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At least 127 records · Page 7Linked to original sources
PubMed2004

Functional topology in a network of protein interactions.

MOTIVATION: The building blocks of biological networks are individual protein-protein interactions (PPIs). The cumulative PPI data set in Saccharomyces cerevisiae now exceeds 78 000. Studying the network of these interactions will provide valuable insight into the inner workings of cells. RESULTS: We performed a systematic graph theory-based analysis of this PPI network to construct computational models for describing and predicting the properties of lethal mutations and proteins participating in genetic interactions, functional groups, protein complexes and signaling pathways. Our analysis suggests that lethal mutations are not only highly connected within the network, but they also satisfy an additional property: their removal causes a disruption in network structure. We also provide evidence for the existence of alternate paths that bypass viable proteins in PPI networks, while such paths do not exist for lethal mutations. In addition, we show that distinct functional classes of proteins have differing network properties. We also demonstrate a way to extract and iteratively predict protein complexes and signaling pathways. We evaluate the power of predictions by comparing them with a random model, and assess accuracy of predictions by analyzing their overlap with MIPS database. CONCLUSIONS: Our models provide a means for understanding the complex wiring underlying cellular function, and enable us to predict essentiality, genetic interaction, function, protein complexes and cellular pathways. This analysis uncovers structure-function relationships observable in a large PPI network.

Algorithms↗
PubMed2026

Neurodevelopmental toxicity of 2-(Methylthio)benzothiazole (MTBT) in zebrafish: Insights into PTGS2- associated dysregulation of the neuroactive ligand-receptor interaction pathway.

2-(Methylthio)benzothiazole (MTBT), an important derivative of benzothiazoles, has extensive applications in industrial processes, pharmaceuticals, and environmental monitoring. It can enter aquatic environments through surface runoff and has been detected at relatively high concentrations in various environmental systems. However, studies investigating the aquatic toxicity of MTBT remain limited. In this study, zebrafish embryos were exposed to MTBT at concentrations of 0, 10, 100, and 1000 μg/L for 144 h to evaluate its developmental and neurotoxic effects. MTBT exposure significantly reduced the survival rate, hatching rate, spontaneous movement, and body length of zebrafish larvae. MTBT also impaired locomotor behavior, reduced fluorescence of Tg(huc:eGFP) larvae in the central nervous system and inhibited motor neuron axonal development. Protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated that MTBT-induced neurotoxicity may be associated with disruption of the neuroactive ligand-receptor interaction pathway. Further validation experiments revealed that MTBT induced oxidative stress, inflammation, and apoptosis, suggesting that these adverse effects may underlie its neurodevelopmental toxicity. Collectively, these findings provide biological evidence that MTBT induces neurodevelopmental toxicity in zebrafish larvae and suggest that dysregulation of the PTGS2-related neuroactive ligand-receptor interaction pathway may be involved in this process.

2-(Methylthio)benzothiazole (MTBT)↗
PubMed2025

Identification of key genes related to bone metastasis of breast cancer using bioinformatics methods and construction of a prognostic model.

Breast cancer (BC) ranks among the most prevalent cancers in females, with bone metastasis significantly compromising patients' quality of life and survival rates. Enhancing our comprehension of BC bone metastasis mechanisms at the molecular level holds promise for improving BC treatment and prognosis. Leveraging bioinformatics tools, we integrated multiple datasets, conducted comprehensive analyses across various databases, identified biomarkers associated with BC bone metastasis, and constructed a prognostic model. Firstly, 3 BC bone metastasis-related datasets were downloaded from gene expression omnibus, the data were merged, and batch effects were removed, followed by identification of differentially expressed genes (DEGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. A protein-protein interaction network was constructed using the STRING database to screen hub genes. Then, survival analysis of hub genes was performed using the Cancer Genome Atlas (TCGA) database. A prognostic model was constructed using key genes with survival differences, and the model was evaluated. Two hundred ninety-two DEGs were identified. Gene ontology and KEGG pathway enrichment analysis yielded 769 biological processes (BPs), 78 cellular components, 43 molecular functions, and 50 KEGG pathways. Fifteen hub genes were selected from the protein-protein interaction network. Survival analysis revealed 6 genes related to BC survival. The prognostic model identified 4 genes with important predictive value for BC prognosis. Our study utilized bioinformatics analysis to identify a series of DEGs related to BC bone metastasis. Based on further selection of hub genes, we constructed a relatively ideal prognostic model for BC, and identified 4 genes (DLGAP5, TPX2, PLK1, and CENPN) with valuable predictive value for BC prognosis.

Humans↗
PubMed2002

Effects of ketamine and apomorphine on inferior colliculus and caudal pontine reticular nucleus evoked potentials during prepulse inhibition of the startle reflex in rats.

Prepulse inhibition (PPI) of the startle reaction to a strong sound is the reduction of this reaction elicited by a weak stimulus, a tone for example, when it precedes the startling sound. Its pharmacological sensitivity has been used to characterize antipsychotic drugs. Not much is known about the level of action of such drugs in the neuronal network involved in PPI. In the present study, evoked potentials from two key structures, the inferior colliculus (IC) and the caudal pontine reticular nucleus (PnC), were obtained in freely moving rats during standard startle and PPI tests, under ketamine (5 mg/kg) or apomorphine (0.5 mg/kg). In the IC, the potential evoked by the noise did not vary whether tested in basic or PPI conditions. Only minor changes were elicited by the drugs. In the PnC, the noise elicited an evoked potential that was reduced under PPI conditions. This alteration of the evoked potential was reversed by ketamine. The results obtained with apomorphine were not homogeneous either when considering the behavioral or the electrophysiological results.

Acoustic Stimulation↗
PubMed1999

Association of Nafion with Polypyrrole Nanoparticles in a Hydrophilic Polymer Network: Effects on Proton Transport.

Proton-conducting polymer composites containing perfluorosulfonic polymer (Nafion) and polypyrrole (PPy) nanoparticles in a polyacrylamide network, P(AAM-MBAM), were synthesized as proton-conducting electrolytes. An investigation into the assembling of Nafion polymer molecules as well as the colloidal PPy-Nafion complexes in the P(AAM-MBAM) network was carried out on the basis of DSC and XRD analysis. It was found that the proton conductivity of the composites was largely affected by the occurrence of the free volume between the P(AAM-MBAM) network and Nafion polymer as well as the concentration of the PPy-Nafion complexes in the composites according to the measurements of the electrical resistance and the frequency-dependent impedance. Copyright 1999 Academic Press.

Journal Article↗
PubMed2001

A neural network approach to the acoustic startle reflex and prepulse inhibition.

Prepulse inhibition (PPI) is the normal suppression of the startle reflex when an intense stimulus is preceded by a weak non-startling prestimulus. PPI is widely used as a model for sensorimotor gating processes and has been shown to be impaired in various neuropsychiatric disorders, including schizophrenia. We have reproduced startle-like behavior and basic PPI modifications with a neural network. The network design was constrained by the attempt (1) to use as few connections as possible and (2) to relate neuroanatomical structures to the simulated network. Performance of the network was evaluated by the behavior of the simulated motor neurons in response to prepulse and pulse stimuli presented with various lead intervals and prepulse intensities. A delayed inhibitory pathway via the pedunculopontine nucleus (PPTg) to the caudal pontine reticular nucleus was found to be a necessary but insufficient requirement to reproduce basic PPI output patterns. Additional requirements included (a) a low threshold at or below the caudal pontine reticular formation, (b) signal amplification in the inhibitory pathway and (c) prolongation of activity in the inhibitory pathway. On the grounds of the most appropriate output patterns of the simulations, we propose a mechanism of sustained activation in the PPTg due to recursive connections. Relations between stimuli, behavior (motor output) and the underlying architecture are discussed. Potentially, this modeling technique can be extended to investigate the impact of drugs and higher brain regions on PPI.

Animals↗
PubMed2003

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.

Here, we describe the development of a mammalian protein-protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks (http://fantom21.gsc.riken.go.jp/PPI/). In the database, we stored the mammalian PPIs identified through our PPI assays (internal PPIs), as well as those we extracted and processed (external PPIs) from publicly available data sources, the DIP and BIND databases and MEDLINE abstracts by using FACTS, a new functional inference and curation system. We integrated the internal and external PPIs into the PPI database, which is linked to the main FANTOM2 viewer. In addition, we incorporated into the PPI Viewer information regarding the luciferase reporter activity of internal PPIs and the data confidence of external PPIs; these data enable visualization and evaluation of the reliability of each interaction. Using the described system, we successfully identified several interactions of biological significance. Therefore, the PPI Viewer is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.

Animals↗
PubMed2004

A novel electrically conductive and biodegradable composite made of polypyrrole nanoparticles and polylactide.

A novel electrically conductive biodegradable composite material made of polypyrrole (PPy) nanoparticles and poly(d,l-lactide) (PDLLA) was prepared by emulsion polymerization of pyrrole in a PDLLA solution, followed by precipitation. The composite was characterized by scanning electron microscopy and X-ray photoelectron spectroscopy. The electrical stability of the composite containing 5 wt% PPy was investigated in a cell culture environment for 1000 h with 100 mV DC applied voltage. Fibroblasts were cultured on the composite membranes and were stimulated with various DC currents. The PPy particles formed aggregations and constituted microdomains and networks embedded in the PDLLA. With the 1-17% increase in the PPy content, the conductivity of the composite increased by six orders of magnitude. The surface resistivity of the PPy/PDLLA membrane with 3% PPy was as low as 1x10(3) Omega/square. The electrical stability was significantly better in the PPy/PDLLA composite than in the PPy-coated polyester fabrics. For the composite with 5% PPy, the test membrane retained 80% and 42% of the initial conductivity in 100 and 400 h, respectively, following the addition of the MEM solution, compared to 5% and 0.1% for the PPy-coated polyester fabrics. Under 100 mV, a composite membrane 3.0x2.5x0.03cm3 in size and containing 5% PPy sustained a biologically meaningful electrical conductivity in a typical cell culture environment for 1000 h. The growth of fibroblasts was up regulated under the stimulation of medium range intensity of DC current.

Adult↗
PubMed2005

Fabrication and biocompatibility of polypyrrole implants suitable for neural prosthetics.

Finding a conductive substrate that promotes neural interactions is an essential step for advancing neural interfaces. The biocompatibility and conductive properties of polypyrrole (PPy) make it an attractive substrate for neural scaffolds, electrodes, and devices. Stand-alone polymer implants also provide the additional advantages of flexibility and biodegradability. To examine PPy biocompatibility, dissociated primary cerebral cortical cells were cultured on PPy samples that had been doped with polystyrene-sulfonate (PSS) or sodium dodecylbenzenesulfonate (NaDBS). Various conditions were used for electrodeposition to produce different surface properties. Neural networks grew on all of the PPy surfaces. PPy implants, consisting of the same dopants and conditions, were surgically implanted in the cerebral cortex of the rat. The results were compared to stab wounds and Teflon implants of the same size. Quantification of the intensity and extent of gliosis at 3- and 6-week time points demonstrated that all versions of PPy were at least as biocompatible as Teflon and in fact performed better in most cases. In all of the PPy implant cases, neurons and glial cells enveloped the implant. In several cases, neural tissue was present in the lumen of the implants, allowing contact of the brain parenchyma through the implants.

Animals↗
PubMed2006

MPact: the MIPS protein interaction resource on yeast.

In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein-protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been called a gold standard because of its quality and comprehensiveness [H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J. D. Han, N. Bertin, S. Chung, M. Vidal and M. Gerstein (2004) Genome Res., 14, 1107-1118]. MPact and the yeast protein localization catalog provide information related to the proximity of proteins in yeast. Beside the integration of high-throughput data, information about experimental evidence for PPIs in the literature was compiled by experts adding up to 4300 distinct PPIs connecting 1500 proteins in yeast. As the interaction data is a complementary part of CYGD, interactive mapping of data on other integrated data types such as the functional classification catalog [A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Güldener, G. Mannhaupt, M. Münsterkötter and H. W. Mewes (2004) Nucleic Acids Res., 32, 5539-5545] is possible. A survey of signaling proteins and comparison with pathway data from KEGG demonstrates that based on these manually annotated data only an extensive overview of the complexity of this functional network can be obtained in yeast. The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of our curated data with high-throughput datasets. The complete dataset as well as user-defined sub-networks can be retrieved easily in the standardized PSI-MI format. The resource can be accessed through http://mips.gsf.de/genre/proj/mpact.

Databases, Protein↗
PubMed2006

Increasing the ordering temperatures in oxalate-based 3D chiral magnets: the series [Ir(ppy)2(bpy)][M(II)M(III)(ox)3] x 0.5 H2O (M(II)M(III) = MnCr, FeCr, CoCr, NiCr, ZnCr, MnFe, FeFe); bpy = 2,2'-bipyridine; ppy = 2-phenylpyridine; ox = oxalate dianion).

The synthesis, structure, and physical properties of a novel series of oxalate-based bimetallic magnets obtained by using the Ir(ppy)2(bpy)]+ cation as a template of the bimetallic [M(II)M(III)(ox)3]- network are reported. The compounds can be formulated as [Ir(ppy)2(bpy)][M(II)Cr(III)(ox)3] x 0.5 H2O (M(II) = Ni, Mn, Co, Fe, and Zn) and [Ir(ppy)2(bpy)]-[M(II)Fe(III)(ox)3] x 0.5 H2O (M(II) = Fe, Mn) and crystallize in the chiral cubic space group P4(1)32 or P4(3)32. They show the well-known 3D chiral structure formed by M(II) and M(III) ions connected through oxalate anions with [Ir(ppy)2(bpy)]+ cations and water molecules in the holes left by the oxalate network. The M(II)Cr(III) compounds behave as soft ferromagnets with ordering temperatures up to 13 K, while the Mn(II)Fe(III) and Fe(II)Fe(III) compounds behave as a weak ferromagnet and a ferrimagnet, respectively, with ordering temperatures of 31 and 28 K. These values represent the highest ordering temperatures so far reported in the family of 3D chiral magnets based on bimetallic oxalate complexes.

Journal Article↗
PubMed1995

Effect of nordidemnin on the cell cycle of sea urchin embryos. Role in synthesis and phosphorylation of proteins and in polyphosphoinositide turnover in mitosis progression.

Nordidemnin (NorD) is a cyclic depsipeptide isolated from a Caribbean tunicate. This drug is thought to affect cell proliferation by acting on protein, RNA, and DNA syntheses. We studied the ability of NorD to arrest sea urchin embryos at the prophase stage. We tested whether NorD could alter the synthesis and phosphorylation of proteins as well as polyphosphoinositide (PPI) metabolism, as the activation of these processes is necessary for progression through the cell cycle. The dose-response effect on protein synthesis and cell cleavage suggests that NorD acts in the same way as emetine, a well-known protein synthesis inhibitor. We observed that treatment of eggs with emetine or NorD, even at concentrations that inhibited DNA and protein synthesis as well as phosphorylation of proteins, led to modifications in the incorporation of 32P into phosphatidylinositol phosphate and phosphatidylinositol bisphosphate without any alteration in the chemical amounts of these lipids. However, fluctuations in the PPI messenger system that occur during the cell cycle were maintained in the presence of either drug. We suggest that proteins and PPI are linked in an intricate network to control mitosis and cellular proliferation.

Animals↗
PubMed2006

NetAlign: a web-based tool for comparison of protein interaction networks.

UNLABELLED: NetAlign is a web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs), which may derive from a common ancestor and disclose conserved topological organization of interactions in evolution. To exemplify the application of NetAlign, we perform two genome-scale comparisons with (1) the Escherichia coli PIN against the Helicobacter pylori PIN and (2) the Saccharomyces cerevisiae PIN against the Caenorrhabditis elegans PIN. Many of the identified CoNSs correspond to known complexes; therefore, cross-species PIN comparison provides a way for discovery of conserved modules. In addition, based on the species-to-species differences in CoNSs, we reformulate the problems of protein-protein interaction (PPI) prediction and species divergence from a network perspective. AVAILABILITY: http://www1.ustc.edu.cn/lab/pcrystal/NetAlign.

Algorithms↗
PubMed2005

A topological measurement for weighted protein interaction network.

High-throughput methods for detecting protein-protein interactions (PPI) have given researchers an initial global picture of protein interactions on a genomic scale. The usefulness of this understanding is, however, typically compromised by noisy data. The effective way of integrating and using these non-congruent data sets has received little attention to date. This paper proposes a model to integrate different data sets. We construct this model using our prior knowledge of data set reliability. Based on this model, we propose a topological measurement to select reliable interactions and to quantify the similarity between two proteins' interaction profiles. Our measurement exploits the small-world network topological properties of protein interaction network. Meanwhile, we discovered some additional properties of the network. We show that our measurement can be used to find reliable interactions with improved performance and to find protein pairs with higher function homogeneity.

Algorithms↗
PubMed2006

Analysis of protein sequence and interaction data for candidate disease gene prediction.

Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimental study: Common Pathway Scanning (CPS) and Common Module Profiling (CMP). CPS is based on the assumption that common phenotypes are associated with dysfunction in proteins that participate in the same complex or pathway. CPS applies network data derived from protein-protein interaction (PPI) and pathway databases to identify relationships between genes. CMP identifies likely candidates using a domain-dependent sequence similarity approach, based on the hypothesis that disruption of genes of similar function will lead to the same phenotype. Both algorithms use two forms of input data: known disease genes or multiple disease loci. When using known disease genes as input, our combined methods have a sensitivity of 0.52 and a specificity of 0.97 and reduce the candidate list by 13-fold. Using multiple loci, our methods successfully identify disease genes for all benchmark diseases with a sensitivity of 0.84 and a specificity of 0.63. Our combined approach prioritizes good candidates and will accelerate the disease gene discovery process.

Algorithms↗
PubMed2005

Neural network model of prepulse inhibition.

The authors introduce a real-time model of acoustic prepulse inhibition (PPI) and facilitation (PPF) in animals and humans. The model incorporates excitatory and facilitatory pathways activated by the positive value of changes in noise level in the environment and an inhibitory pathway activated by the absolute value of changes in noise level. Whereas excitation and facilitation are exponential functions, inhibition is a linear function of the input noise expressed in decibels. The model describes many properties of PPI and PPF that include, among others, their dependency on prepulse intensity and duration, duration of the lead interval, and changes in background noise. The model also describes how specific brain lesions enhance the strength of the startle response and impair PPI. Finally, the model correctly predicts how PPI depends on pulse intensity.

Acoustic Stimulation↗
PubMed2001

Rational design of three-dimensional (3D) optically active molecule-based magnets: synthesis, structure, optical and magnetic properties of ([Ru(bpy)3](2+), ClO4(-), [Mn(II) Cr(III)(ox)3](-))n and ([Ru(bpy)2ppy](+), [M(II)Cr(III)(ox)3](-))n, with M(II) = Mn(II), Ni(II). X-ray structure of ([deltaRu(bpy)3](2+), ClO4(-), [deltaMn(II)DeltaCr(III)(ox)3](-))n and ([lambdaRu(bpy)2ppy)](+), [lambdaMn(II)lambdaCr(III)(ox)3](-))n.

To elucidate the relation between structural and magnetic properties, we have synthesized molecular materials having both Cotton effects and a ferromagnetic long range order. Such optically active 3D molecule-based magnets were rationally designed using the enantioselective template effect of optically active cations, namely Delta or Lambda [Ru(bpy)3, ClO4](+) or Delta or Lambda [Ru(bpy)3ppy](+) (bpy = bipyridine; ppy = phenylpyridine). Such cations are able to template the formation of optically active 3D anionic networks in which transition metal ions (Cr-Mn) and (Cr-Ni) are connected by oxalate ligands (ox). Following this strategy, we described the synthesis of ([Ru(bpy)3](2+), ClO4(-), [Mn(II)Cr(III)(ox)3](-))n and ([Ru(bpy)2ppy](+), [M(II)Cr(III)(ox)3](-))n with M(II) = Mn(II), Ni(II) in their optically active forms. In these 3D networks, all of the metallic centers have the same configuration, Delta or Lambda, as the template cation. We have determined the structure of ([DeltaRu(bpy)3][ClO4][DeltaMnDeltaCr(ox)3])n and ([LambdaRu(bpy)2ppy](+), [LambdaMn(II)LambdaCr(III)(ox)3](-))n by X-ray diffraction studies. These optically active networks show the Cotton effect and long-range ferromagnetic order at low temperatures. The magnetic circular dichroism of ([Ru(bpy)3](2+), ClO4(-), [Mn(II)Cr(III)(ox)3](-))n at 2 K is reported.

Journal Article↗
PubMed2006

Enhanced c-Fos expression in the rostral ventral respiratory complex and rostral parapyramidal region by inhibition of the Na+/H+ exchanger type 3.

Previous studies have shown that selective inhibition of Na+/H+ exchanger type 3 (NHE3) induces intracellular acidification and activates CO2/H+-sensitive medullary neurons, mimicking the responses evoked by hypercapnic stimuli. In addition, NHE3 blockers administration decreases the duration of apnoea induced by laryngeal stimulation, presumably by means of central chemoreceptor activation. To test the hypothesis that the central chemoreceptor network may be affected by NHE3 inhibition, brainstem c-Fos immunoreactive cell counting was performed after systemic administration of the NHE3 blocker AVE1599 (Aventis Pharma Deutschland GmbH) (2 mg/kg). The rostro-caudal quantitative c-Fos analysis showed a significant increase in the number of c-Fos positive cells in the rostral part of the ventral respiratory complex (VRC) as well as in the rostral part of the parapyramidal (Ppy) region. The VRC activated region (-4.2 to -3.2mm interaural) included the pre-Bötzinger complex, the rostral ventral respiratory group and the rostral ventrolateral medulla, all of them involved in cardiorespiratory control. The activated Ppy region corresponded with the rostral chemosensitive area, which elicits the strongest ventilatory response upon ventral medullary surface stimulation with H+/CO2. Most cells activated in Ppy after NHE3 inhibition were serotonergic. Hence, systemic application of NHE3 blockers may induce central chemoreceptors activation and an increase in the respiratory network activity in a similar way to known physiological stimuli such as hypercapnia. On the other hand, selective NHE3 blockers could be excellent tools for treatment of pathological states where central chemoreceptor function is diminished or absent, such as central hypoventilation syndrome or sudden infant death syndrome.

Animals↗