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PubMed1988

The interaction of Escherichia coli integration host factor with the cohesive end sites of phages lambda and 21.

The interaction of E. coli integration host factor (IHF) with the cohesive end sites (cos's) of phages lambda and 21 has been studied by the DNAase I footprinting technique. Six potential sites in cos lambda differ from the consensus IHF binding sequence by 1 to 3 base pairs. Of the six, one site, I1, binds IHF strongly. The I1 segment protected by IHF contains two sequences that closely match the IHF consensus binding sequence. Another site, I2, binds IHF moderately well, and three sites: 10', 13 and 14 bind IHF very weakly. The 10 site does not bind IHF under the conditions used here. In phage 21 the DNA segment extending to the right from the cohesive ends, which contains three potential IHF binding sites, was examined. Two sites bind IHF well; I1, the 21 analogue of one of the lambda I1 sites, and I0, a site not analogous to a lambda site. The third 21 site, I2, binds IHF moderately well, as does the analogous I2 site in lambda. The significance of the results for lambda DNA packaging is discussed.

Bacterial Proteins↗
PubMed1998

Cellular and molecular partners involved in gut morphogenesis and differentiation.

The intestinal mucosa represents an interesting model to study the cellular and molecular basis of epithelial-mesenchymal cross-talk participating in the development and maintenance of the digestive function. This cross-talk involves extracellular matrix molecules, cell-cell and cell-matrix adhesion molecules as well as paracrine factors and their receptors. The cellular and molecular unit is additionally regulated by hormonal, immune and neural inputs. Such integrated cell interactions are involved in pattern formation, in proximodistal regionalization, in maintenance of a gradient of epithelial proliferation and differentiation, and in epithelial cell migration. We focus predominantly on two aspects of these integrated interactions in this paper: (i) the role of basement membrane molecules, namely laminins, in the developmental and spatial epithelial behaviour; and (ii) the importance of the mesenchymal cell compartment in these processes.

Animals↗
PubMed2004

Omic space: coordinate-based integration and analysis of genomic phenomic interactions.

MOTIVATION: With the recent progress in genomics, various data sets of omic interactions describing networks of omic elements have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of data sets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic, metabolomic, phenomic and other omic planes are defined by two orthogonal genomic-coordinate axes. RESULTS: We show that the omic space concept helps us to assimilate biological findings comprehensively into hypotheses or models combining higher-order phenomena and lower-order mechanisms by demonstrating that a comprehensive ranking of correspondences among interactions in the space can be used effectively for estimating candidates of responsible gene pairs for epistatic interacting loci of tumors in mice. We also show that the omic space offers a convenient framework for database integration, by presenting a system named the 'Genome <==> Phenome Superhighway' (GPS) that serves as a framework for integration and visualization of omic interactions based on omic spaces of some model species including Homo sapiens, Mus musculus, Caenorhabditis elegans and Arabidopsis thaliana. AVAILABILITY: For the GPS web site, see http://omicspace.riken.jp/gps/.

Algorithms↗
PubMed1989

The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending.

The interaction of E. coli's integration Host Factor (IHF) with fragments of lambda DNA containing the cos site has been studied by gel-mobility retardation and electron microscopy. The cos fragment used in the mobility assays is 398 bp and spans a region from 48,298 to 194 on the lambda chromosome. Several different complexes of IHF with this fragment can be distinguished by their differential mobility on polyacrylamide gels. Relative band intensities indicate that the formation of a complex between IHF and this DNA fragment has an equilibrium binding constant of the same magnitude as DNA fragments containing lambda's attP site. Gel-mobility retardation and electron microscopy have been employed to show that IHF sharply bends DNA near cos and to map the bending site. The protein-induced bend is near an intrinsic bend due to DNA sequence. The position of the bend suggests that IHF's role in lambda DNA packaging may be the enhancement of terminase binding/cos cutting by manipulating DNA structure.

Bacterial Proteins↗
PubMed2006

Struct2net: integrating structure into protein-protein interaction prediction.

UNLABELLED: This paper presents a framework for predicting protein-protein interactions (PPI) that integrates structure-based information with other functional annotations, e.g. GO, co-expression and co-localization, etc., Given two protein sequences, the structure-based interaction prediction technique threads these two sequences to all the protein complexes in the PDB and then chooses the best potential match. Based on this match, structural information is incorporated into logistic regression to evaluate the probability of these two proteins interacting. This paper also describes a random forest classifier which can effectively combine the structure-based prediction results and other functional annotations together to predict protein interactions. Experimental results indicate that the predictive power of the structure-based method is better than many other information sources. Also, combining the structure-based method with other information sources allows us to achieve a better performance than when structure information is not used. We also tested our method on a set of approximately 1000 yeast genes and, interestingly, the predicted interaction network is a scale-free network. Our method predicted some potential interactions involving yeast homologs of human disease-related proteins. SUPPLEMENTARY INFORMATION: http://theory.csail.mit.edu/struct2net

Algorithms↗
PubMedDate not supplied

A real-time, interactive steering environment for integrated ground water modeling.

We present in this note an innovative software environment, called Interactive Ground Water (IGW), for unified deterministic and stochastic ground water modeling. Based on efficient computational algorithms, IGW allows simulating three-dimensional (3D) unsteady flow and transport in saturated media subject to systematic and "random" stresses and geological and chemical heterogeneity. Adopting a new computing paradigm, IGW eliminates the fragmentation in the traditional modeling schemes and allows fully utilizing today's dramatically increased computing power. For many problems, IGW enables real-time modeling, visualization, mapping, and analysis. The software environment functions as a "numerical laboratory" in which an investigator may freely explore the following: creating visually an aquifer system of desired configurations, interactively applying stresses and boundary conditions, and then investigating and visualizing on the fly the geology and flow and transport dynamics. At any time, a researcher can pause to interact dynamically with virtually any aspects of the modeling process and then resume the integrated visual exploration; he or she can initiate, pause, or resume particle tracking, plume modeling, subscale modeling, stochastic modeling, monitoring, and budget analyses. IGW continually provides results that are dynamically processed, overlaid, and displayed. It dynamically merges modeling inputs and outputs into composite two-dimensional/3D images-integrating related data to provide a more complete view of the complex interplay among the geology, hydrology, flow system, and transport. These unique capabilities of real-time modeling, steering, analysis, and mapping expand the utility of models as tools for research, education, and professional investigations.

Computer Simulation↗
PubMed1986

Interactive multi-window integration of two-parameter flow cytometric data fields.

Integration is necessary to determine the particle content of regions of interest of flow cytometric two-parameter fields. The improved program of the Cytomic 12 analyzer (1) offers: window trace integration for relatively simple window structures. The field of interest is surrounded by an integration trace (window). Eight independent windows can be stored and successively evaluated. It also offers painted field integration for complicated window structures. The pointer or a small window is interactively moved over the structures to be integrated like the brush of a painter. The "painted field" defines the window to be integrated. Window sets and painted fields can be stored on a floppy disk. Painted fields can be added and may also serve as look up tables for sorting.

Cell Count↗
PubMed2006

Towards an integrated protein-protein interaction network: a relational Markov network approach.

Protein-protein interactions play a major role in most cellular processes. Thus, the challenge of identifying the full repertoire of interacting proteins in the cell is of great importance and has been addressed both experimentally and computationally. Today, large scale experimental studies of protein interactions, while partial and noisy, allow us to characterize properties of interacting proteins and develop predictive algorithms. Most existing algorithms, however, ignore possible dependencies between interacting pairs and predict them independently of one another. In this study, we present a computational approach that overcomes this drawback by predicting protein-protein interactions simultaneously. In addition, our approach allows us to integrate various protein attributes and explicitly account for uncertainty of assay measurements. Using the language of relational Markov networks, we build a unified probabilistic model that includes all of these elements. We show how we can learn our model properties and then use it to predict all unobserved interactions simultaneously. Our results show that by modeling dependencies between interactions, as well as by taking into account protein attributes and measurement noise, we achieve a more accurate description of the protein interaction network. Furthermore, our approach allows us to gain new insights into the properties of interacting proteins.

Algorithms↗
PubMed1995

Mechanochemistry of protein 4.1's spectrin-actin-binding domain: ternary complex interactions, membrane binding, network integration, structural strengthening.

Mechanical strength of the red cell membrane is dependent on ternary interactions among the skeletal proteins, spectrin, actin, and protein 4.1. Protein 4.1's spectrin-actin-binding (SAB) domain is specified by an alternatively spliced exon encoding 21 amino acid (aa) and a constitutive exon encoding 59 aa. A series of truncated SAB peptides were engineered to define the sequences involved in spectrin-actin interactions, and also membrane strength. Analysis of in vitro supramolecular assemblies showed that gelation activity of SAB peptides correlates with their ability to recruit a critical amount of spectrin into the complex to cross-link actin filaments. Also, several SAB peptides appeared to exhibit a weak, cooperative actin-binding activity which mapped to the first 26 residues of the constitutive 59 aa. Fluorescence-imaged microdeformation was used to show SAB peptide integration into the elastic skeletal network of spectrin, actin, and protein 4.1. In situ membrane-binding and membrane-strengthening abilities of the SAB peptides correlated with their in vitro gelation activity. The findings imply that sites for strong spectrin binding include both the alternative 21-aa cassette and a conserved region near the middle of the 59 aa. However, it is shown that only weak SAB affinity is necessary for physiologically relevant action. Alternatively spliced exons can thus translate into strong modulation of specific protein interactions, economizing protein function in the cell without, in and of themselves, imparting unique function.

Actins↗
PubMed2006

An integrated approach to the prediction of domain-domain interactions.

BACKGROUND: The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain interactions, it is crucial to understand protein interactions at the level of the domains. The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets. RESULTS: We combine protein interaction data sets from multiple species, molecular sequences, and gene ontology to construct a set of high-confidence domain-domain interactions. First, we propose a new measure, the expected number of interactions for each pair of domains, to score domain interactions based on protein interaction data in one species and show that it has similar performance as the E-value defined by Riley et al. Our new measure is applied to the protein interaction data sets from yeast, worm, fruitfly and humans. Second, information on pairs of domains that coexist in known proteins and on pairs of domains with the same gene ontology function annotations are incorporated to construct a high-confidence set of domain-domain interactions using a Bayesian approach. Finally, we evaluate the set of domain-domain interactions by comparing predicted domain interactions with those defined in iPfam database that were derived based on protein structures. The accuracy of predicted domain interactions are also confirmed by comparing with experimentally obtained domain interactions from H. pylori. As a result, a total of 2,391 high-confidence domain interactions are obtained and these domain interactions are used to unravel detailed protein and domain interactions in several protein complexes. CONCLUSION: Our study shows that integration of multiple biological data sets based on the Bayesian approach provides a reliable framework to predict domain interactions. By integrating multiple data sources, the coverage and accuracy of predicted domain interactions can be significantly increased.

Algorithms↗
PubMed2006

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model.

BACKGROUND: Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. RESULTS: By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. CONCLUSION: IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at http://hanlab.genetics.ac.cn/IntNetDB.htm. Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer.

Algorithms↗
PubMed1986

Mutational analysis of integrase arm-type binding sites of bacteriophage lambda. Integration and excision involve distinct interactions of integrase with arm-type sites.

Integrative recombination between specific attachment (att) regions of the bacteriophage lambda genome (attP) and the Escherichia coli genome (attB) results in a prophage flanked by the hybrid recombinant sites attL and attR. Each att site contains sequences to which proteins involved in recombination bind. Using site-directed mutagenesis, we have constructed a related set of point mutations within each of the five Int "arm-type" binding sites located within attP, attL and attR. Footprint analyses of binding demonstrate that mutating the arm-type sites significantly disrupts the binding of Int. Recombination analyses of mutant att sites in vivo and in vitro demonstrate that only three wild-type arm-type sites within attP are required for efficient integrative recombination. Similar analyses demonstrate that efficient excision can occur with two other different sets of wild-type arm-type sites in attL and attR. These results demonstrate that integrative and excisive recombination may involve interactions of Int with distinct and different subsets of arm-type sites.

Attachment Sites, Microbiological↗
PubMed1993

Biologic and immunologic approaches to comprehensive therapy for pediatric malignant conditions. Laboratory-clinical interaction.

Cooperative integration of laboratory and clinical trial data has provided striking improvement in the treatment of pediatric malignant conditions over the last 2 decades. If attempts are made to individualize therapy to the specific disease and prognostic treatment subgroups for each pediatric malignant condition, the combination of surgery, radiation therapy, and chemotherapy can put the vast majority of patients into a complete clinical remission, with apparent cure for more than half of these patient. Depending on the disease type, treatment failure, when it occurs, is usually the result of recurrent, distant, metastatic disease that is refractory to prior treatment and simultaneously refractory to treatment approaches not yet used for the patient who has had a relapse. The clinical research challenge with these pediatric malignant neoplasms is to identify those children who are harboring microscopic amounts of residual tumor before their relapse and develop effective combined well-tolerated treatment approaches that can be initiated in those patients. These additional treatment approaches should complement rather than duplicate the biologic mechanisms that had been used to initiate remission to eradicate residual tumor without cross resistance. Ongoing laboratory and clinical research approaches are developing and testing the potential of biologic/immunologic therapeutics. The broad application of these principles to clinical oncology will be facilitated by the integrated laboratory-clinical testing that is being accomplished through cooperative pediatric clinical research trials.

Antibodies, Monoclonal↗
PubMed2006

Early experience determines how the senses will interact.

Multisensory integration refers to the process by which the brain synthesizes information from different senses to enhance sensitivity to external events. In the present experiments, animals were reared in an altered sensory environment in which visual and auditory stimuli were temporally coupled but originated from different locations. Neurons in the superior colliculus developed a seemingly anomalous form of multisensory integration in which spatially disparate visual-auditory stimuli were integrated in the same way that neurons in normally reared animals integrated visual-auditory stimuli from the same location. The data suggest that the principles governing multisensory integration are highly plastic and that there is no a priori spatial relationship between stimuli from different senses that is required for their integration. Rather, these principles appear to be established early in life based on the specific features of an animal's environment to best adapt it to deal with that environment later in life.

Adaptation, Physiological↗
PubMed2000

Use of G-protein fusions to monitor integral membrane protein-protein interactions in yeast.

The control of protein-protein interactions is a fundamental aspect of cell regulation. Here we describe a new approach to detect the interaction of two proteins in vivo. By this method, one binding partner is an integral membrane protein whereas the other is soluble but fused to a G-protein gamma-subunit. If the binding partners interact, G-protein signaling is disrupted. We demonstrate interaction between known binding partners, syntaxin 1a with neuronal Sec1 (nSec1), and the fibroblast-derived growth factor receptor 3 (FGFR3) with SNT-1. In addition, we describe a genetic screen to identify nSec1 mutants that are expressed normally, but are no longer able to bind to syntaxin 1a. This provides a convenient method to study interactions of integral membrane proteins, a class of molecules that has been difficult to study by existing biochemical or genetic methods.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Structure and effective interactions in polymer nanocomposite melts: an integral equation theory study.

The polymer reference interaction site model from integral equation theory is used to investigate the structure and effective interactions in polymer nanocomposite melts where strong nanoparticle-monomer interactions are principally considered in this work. For finite particle volume fraction, the compromise for the interference between polymers and nanoparticles results in an optimum particle volume fraction for nanoparticle dispersion in polymer melts. At constant particle volume fraction, the effects of degree of polymerization become insignificant when it reaches a threshold value, below which quantitative effects on the organization states of polymer nanocomposite melts are found and help nanoparticles to well disperse in polymer. The aggregation of large nanoparticles decreases with the increase of the nanoparticle-monomer attraction strength. These observations may provide useful information for the development of new polymer materials.

Journal Article↗
PubMed2005

Integration requires a specific interaction of the donor DNA terminal 5'-cytosine with glutamine 148 of the HIV-1 integrase flexible loop.

Integration is essential for retroviral replication and gene therapy using retroviral vectors. Human immunodeficiency virus, type 1 (HIV-1), integrase specifically recognizes the terminal sequences of each long terminal repeat (LTR) and cleaves the 3'-end terminal dinucleotide 5'-GT. The exposed 3'-hydroxyl is then positioned for nucleophilic attack and subsequent strand transfer into another DNA duplex (target or chromosomal DNA). We report that both the terminal cytosine at the protruding 5'-end of the long terminal repeats (5'-C) and the integrase residue Gln-148 are critical for strand transfer. Proximity of the 5'-C and Gln-148 was demonstrated by disulfide cross-linking. Cross-linking is inhibited by the inhibitor 5CITEP 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone. We propose that strand transfer requires a conformational change of the integrase-viral (donor) DNA complex with formation of an H-bond between the N-3 of the 5'-C and the amine group of Gln-148. These findings have implications for the molecular mechanisms coupling 3'-processing and strand transfer as well as for the molecular pharmacology of integrase inhibitors.

Conserved Sequence↗