. We hypothesized that genes expressed by first-trimester chorionic villi constitute critical regulators of placentation and hence of early human development. Our objective was therefore to isolate and characterize genes, both known and unknown, expressed by the human placenta during the first trimester. STUDY DESIGN: Tissues collected consisted of placental material collected during first-trimester elective pregnancy terminations. Fetal chorionic villi were separated grossly from maternal decidual and quickly frozen in liquid nitrogen for ribonucleic acid preservation. Tissues from different gestational ages were kept separate. Total ribonucleic acid was extracted, messenger ribonucleic acid was isolated, and complementary deoxyribonucleic acid was synthesized. Complementary deoxyribonucleic acid was cloned into the ZAP Express lambda vector (Stratagene, La Jolla, Calif). Automated sequencing of random plaques was done. Sequence homology was searched for with the Basic Local Assignment Search Tool to search the Genbank database (National Center for Biotechnology Institute, Bethesda, Md). In the event that a known gene sequence was derived, no further workup was undertaken. If no homology was identified, the complete complementary deoxyribonucleic acid insert was sequenced in its entirety. Novel genes were further characterized by tissue-specific patterns, cellular localization, and chromosomal location. Expression by fetal villi was confirmed by reverse transcriptase polymerase chain reaction. RESULTS: We isolated a number of genes known to be expressed at the maternal-fetal interface. Seventeen of 186 random clones were >1 kilobase in length and did not display homology with known genes, and these may therefore constitute novel genes critical for placentation. One of the clones from a human chorionic villi complementary deoxyribonucleic acid library at 12 weeks' gestation is a 7-kilobase gene that is also abundantly expressed in human fetal brain, lung, liver, and kidney. In situ hybridization localized the transcript to the fetal renal glomerulus. CONCLUSIONS: Our findings indicate that the placenta serves as a rich source for potential novel gene expression. Seventeen clones were >1 kilobase in length and are potential novel genes involved in early first-trimester placentation. One of these 17 potential novel genes is expressed in abundance in several fetal tissues, which suggests a role in early human fetal development. Other potential novel genes are currently being characterized. The powerful molecular techniques that we used to isolate genes expressed by early fetal chorionic villi will lead us to a better understanding of the genetic control of normal human reproduction. They also may be used to study obstetric and other human disease.

Adult↗

A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity.

Full details of the development of a simple, nondestructive, and high-throughput method for establishing DNA binding affinity and sequence selectivity are described. The method is based on the loss of fluorescence derived from the displacement of ethidium bromide or thiazole orange from the DNA of interest or, in selected instances, the change in intrinsic fluorescence of a DNA binding agent itself and is applicable for assessing relative or absolute DNA binding affinities. Enlisting a library of hairpin deoxyoligonucleotides containing all five base pair (512 hairpins) or four base pair (136 hairpins) sequences displayed in a 96-well format, a compound's rank order binding to all possible sequences is generated, resulting in a high-resolution definition of its sequence selectivity using this fluorescent intercalator displacement (FID) assay. As such, the technique complements the use of footprinting or affinity cleavage for the establishment of DNA binding selectivity and provides the information at a higher resolution. The merged bar graphs generated by this rank order binding provide a qualitative way to compare, or profile, DNA binding affinity and selectivity. The 96-well format assay (512 hairpins) can be conducted at a minimal cost (presently ca. $100 for hairpin deoxyoligonucleotides/assay with ethiduim bromide or less with thiazole orange), with a rapid readout using a fluorescent plate reader (15 min), and is adaptable to automation (Tecan Genesis Workstation 100 robotic system). Its use in generating a profile of DNA binding selectivity for several agents including distamycin A, netropsin, DAPI, Hoechst 33258, and berenil is described. Techniques for establishing binding constants from quantitative titrations are compared, and recommendations are made for use of a Scatchard or curve fitting analysis of the titration binding curves as a reliable means to quantitate the binding affinity.

Base Pairing↗

Microcomputer system for automatic identification of the Cryptococcus neoformans and its clinical application.

In this study, microcomputer image processing and pattern recognition technology, and the knowledge of morphology and optical characteristics of Cryptococcus neoformans were used for identification of Cryptococcus neoformans. Four groups of mice were lethally infected with standard strain, Wuhan strain, American B-2643 strain and Var. Shanghainesis of the Cryptococcus neoformans. The samples collected included mice brain, lung, kidney, liver, small intestine tissue and were observed under a light microscope. More than 600 images of the fungus were input into a microcomputer. A system of computer for automatic identification of the Cryptococcus neoformans was developed. The technique involved image preprocessing, image segmenting, coding of line-length on the edge, curve fitting, extracting of image feature, building of image library and feature data bank etc.. And then, 768 images of the clinical samples and other fungus samples whose morphological features tend to be confused with Cryptococcus neoformans were input into microcomputer and subjected to automatic identification. The Cryptococcus neoformans was accurately identified within 15 min, and the consistency rate with results of routine culture was 98%.

Animals↗