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Results for “Integrative interaction”

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At least 1,063 records · Page 59Linked to original sources

PubMed2002

Interhemispheric stroop-like interference in number comparison: evidence for strong interhemispheric integration of semantic number information.

Three experiments investigated interhemispheric interactions in number comparison using the interhemispheric Stroop-like paradigm (E. Ratinckx, M. Brysbaert, & B. Reynvoet, 2001). In all experiments, a target was presented in I visual field simultaneously with a distractor in the other visual field. In Experiment 1, both target and distractor were of the same modality (Arabic digits), whereas in Experiment 2, target and distractor were of different modalities (Arabic digits and word numerals). In Experiment 3, the interhemispheric Stroop-like task of Experiment 1 was combined with intrahemispheric conditions to evaluate the strength of the interhemispheric interactions. Overall, the results point to strong interhemispheric integration during semantic access and response preparation with very weak lateralization of the semantic number system.

Adolescent↗

PubMed1998

Two distinct types of repression domain in engrailed: one interacts with the groucho corepressor and is preferentially active on integrated target genes.

Active transcriptional repression has been characterized as a function of many regulatory factors. It facilitates combinatorial regulation of gene expression by allowing repressors to be dominant over activators under certain conditions. Here, we show that the Engrailed protein uses two distinct mechanisms to repress transcription. One activity is predominant under normal transient transfection assay conditions in cultured cells. A second activity is predominant in an in vivo active repression assay. The domain mediating the in vivo activity (eh1) is highly conserved throughout several classes of homeoproteins and interacts specifically with the Groucho corepressor. While eh1 shows only weak activity in transient transfections, much stronger activity is seen in culture when an integrated target gene is used. In this assay, the relative activities of different repression domains closely parallel those seen in vivo, with eh1 showing the predominant activity. Reducing the amounts of repressor and target gene in a transient transfection assay also increases the sensitivity of the assay to the Groucho interaction domain, albeit to a lesser extent. This suggests that it utilizes rate-limiting components that are relatively low in abundance. Since Groucho itself is abundant in these cells, the results suggest that a limiting component is recruited effectively by the repressor-corepressor complex only on integrated target genes.

Amino Acid Sequence↗

PubMed2002

Protein kinase signaling in the modulation of microvascular permeability.

The permeability of exchange microvessels is regulated through complex interactions between signaling molecules and structural proteins in the endothelium. Endothelial barrier integrity is maintained by adhesive interactions occurring at the cell-cell and cell-matrix contacts via junctional proteins and focal adhesion complexes that are anchored to the cytoskeleton. Cyclic AMP (cAMP) and cAMP-dependent kinase counteract with the nitric oxide (NO)-cyclic GMP (cGMP) pathway to protect the basal barrier function. Upon stimulation by physical stress, growth factors, or inflammatory agents, endothelial cells undergo a series of intracellular signaling reactions involving activation of protein kinase C (PKC), protein kinase G (PKG), mitogen-activated protein kinases (MAPK), and/or protein tyrosine kinases. The phosphorylation cascades trigger biochemical and conformational changes in the barrier structure and ultimately lead to an opening of the paracellular pathway. In particular, myosin light chain kinase (MLCK) activation and subsequent myosin light chain (MLC) phosphorylation in endothelial cells directly result in cell contraction and shape changes. The phosphorylation of beta-catenin may cause disorganization of adherens junctions or dissociation of vascular endothelial (VE)-cadherin-catenin complex from its cytoskeletal anchor, leading to loose or opened intercellular junctions. Additionally, focal adhesion kinase (FAK) phosphorylation-coupled focal adhesion assembly and redistribution provide an anchorage support for the conformational changes occurring in the cells and at the cell junctions. The Src family tyrosine kinases may serve as common signals that coordinate these molecular events to facilitate the paracellular transport of macromolecules. The critical roles of protein kinases in endothelial hyperpermeability implicate the therapeutic significance of protein kinase inhibitors in the prevention and treatment of diseases and injuries that are associated with microvascular barrier dysfunction.

Adherens Junctions↗

PubMed1997

Observed family interaction during clinical interviews: a comparison of families containing preschool boys with and without disruptive behavior.

The clinical intake interview is an opportunity to observe family interactions and formulate hypotheses about their influence on presenting problems. In this study family interactions were assessed during an unstructured segment of a clinical intake. Families with disruptive preschool boys were compared with those having nonproblem boys. Mother's and fathers' reports of marital satisfaction, parenting involvement, and child behavior problems were examined in relation to observed behavior during intake. Patterns of family interaction emerged which were consistent with previous research and with family systems theory. Clinic boys oriented more toward mothers than fathers and interacted more negatively with their fathers than did comparison boys. Implications for integrating the assessment of family interactions into clinical practice and research with behavior problem children are discussed.

Adult↗

PubMed2006

The role of junctional adhesion molecules in interactions between vascular cells.

Adhesive interactions between cells regulate tissue integrity as well as the process of inflammatory cell recruitment. Such intercellular interactions are regulated by adhesion receptors and can be homotypic, that is, between cells of the same type, for example, between adjacent endothelial cells in the vasculature, as well as heterotypic, that is, between different cells, such as the leukocyte endothelial interactions that take place during leukocyte extravasation. Emerging evidence points to the importance of the family of junctional adhesion molecules (JAMs), which are localized in interendothelial contacts and are implicated in the regulation of leukocyte extravasation. JAMs are members of the immunoglobulin superfamily and can undergo both homophilic and heterophilic interactions. This chapter deals with the role of JAMs in the regulation of adhesive interactions between vascular cells.

Animals↗

PubMed2002

Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair.

Protein-protein interaction plays a critical role in biological processes. The identification of interacting proteins by computational methods can provide new leads in functional studies of uncharacterized proteins without performing extensive experiments. We developed a database for the potentially interacting domain pairs (PID) extracted from a dataset of experimentally identified interacting protein pairs (DIP: database of interacting proteins) with InterPro, an integrated database of protein families, domains and functional sites. In developing protein interaction databases and predictive methods, sensitive statistical scoring systems is critical to provide a reliability index for accurate functional analysis of interaction networks. We present a statistical scoring system, named "PID matrix score" as a measure of the interaction probability (interactability) between domains. This system provided a valuable tool for functional prediction of unknown proteins. For the evaluation of PID matrix, cross validation was performed with subsets of DIP data. The prediction system gives about 50% sensitivity and more than 98% specificity, which implies that the information for interacting proteins pairs could be enriched about 30 fold with the PID matrix. It is demonstrated that mapping of the genome-wide interaction network can be achieved by using the PID matrix.

Algorithms↗

PubMed1993

Relevance of charged groups for the integrity of the S-layer from Bacillus coagulans E38-66 and for molecular interactions.

In this paper, the importance of charged amino and carboxyl groups for the integrity of the cell surface layer (S-layer) lattice from Bacillus coagulans E38-66 and for the self-assembly of the isolated subunits was investigated. Amidination of the free amino groups which preserved their positive net charge had no influence on both. On the other hand, acetylation and succinylation, which converted the amino groups into either neutral or negatively charged groups, and amidation of carboxyl groups were accompanied by the disintegration or at least by the loss of the regular structure of the S-layer lattice. Treatment of S-layer monolayers with the zero-length cross-linker carbodiimide led to the introduction of peptide bonds between activated carboxyl groups and amino groups from adjacent subunits. This clearly indicated that in the native S-layer lattice the charged groups are located closely enough for direct electrostatic interactions. Under disrupting conditions in which the S-layer polypeptide chains were unfolded, 58% of the Asx and Glx residues could be amidated, indicating that they occur in the free carboxylic acid form. As derived from chemical modification of monolayer self-assembly products, about 90% of the lysine and 70% of the aspartic and glutamic acid residues are aligned on the surface of the S-layer protein domains. This corresponded to 45 amino groups and to 63 carboxyl groups per S-layer subunit. Labelling experiments with macromolecules with different sizes and charges and adsorption studies with ion-exchange particles revealed a surplus of free carboxyl groups on the inner and on the outer faces of the S-layer lattice. Since the carboxyl groups on the outer S-layer face were accessible only for protein molecules significantly smaller then the S-layer protomers or for positively charged, thin polymer chains extending from the surface of ion-exchange beads, the negatively charged sites must be located within indentations of the corrugated S-layer protein network. This was in contrast to the carboxyl groups on the inner S-layer face, which were found to be exposed on elevations of the S-layer protein domains (D. Pum, M. Sára, and U.B. Sleytr, J. Bacteriol. 171:5296-5303, 1989).

Amino Acids↗

PubMed1987

Donnan membrane equilibrium, sedimentation equilibrium, and coil expansion of DNA in salt solutions.

This is a review of applications of the McMillan-Mayer-Hill virial theory and the ionic double-layer theory to dilute colloidal solutions, in particular, solutions of DNA. Interactions of highly charged colloidal rods are developed in terms of the second virial coefficients between two rods, and between one rod and one small co-ion. The relevant cluster integrals are evaluated with interaction potentials based on the Poisson-Boltzmann equation. The treatment is extended to the intrachain repulsion responsible for the statistical swelling of coiled DNA (excluded volume effect). The theory is compared with three sets of experimental data: The salt distribution in Donnan membrane equilibria of DNA-salt solutions, sedimentation equilibria of short DNA fragments at different ionic strengths, and the intrinsic viscosity of T7 DNA in NaCl solutions. In all cases the theory agrees well with the experiments. The agreement is not convincing for the sedimentation equilibrium at low ionic strength, because here the experimental DNA concentration is too high for the truncated dilute solution expansion of the DNA-salt repulsion.

Biophysical Phenomena↗

PubMed2004

Visualizations for taxonomic and phylogenetic trees.

MOTIVATION: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain. RESULTS: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces.

Algorithms↗

PubMed2005

Detecting silent pauses in speech: a new tool for measuring on-line lexical and semantic processing.

In this study, we introduce pause detection (PD) as a new tool for studying the on-line integration of lexical and semantic information during speech comprehension. When listeners were asked to detect 200-ms pauses inserted into the last words of spoken sentences, their detection latencies were influenced by the lexical-semantic information provided by the sentences. Listeners took longer to detect a pause when it was inserted within a word that had multiple potential endings, rather than a unique ending, in the context of the sentence. An event-related potential (ERP) variant of the PD procedure revealed brain correlates of pauses as early as 101 to 125 ms following pause onset and patterns of lexical-semantic integration that mirrored those obtained with PD within 160 ms of pause onset. Thus, both the behavioral and the electrophysiological responses to pauses suggest that lexical and semantic processes are highly interactive and that their integration occurs rapidly during speech comprehension.

Humans↗

PubMed2003

Identification and characterization of an adeno-associated virus integration site in CV-1 cells from the African green monkey.

Adeno-associated virus (AAV) is a classification given to a group of nonpathogenic, single-stranded DNA viruses known to reside latently in primates. During latency in humans, AAV type 2 (AAV2) preferentially integrates at a site on chromosome 19q13.3ter by targeting a sequence composed of an AAV Rep binding element (RBE), a spacer, and a nicking site. Here, we report the DNA sequence of an African green monkey AAV integration site isolated from CV-1 cells. Overall, it has 98% homology to the analogous human site, including identical spacer and nicking sequences. However, the simian RBE is expanded, having five perfect directly repeated GAGC tetramers. We carried out a number of in vitro and in vivo assays to determine the effect of this expanded RBE sequence on the Rep-RBE interaction and AAV targeted integration. Using electromobility shift assays it was demonstrated that AAV4 Rep68 bound the expanded RBE with a sixfold-greater affinity than the human RBE. To determine the basis for the affinity increase, DNase I protection and methylation interference (MI) assays were performed. Comparison of footprints on both the human and simian RBEs revealed nearly identical protection; however, MI analysis suggested greater interaction with the guanine nucleotides of the expanded RBE, thus providing a biochemical basis for the increased binding activity. In vivo, integration targeted to the simian RBE was demonstrated by PCR analysis of latently infected Cos-7 cells. Interestingly, the frequency of site-specific integration was twofold greater in Cos-7 cells than in HeLa cells. Overall, these experiments establish that the simian RBE, identified in CV-1 cells, functions analogously to the human RBE and provide further evidence for a developing model that proposes individual roles for the RBE and the spacer and nicking site elements.

Animals↗

PubMed2004

Computational method for multidimensional quantal dynamics of polynomially interacting oscillator systems.

We propose a numerical algorithm for computing quantal dynamics, which is tailored for a generic multidimensional model of low-energy dynamics, i.e., polynomially interacting oscillator system. This algorithm evaluates symplectic integrators effectively, by using block tridiagonality of the interaction operator, and thus accurately preserves unitarity with time. A practical advantage of this method is that high-order integrators are easily implemented even for time-dependent parameter systems. We demonstrate the accuracy and usefulness by applying it to a phi(4) model.

Journal Article↗

PubMed1997

[15O]-water PET and intraoperative brain mapping: a comparison in the localization of eloquent cortex.

[15O]-water PET was performed on 12 patients with structural lesions for localization of the motor (n = 5), language (receptive and expressive; n = 6), and visual cortex (n = 1). All these patients underwent interactive image-guided surgery using an infrared digitizer and intraoperative electrical stimulation mapping for motor, sensory, language, and visual cortex location. MRI-PET coregistration was performed using a surface matching approach that integrated functional information with interactive image guidance during the surgical procedure. An awake craniotomy with motor and sensory intraoperative stimulation was performed using a registered bipolar electrode that was tracked on real-time during the surgical procedure. Intraoperative functional findings were displayed and saved on the registered MRI images. The sites of functional PET activation during the performance of motor, visual and language tasks were then compared to the results of intraoperative cortical stimulation in 11 patients and visual evoked potentials in one. The results of the PET activation studies were concordant with the findings of intraoperative stimulation in all cases. During resection of the structural lesions, intraoperative stimulation was continued in the subcortical pathways, and five patients had positive responses on areas not identified by the functional PET. Furthermore, 3 patients showed transitory changes in function (speech arrest 1, naming difficulty 1, and motor weakness 1) that were reversible after changing the dissection technique or a brain retractor. [15O]-water PET was reliable in identifying the motor, visual, and language cortex. Language-related rCBF increases were highly distributive, although only part of these activations were subjected to intraoperative stimulation. We conclude that [15O]-water PET can be used for preoperative noninvasive identification of functional cortex and may be useful in neurosurgical preplanning. Intraoperative mapping still remains the main means to avoid neurological damage as it can be performed during the entire surgical procedure to avoid damage to cortex, pathways, and damage secondary to ischemia or edema (brain retraction).

Adolescent↗

PubMed2006

Integrating two-dimensional paths: do desert ants process distance information in the absence of celestial compass cues?

When performing foraging trips desert ants of the genus Cataglyphis continuously process and update a ;home vector' that enables them to return to their nest on the shortest route. This capacity of path integration requires two types of information: (i) information about the travelling directions, and (ii) odometric information about the distances travelled in a particular direction. We have investigated how these two necessary pieces of information interact within the path integration processor. The specific question is: how do the ants process distance information if there is no simultaneous input from the sky compass available. Ants were trained to forage in a ;Z'-shaped channel system, the three segments of which joined at right angles. Individual animals were transferred from the feeder to a test field where their homing paths could be observed. In the crucial tests the middle segment of the maze was covered by orange Perspex that did not transmit the UV part of the spectrum, and thus precluded the perception of polarization patterns. Changes of the ant's processing of odometric information within this channel segment directly translate into a change in homing direction on the test field. The results indicate that the odometric information about travelling distance is largely ignored for path integration if there is no simultaneous input from the sky-view-based compass. They further show that idiothetic information cannot adequately substitute for the polarization compass to infer travelling directions.

Animals↗

PubMed1998

Src can regulate carboxy terminal interactions with AFAP-110, which influence self-association, cell localization and actin filament integrity.

The SH2 and SH3 binding partner AFAP-110 is a tyrosine phosphorylated substrate of Src. AFAP-110 has been hypothesized to link Src to actin filaments, which may contribute to the effects of Src upon actin filament integrity. However, it has been unclear what effect activated Src (Src527F) has upon AFAP-110 structure or function and whether AFAP-110 plays a role in actin filament integrity. We report here that the carboxy terminal 127 amino acids of AFAP-110 are comprised of an alpha-helical region that contains a leucine zipper motif. This indicated the potential of AFAP-110 to self-associate. Expression of the carboxy terminus as a fusion protein (GST-cterm) will permit affinity absorption of cellular AFAP-110. The integrity of the alpha-helical leucine zipper motif in GST-cterm is required for affinity absorption, but binding is not due to a classical leucine zipper interaction. Co-expression of Src527F, unlike cSrc, will abrogate affinity absorption of AFAP-110 with GST-cterm. These data indicate that Src527F has affected a change in the carboxy terminal structure that renders AFAP-110 unavailable for affinity absorption. Superose chromatography demonstrate that AFAP-110 will fractionate as a monomer or multimer, indicating AFAP-110 can be detected in a self-associated form in cell lysates. Co-expression of Src527F resulted in AFAP-110 fractionating with a molecular weight that predicts only a multimeric population. Deletional mutagenesis also indicate a biological role for the carboxy terminus in cellular localization and actin filament integrity. Deletion of the entire carboxy terminal alpha-helix (84 amino acids) will not permit AFAP-110 to efficiently colocalize with actin filaments or the cell membrane. Deletion of only the leucine zipper region of the carboxy terminal alpha-helix (44 amino acids) from AFAP-110 (AFAPAdeltazip) demonstrate that both AFAPdeltalzip and actin filaments are repositioned into rosette-like structures, similar to the effects of Src527F, while co-expression of AFAP-110 with cSrc will not affect actin filaments. These data indicate that AFAP-110 can play an important role in modulating actin filament integrity through carboxy terminal interactions that can be affected by Src527F.

Actin Cytoskeleton↗

PubMed2003

Global snapshot of a protein interaction network-a percolation based approach.

MOTIVATION: Biologically significant information can be revealed by modeling large-scale protein interaction data using graph theory based network analysis techniques. However, the methods that are currently being used draw conclusions about the global features of the network from local connectivity data. A more systematic approach would be to define global quantities that measure (1) how strongly a protein ties with the other parts of the network and (2) how significantly an interaction contributes to the integrity of the network, and connect them with phenotype data from other sources. In this paper, we introduce such global connectivity measures and develop a stochastic algorithm based upon percolation in random graphs to compute them. RESULTS: We show that, in terms of global connectivities, the distribution of essential proteins is distinct from the background. This observation highlights a fundamental difference between the essential and the non-essential proteins in the network. We also find that the interaction data obtained from different experimental methods such as immunoprecipitation and two-hybrid techniques contribute differently to network integrities. Such difference between different experimental methods can provide insight into the systematic bias present among these techniques. SUPPLEMENTARY INFORMATION: The full list of our results can be found in the supplemental web site http://www.nas.nasa.gov/Groups/SciTech/nano/msamanta/projects/percolation/index.php

Algorithms↗

PubMed2006

Hypothesis: Huntingtin may function in membrane association and vesicular trafficking.

Huntington's disease is a progressive neurodegenerative genetic disorder that is caused by a CAG triplet-repeat expansion in the first exon of the IT15 gene. This CAG expansion results in polyglutamine expansion in the 350 kDa huntingtin protein. The exact function of huntingtin is unknown. Understanding the pathological triggers of mutant huntingtin, and distinguishing the cause of disease from downstream effects, is critical to designing therapeutic strategies and defining long- and short-term goals of therapy. Many studies that have sought to determine the functions of huntingtin by determining huntingtin's protein-protein interactions have been published. Through these studies, huntingtin has been seen to interact with a large number of proteins, and is likely a scaffolding protein for protein-protein interactions. Recently, using imaging, integrative proteomics, and cell biology, huntingtin has been defined as a membrane-associated protein, with activities related to axonal trafficking of vesicles and mitochondria. These functions have also been attributed to some huntingtin-interacting proteins. Additionally, discoveries of a membrane association domain and a palmitoylation site in huntingtin reinforce the fact that huntingtin is membrane associated. In Huntington's disease mouse and fly models, axonal vesicle trafficking is inhibited, and lack of proper uptake of neurotrophic factors may be an important pathological trigger leading to striatal cell death in Huntington's disease. Here we discuss recent advances from many independent groups and methodologies that are starting to resolve the elusive function of huntingtin in vesicle transport, and evidence that suggests that huntingtin may be directly involved in membrane interactions.

Cell Membrane↗

PubMed2003

Correlated discharge among cell pairs within the oculomotor horizontal velocity-to-position integrator.

In the oculomotor system, temporal integration of velocity commands into position signals may depend on synaptic feedback among neurons of a bilateral brainstem cell assembly known as the "neural integrator." Both ipsilateral excitatory and contralateral inhibitory projections between eye position-related integrator cells are hypothesized as a substrate for positive feedback supporting integration. Presence of feedback interactions should be evident in cross-correlation functions of neuron pairs. Here, unilateral and bilateral paired recordings were obtained during fixation behavior from neurons in goldfish brainstem area I, a key element of the integrator. During fixations, discharge of most unilateral pairs, composed of cells with eye position sensitivities of the same sign, was positively correlated with lag of 0-10 msec (n = 11 of 14 significant). Typically, a very narrow peak (mean half-width <4 msec) near zero lag was observed. Discharge of bilateral pairs, composed of cells with position sensitivities of the opposite sign, was either negatively correlated with lag of 0-10 msec (n = 5 of 13 significant) or not correlated. Troughs in negative correlations always had minima between 3 and 5 msec lag. These results are consistent with the feedback hypothesis of temporal integration, highlighting excitation unilaterally and inhibition bilaterally. Absence of visual input did not weaken correlations, but other sources of correlated input extrinsic to area I were not ruled out. Triplet recordings revealed that unilateral pairwise correlations were primarily independent. Correlation between unilateral pairs systematically decreased with increasing eye position, demonstrating that synchrony is not necessary for persistent activity at high firing rates.

Action Potentials↗