The Experts below are selected from a list of 300 Experts worldwide ranked by ideXlab platform
Erland Jungert - One of the best experts on this subject based on the ideXlab platform.
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VISUAL - Spatial/Temporal Query Processing for Information Fusion Applications
Lecture Notes in Computer Science, 2000Co-Authors: Shi-kuo Chang, Gennaro Costagliola, Erland JungertAbstract:To support the retrieval and fusion of multimedia information from multiple sources and databases, a spatial/temporal query language called ?QL was proposed. ?QL is based upon the ?-Operator Sequence and in practice expressible in SQL-like syntax. ?QL allows a user to specify powerful spatial/temporal queries for both multimedia data sources and multimedia databases, eliminating the need to write different queries for each. In this paper, we illustrate this approach by query processing examples for information fusion applications.
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Multimedia Information Analysis and Retrieval - A Spatial Query Language for Multiple Data Sources Based on s-Operator Sequences
Lecture Notes in Computer Science, 1998Co-Authors: Shi-kuo Chang, Erland JungertAbstract:To support the retrieval, fusion and discovery of visual Umultimedia information, a spatial query language for multiple data sources is needed. In this paper we describe a spatial query language which is based upon the σ-Operator Sequence and in practice expressible in an SQL-like syntax. The general 6-Operator and temporal σ-Operator are explained, and applications of the σ-query language to vertical/horizontal reasoning and hypermapped virtual world are explored.
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A SPATIAL/TEMPORAL QUERY LANGUAGE FOR MULTIPLE DATA SOURCES IN A HETEROGENEOUS INFORMATION SYSTEM ENVIRONMENT
International Journal of Cooperative Information Systems, 1998Co-Authors: Shi-kuo Chang, Erland JungertAbstract:To support the retrieval, fusion and discovery of multimedia information, a spatial/temporal query language for multiple data sources is needed. In this paper we describe a spatial/temporal query language, the ∑QL, which is based upon the σ-Operator Sequence and in practice expressible in an SQL-like syntax. The general σ-Operator and temporal σ-Operator are explained, and applications of the σ-query language to vertical/horizontal reasoning and hypermapped virtual world are discussed.
Larry W. Mclaughlin - One of the best experts on this subject based on the ideXlab platform.
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Probing the Interface of the trp Repressor–Operator Complex Using Operator Sequences Containing Isosteric Base-Pair Analogues☆
Bioorganic Chemistry, 1999Co-Authors: Stephen A. Smith, Larry W. MclaughlinAbstract:Abstract A series of base pair analogues, dI-dM and dD-dU, have been used in place of the native dA-dT and dG-dC residues to probe the interface between the trp repressor and its Operator Sequence. Both analogues maintain the interstrand hydrogen bond character that correlates with the corresponding native base pair, but alters the relative positions of the amino and carbonyl residues of the base pairs that extend into the major groove of B-form DNA. None of the Sequences tested exhibit native-like binding with the trp repressor. Although functional group contacts between complementary hydrogen bond donors and acceptors could account for these differences, such a scenario is not consistent with the published crystal structures. Differences in binding by these analogue Sequences is suggested to result from incremental differences in the van der Waals contacts at the interface between the protein and the nucleic acid. Although this surface would appear to be nonspecific in nature, previous studies have indicated that the state of hydration in the major groove for the free and complexed Operators is in part conserved. These bound water molecules alter the nature of the van der Waals surface and could function as an extension of the van der Waals surface of the major groove. Either of the base pair analogues, dI-dM or dD-dU, results in either the loss of a conserved site of hydration, or the introduction of a new hydration site. Either effect would alter the van der Waals surface relative to the native Operator and result in reduced affinity between the protein and nucleic acid. Additional analogues designed to alter the nature of the van der Waals surface by removing polar functional groups (adenine → purine) result in some cases in higher affinity binding than is observed with the native Operator Sequence.
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Probing contacts to the DNA backbone in the trp repressor-Operator Sequence-specific protein-nucleic acid complex using diastereomeric methylphosphonate analogues.
Biochemistry, 1997Co-Authors: Stephen A. Smith, Larry W. MclaughlinAbstract:Fourteen analogue DNA Sequences containing the trp Operator Sequence and a single diastereomeric methylphosphonate linkage are each prepared from the stereochemically pure nucleoside methylphosphonate dimer building block, prepared as a phosphoramidite. The analogue Sequences are shown to be single diastereomers on the basis of HPLC analysis of the digestion mixture; in each case, only a single diastereomeric dimer is present. These analogue Sequences can be used effectively to probe for interactions to either of the prochiral phosphate oxygens as illustrated by their use to identify critical interactions in the trp repressor−Operator complex. In a number of cases, the pairs of diastereomeric analogue Sequences exhibit variable binding affinities that can be used to identify one of the prochiral phosphate oxygens as a critical site for complex-stabilizing interactions. Upon the basis of dissociation constants, apparent incremental binding energies are assigned to specific interactions. In all but one exam...
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Interactions between the trp repressor and its Operator Sequence as studied by base analogue substitution.
Biochemistry, 1992Co-Authors: Joan M. Mazzarelli, Sharanabasava B. Rajur, Patricia L. Iadarola, Larry W. MclaughlinAbstract:A series of modified trp Operator Sequences has been prepared by the incorporation of seven different base analogues. Four of the analogues allow the site-specific deletion of functional groups present on the dA-dT and dT-dA base pairs at positions -4/+4 and -5/+5 in the trp Operator. The remaining three analogues permit the incorporation of structural analogues of the native dA-dT or dG-dC base pairs. The duplex Operator Sequences all exhibit Tm values well above ambient temperature (48-70 degrees C), and these values generally correlate very well with the number of interstrand hydrogen bonds present. The affinity between the trp repressor and 14 modified Operator Sequences was examined using a recently developed alkaline phosphatase protection assay. The results from the analogue Sequences used in this study suggest that the structure of the dA-dT or dT-dA base pairs at positions -4/+4 and -5/+5, respectively, has relatively little effect upon the solution binding by the trp repressor, but the protein is very sensitive to the orientation of the amino and carbonyl functional groups at the -4/+4 positions, which are involved in the formation of an interbase hydrogen bond present in the major groove. (The term structure in this case refers to the hydrogen bonding structure of the base pairs. We recognize that the introduction of conservative functional group deletions or reversals may affect other structural criteria such as hydration.) The deletion of individual functional groups from the Operator Sequence suggests that the carbonyl at dT+4 is critical for formation of the high-affinity Sequence-specific complex. Additionally, the thymine methyl group at dT+4 and the N7 nitrogen of dA+5 appear to be critical contacts necessary for high-affinity binding by the repressor. The thymine carbonyl and the adenine N7 nitrogen are each responsible for approximately -1.5 kcal/mol of apparent free energy of binding. The thymine methyl provides a somewhat smaller contribution of -0.7 kcal/mol. Deletion of either of the adenine amino groups at dA-4 or dA+5 results in a Sequence that binds to the repressor with a higher affinity than observed with the native Sequence; this can be explained in that the functional groups lost are not critical for binding, and the resulting increased flexibility of the Operator, or the creation of a more hydrophobic surface at these sites, enhances van der Waals contacts between the protein and the nucleic acid.
Shi-kuo Chang - One of the best experts on this subject based on the ideXlab platform.
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VISUAL - Spatial/Temporal Query Processing for Information Fusion Applications
Lecture Notes in Computer Science, 2000Co-Authors: Shi-kuo Chang, Gennaro Costagliola, Erland JungertAbstract:To support the retrieval and fusion of multimedia information from multiple sources and databases, a spatial/temporal query language called ?QL was proposed. ?QL is based upon the ?-Operator Sequence and in practice expressible in SQL-like syntax. ?QL allows a user to specify powerful spatial/temporal queries for both multimedia data sources and multimedia databases, eliminating the need to write different queries for each. In this paper, we illustrate this approach by query processing examples for information fusion applications.
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Multimedia Information Analysis and Retrieval - A Spatial Query Language for Multiple Data Sources Based on s-Operator Sequences
Lecture Notes in Computer Science, 1998Co-Authors: Shi-kuo Chang, Erland JungertAbstract:To support the retrieval, fusion and discovery of visual Umultimedia information, a spatial query language for multiple data sources is needed. In this paper we describe a spatial query language which is based upon the σ-Operator Sequence and in practice expressible in an SQL-like syntax. The general 6-Operator and temporal σ-Operator are explained, and applications of the σ-query language to vertical/horizontal reasoning and hypermapped virtual world are explored.
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A SPATIAL/TEMPORAL QUERY LANGUAGE FOR MULTIPLE DATA SOURCES IN A HETEROGENEOUS INFORMATION SYSTEM ENVIRONMENT
International Journal of Cooperative Information Systems, 1998Co-Authors: Shi-kuo Chang, Erland JungertAbstract:To support the retrieval, fusion and discovery of multimedia information, a spatial/temporal query language for multiple data sources is needed. In this paper we describe a spatial/temporal query language, the ∑QL, which is based upon the σ-Operator Sequence and in practice expressible in an SQL-like syntax. The general σ-Operator and temporal σ-Operator are explained, and applications of the σ-query language to vertical/horizontal reasoning and hypermapped virtual world are discussed.
Charles T. Campbell - One of the best experts on this subject based on the ideXlab platform.
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Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy.
Analytical chemistry, 2004Co-Authors: Jennifer S. Shumaker-parry, Ruedi Aebersold, Charles T. CampbellAbstract:Quantitative, real-time measurement of kinetics of Sequence-specific binding of DNA-binding proteins to double-stranded DNA (dsDNA) immobilized in a 10 × 12 array on a planar gold surface is demonstrated using surface plasmon resonance (SPR) microscopy. This binding of the yeast transcription factor Gal4 to a 120-spot dsDNA array made with alternating 200-μm spots of its dsDNA Operator Sequence and an unrelated DNA Sequence proves that this method could be used to simultaneously monitor the kinetics of binding of proteins to 120 different dsDNA Sequences with a sensitivity to ∼0.5 pg (
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parallel quantitative measurement of protein binding to a 120 element double stranded dna array in real time using surface plasmon resonance microscopy
Analytical Chemistry, 2004Co-Authors: Jennifer S Shumakerparry, Ruedi Aebersold, Charles T. CampbellAbstract:Quantitative, real-time measurement of kinetics of Sequence-specific binding of DNA-binding proteins to double-stranded DNA (dsDNA) immobilized in a 10 × 12 array on a planar gold surface is demonstrated using surface plasmon resonance (SPR) microscopy. This binding of the yeast transcription factor Gal4 to a 120-spot dsDNA array made with alternating 200-μm spots of its dsDNA Operator Sequence and an unrelated DNA Sequence proves that this method could be used to simultaneously monitor the kinetics of binding of proteins to 120 different dsDNA Sequences with a sensitivity to ∼0.5 pg (<2 × 107 molecules) of bound protein in each array spot at a time resolution of 1 s. The method is label free and also allows absolute quantitative determination of the binding stoichiometry (i.e., the number of proteins bound per dsDNA) at each time. The dsDNA array was fabricated using a robotic microspotting system to deliver nanoliter droplets of biotinylated dsDNA solutions onto a streptavidin linker layer immobilized w...
Jan Vijg - One of the best experts on this subject based on the ideXlab platform.
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Plasmid rescue from transgenic mouse DNA using LacI repressor protein conjugated to magnetic beads.
BioTechniques, 1993Co-Authors: Jan A. Gossen, W. J. F. De Leeuw, A. C. Molijn, Jan VijgAbstract:A method for the efficient rescue of lac Operator containing plasmids from transgenic mouse genomic DNA is described. The method is based on the high affiny of the LacI repressor protein for the lac Operator Sequence. Using the LacI repressor protein conjugated to magnetic beads, more than 95% of plasmid Sequences could be purified from restriction enzyme digested genomic DNA. After circularization, the plasmids were introduced into Escherichia coli by means of electroporation. Since the plasmid was cloned into a bacteriophage λ vector, the efficiency of plasmid rescue could easily be compared with in vitro packaging
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Plasmid rescue from transgenic mouse DNA using LacI repressor protein conjugated to magnetic beads
BioTechniques, 1993Co-Authors: Jan A. Gossen, W. J. F. De Leeuw, A. C. Molijn, Jan VijgAbstract:A method for the efficient rescue of lac Operator containing plasmids from transgenic mouse genomic DNA is described. The method is based on the high affinity of the LacI repressor protein for the lac Operator Sequence. Using the LacI repressor protein conjugated to magnetic beads, more than 95% of plasmid Sequences could be purified from restriction enzyme digested genomic DNA. After circularization, the plasmids were introduced into Escherichia coli by means of electroporation. Since the plasmid was cloned into a bacteriophage lambda vector, the efficiency of plasmid rescue could easily be compared with in vitro packaging. Our results indicate that plasmid rescue is about 25 times more efficient. Application of this method should be especially useful with transgenic mouse models harboring LacZ plasmid shuttle vectors for studying spontaneous or induced mutations in vivo.