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Results for “Functional perturbation”

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PubMed2001

Microscopic approach for the site distribution and thermodynamic properties of a single-component polymer subjected to an external field.

A microscopic statistical mechanics approach is proposed for a nonuniform single-component freely jointed tangential hard-sphere polymer in the framework of density-functional theory. The present approach avoids the use of single-chain simulation in the theory by treating bonding interaction on the basis of the properties of the Dirac delta function. The present excess free energy includes all terms of functional perturbative expansion around the uniform bulk fluid in the form of the Verlet-modified bridge function. The second-order direct correlation function of a uniform polymer melt as the input parameter is obtained by solving numerically the polymer-reference-interaction-site-model integral equation with the Percus-Yevick closure. Predictions of the present approach for such microscopic structural and thermodynamics properties as the site density distribution, the partition coefficient, and the adsorption isotherm near a hard wall or between two hard walls are compared with computer-simulation results and with those of previous theories. The comparison indicates that the present approach is more accurate than the previous integral equation theory and the most accurate Monte Carlo density-functional theories. The predicted oscillations of the medium-induced force between two hard walls immersed in polymer melts are consistent with the experimental results available in the literature. The relation of the present approach with self-consistent-field theory, as well as the differences between the two, are discussed.

Journal Article↗

PubMed2004

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway.

Signal transduction pathways are modular composites of functionally interdependent sets of proteins that act in a coordinated fashion to transform environmental information into a phenotypic response. The pro-inflammatory cytokine tumour necrosis factor (TNF)-alpha triggers a signalling cascade, converging on the activation of the transcription factor NF-kappa B, which forms the basis for numerous physiological and pathological processes. Here we report the mapping of a protein interaction network around 32 known and candidate TNF-alpha/NF-kappa B pathway components by using an integrated approach comprising tandem affinity purification, liquid-chromatography tandem mass spectrometry, network analysis and directed functional perturbation studies using RNA interference. We identified 221 molecular associations and 80 previously unknown interactors, including 10 new functional modulators of the pathway. This systems approach provides significant insight into the logic of the TNF-alpha/NF-kappa B pathway and is generally applicable to other pathways relevant to human disease.

Animals↗

PubMed2000

Astrocytic alterations induced by HTLV type 1-infected T lymphocytes: a role for Tax-1 and tumor necrosis factor alpha.

In the neurological disease associated with HTLV-1 infected T lymphocytes infiltrated within the CNS are suspected of playing a prominent role in pathogenesis via inflammatory cytokines and the viral protein Tax-1. We hypothesized that T lymphocytes initiate functional perturbation in astrocytes, resulting in neuronal alteration as glial cells have a crucial role in CNS homeostasis. In particular, astrocytes manage the steady state level of glutamate and continuously provide metabolite precursors to neurons and oligodendrocytes. Using a model system of HTLV-1-infected T cells-astrocytes interaction, we show that after contact with T cells, astrocyte acquire a phenotype typical of gliosis: secretion of proinflammatory cytokines (TNF-alpha, IL-1alpha, IL-6) and matrix metalloproteinases (MMP-9, MMP-3). The concomitant increase in the expression of MMPs and of their endogenous inhibitors (TIMP-1 and TIMP-3) suggests a perturbation in MMP/TIMP balance. This may alter the extracellular matrix and, in turn, the cell environment. At a functional level, glutamate transport and catabolism are impaired in astrocytes. A decrease in glutamate uptake is associated with downregulated expression of glutamate transporters GLAST and GLT1. The expression of astrocytic enzyme of glutamate metabolism is modified with up-regulation of glutamine synthetase and down-regulation of glutamate dehydrogenase. The involvement of Tax-1 in these alterations, directly or indirectly via TNF-alpha, is shown. Altered glutamate uptake and catabolism associated with impairment in cell connectivity via MMP/TIMP imbalance could compromise the functional integrity of the CNS in general and that of neurons and oligodendrocytes in particular.

Animals↗

PubMed2004

Pedunculopontine nucleus and basal ganglia: distant relatives or part of the same family?

The basal ganglia are more highly interconnected with the pedunculopontine tegmental nucleus (PPN) than with any other brain region. Regulation and relay of basal ganglia activity are two key functions of the PPN. The PPN provides an interface for the basal ganglia to influence sleep and waking, and the two structures are similarly implicated in learning, reward and other cognitive functions. Perturbations of basal ganglia activity have consequences for the PPN and vice versa, exemplified by their interdependencies in motor function and Parkinson's disease. Thus, close anatomical and physiological links between the PPN and basal ganglia make it increasingly difficult to consider the two as separate functional entities.

Animals↗

PubMed2005

Variational optimization of effective atom centered potentials for molecular properties.

In plane wave based electronic structure calculations the interaction of core and valence electrons is usually represented by atomic effective core potentials. They are constructed in such a way that the shape of the atomic valence orbitals outside a certain core radius is reproduced correctly with respect to the corresponding all-electron calculations. Here we present a method which, in conjunction with density functional perturbation theory, allows to optimize effective core potentials in order to reproduce ground-state molecular properties from arbitrarily accurate reference calculations within standard density functional calculations. We demonstrate the wide range of possible applications in theoretical chemistry of such optimized effective core potentials (OECPs) by means of two examples. We first use OECPs to tackle the link atom problem in quantum mechanics/molecular mechanics (QM/MM) schemes proposing a fully automatized procedure for the design of link OECPs, which are designed in such a way that they minimally perturb the electronic structure in the QM region. In the second application, we use OECPs in two sample molecules (water and acetic acid) such as to reproduce electronic densities and derived molecular properties of hybrid (B3LYP) quality within general gradient approximated (BLYP) density functional calculations.

Journal Article↗

PubMed1979

Control of stiffness by the medium latency electromyographic response to limb perturbation.

It is hypothesized that the medium latency electromyographic (EMG) response (ML) to limb perturbation functions to preset limb stiffness to a constant initial level. Three predictions are derived from this hypothesis: Firstly, in the presence of an instruction calling for opposition to limb perturbation, a control signal, ML, will be observed and will lead to the establishment of a constant level of limb stiffness. Secondly, in the absence of an instruction to oppose, no control signal will be observed and correspondingly a constant stiffness will not be generated. Thirdly, the latency of onset of stiffness control will covary with the latency of onset of ML. These predictions were tested in experiments involving perturbation of the human forearm about the elbow joint, with surface EMG measurements and computation of the limb stiffness function. The results are in accord with these predictions, and support the hypothesis that ML functions in the feedforward control of limb stiffness.

Adult↗

PubMed2004

Optimization of effective atom centered potentials for london dispersion forces in density functional theory.

We add an effective atom-centered nonlocal term to the exchange-correlation potential in order to cure the lack of London dispersion forces in standard density functional theory. Calibration of this long-range correction is performed using density functional perturbation theory and an arbitrary reference. Without any prior assignment of types and structures of molecular fragments, our corrected generalized gradient approximation density functional theory calculations yield correct equilibrium geometries and dissociation energies of argon-argon, benzene-benzene, graphite-graphite, and argon-benzene complexes.

Biopolymers↗

PubMed1983

The microenvironment of the spinal ganglion neuron in the rat during aging.

The environment and particularly the glial sheath of the spinal ganglion neurons was systematically studied by light and electron microscopy in the young and senescent rat. Experiments using radioactive tracers tested the consequences of the functional perturbations associated with structural impairments. The results suggested the possibility that the glial sheath and the neuron aged differently. Whereas the glial sheath maintained its functional capacity relatively intact, neuronal performance was markedly and more rapidly impeded. The morphology and volume of the extracellular space were unchanged. Therefore, impairment of the glioneuronal units in the spinal ganglion during aging cannot be assigned to environmental and vascular phenomena.

Aging↗

PubMed2002

Post-insult exposure to (+/-) kavain potentiates N-methyl-D-aspartate toxicity in the developing hippocampus.

Kavapyrone extracts of the pepper plant Piper methysticum Forst. have been reported to be pharmacologically active in the brain by modulating the function of several ionotropic receptor systems and voltage-sensitive ion channels. While kavapyrones have previously demonstrated neuroprotective effects against several forms of neurotoxicity, the possibility remains that perturbed function of neuronal ion transport may prove to be neurotoxic in some instances. The present studies were designed to examine the effects of the kavapyrone, (+/-) kavain, on viability of organotypic hippocampal explants exposed to the excitotoxin N-methyl-D-aspartate (NMDA). Exposure to (+/-) kavain (1-600 microM) for 24 h did not alter neuronal viability in the CA1, CA3, or dentate gyrus regions of hippocampal explants. However, higher concentrations of (+/-) kavain (> or =300 microM) produced marked neurotoxicity in the lacunosum moleculare layer of the hippocampus. One hour of exposure to NMDA (20 microM) produced significant neuronal death in both the CA3 and CA1 pyramidal cell regions, effects prevented by co-exposure to MK-801 (30 microM). Co-exposure of explants to (+/-) kavain (1-100 microM) with NMDA did not alter the severity of NMDA-induced neurotoxicity. However, exposure of NMDA-treated explants to (+/-) kavain (> or =10 microM) for 24 h after insult produced significant increases in neurotoxicity in the CA1 and dentate gyrus regions of explants. In conclusion, while the kavapyrone (+/-) kavain is neurotoxic only at high concentrations when exposed alone to the developing hippocampus, it appears to adversely affect neuronal recovery following excitotoxic insults.

Animals↗

PubMed2006

[Brain profile of hypometabolism in early Alzheimer's disease: relationships with cognitive deficits and atrophy].

While accurate and early prediction of patients that will develop Alzheimer's disease (AD) in the near future is urgently needed, the amnestic Mild Cognitive Impairment (MCI) state is of particular interest since it most conveniently represents the pre-dementia stage of AD. Consistently, the profile of brain functional alteration constantly evidenced in resting-state SPECT and PET studies is similar to that observed in mild AD, mainly involving the posterior cingulate and temporo-parietal regions. While the former is a characteristic feature of MCI, since it is present in each patient at this stage, the latter seems specifically associated with the future conversion to AD. Moreover, right temporo-parietal hypometabolism has been found to be the best predictor of subsequent global cognitive decline, over and above neuropsychological and MRI volumetric measurements. This review also presents a discussion on the relationships between the brain profile of hypometabolism on the one hand, and cognitive impairment as well as cerebral structural alterations on the other. Thus, firstly, while functional impairment in the posterior cingulate region seems to be associated with deficits in retrieval of episodic memories in MCI, the relationship between right temporo-parietal hypometabolism and cognitive impairment is still obscure. However, several arguments point to its relation with visuo-spatial deficits, which are often associated with future conversion to AD. Secondly, the discordance between brain areas of major functional changes, and those of highest structural alterations, leads to some relevant questions about the relations between both pathological manifestations and their underlying mechanisms. More specifically, additional hypometabolism-inducing factors could occur in areas of highest hypometabolism compared to atrophy, i.e. mainly in posterior associative cortical regions, leading to genuine functional perturbation in early AD before the development of real atrophy and perhaps of disease as well. By contrast, the hippocampus is the main site of atrophy while its functional alteration is still debated, suggesting that compensation/protective mechanisms probably specifically occur in this structure to maintain a high level of metabolism relative to its structural alteration.

Alzheimer Disease↗

PubMed2026

Genome-wide identification and expression profiling of HSD3B and SDR42E1 genes in the Pacific oyster (Crassostrea gigas): potential associations with gonadal development.

Sex steroids are lipid-soluble signaling molecules that regulate sex differentiation, reproductive development and physiological homeostasis in animals. 3β-Hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase (3β-HSD) is a key steroidogenic enzyme, whereas SDR42E1, an extended short-chain dehydrogenase/reductase, has been implicated in sterol- and steroid-related metabolism. However, the composition, evolutionary relationships and expression patterns of the HSD3B- and SDR42E1-related genes in bivalve gonadal development remain poorly characterized. In this study, five PF01073-containing genes, comprising three CgHsd3b and two CgSdr42e1 genes, were identified in the Pacific oyster Crassostrea gigas. Phylogenetic analysis separated the proteins into HSD3B-related and SDR42E1-related groups, and gene-structure and motif analyses indicated subfamily-level divergence. All five proteins retained the SDR domain but differed in exon-intron structure and motif composition. Each contained the extended-SDR TGxxGxxG motif, whereas exact classical [ST]GxxxGxG and NNAG motifs were absent. Tyr- and Lys-equivalent residues were conserved, while the HSD3B1 Ser-equivalent position contained Thr in two C. gigas proteins and Ser in one. These features support their classification as extended-SDR proteins but do not establish enzymatic activity or substrate specificity. The three CgHsd3b genes were dispersed on one chromosome, whereas CgSdr42e1-1 and CgSdr42e1-2 were adjacent on another chromosome, suggesting a possible local duplication event for the CgSdr42e1 pair. Public RNA-seq data showed distinct tissue- and gonadal-stage expression patterns, with several genes displaying gonad-biased or female-stage-associated expression. Independent RT-qPCR profiling of the representative genes CgHsd3b-3 and CgSdr42e1-1 detected stage-dependent expression, although tissue rankings differed from those in the public RNA-seq datasets. These differences may reflect the use of independent biological samples, tissue composition, normalization procedures, and platform-specific measurements. Because enzymatic assays, metabolite measurements, cellular localization, and functional perturbation were not performed, the results identify candidate genes whose expression is associated with gonadal development rather than demonstrating regulatory roles. This study provides a comparative framework for future functional investigation of sterol- and steroid-related metabolism in bivalves.

Animals↗

PubMed1990

Unification of perturbation measures in speech signals.

Voice perturbation measures, formerly defined in a somewhat ad hoc fashion, are discussed within the framework of signal theory. An attempt is made to unify a variety of existing jitter, shimmer, and noise measures on the basis of common underlying perturbation functions and their derivatives. Some simple modulations (sinusoid, Gaussian noise, linear trend) are imposed on cyclic parameters in phonation (e.g., amplitude and fundamental frequency) to test the ability of perturbation measures to detect or reject these types of modulations. It is expected that this systematic approach to perturbation analysis will be helpful in identifying the sources of irregularity in the voice and, thereby, in the detection of laryngeal disorders.

Humans↗

PubMed1999

Adhesion and migration of avian neural crest cells on fibronectin require the cooperating activities of multiple integrins of the (beta)1 and (beta)3 families.

Based on genetic, functional and histological studies, the extracellular matrix molecule fibronectin has been proposed to play a key role in the migration of neural crest cells in the vertebrate embryo. In the present study, we have analyzed in vitro the repertoire and function of integrin receptors involved in the adhesive and locomotory responses of avian truncal neural crest cells to fibronectin. Immunoprecipitation experiments showed that neural crest cells express multiple integrins, namely (alpha)3(beta)1, (alpha)4(beta)1, (alpha)5(beta)1, (alpha)8(beta)1, (alpha)v(beta)1, (alpha)v(beta)3 and a (beta)8 integrin, as potential fibronectin receptors, and flow cytometry analyses revealed no major heterogeneity among the cell population for expression of integrin subunits. In addition, the integrin repertoire expressed by neural crest cells was found not to change dramatically during migration. At the cellular level, only (alpha)v(beta)1 and (alpha)v(beta)3 were concentrated in focal adhesion sites in connection with the actin microfilaments, whereas the other integrins were predominantly diffuse over the cell surface. In inhibition assays with function-perturbing antibodies, it appeared that complete abolition of cell spreading and migration could be achieved only by blocking multiple integrins of the (beta)1 and (beta)3 families, suggesting possible functional compensations between different integrins. In addition, these studies provided evidence for functional partitioning of integrins in cell adhesion and migration. While spreading was essentially mediated by (alpha)v(beta)1 and (alpha)8(beta)1, migration involved primarily (alpha)4(beta)1, (alpha)v(beta)3 and (alpha)8(beta)1 and, more indirectly, (alpha)3(beta)1. (alpha)5(beta)1 and the (beta)8 integrin were not found to play any major role in either adhesion or migration. Finally, consistent with the results of inhibition experiments, recruitment of (alpha)4(beta)1 and (alpha)v(beta)3, individually or in combination using antibodies or recombinant VCAM-1 and PECAM-1 molecules as a substratum, was required for migration but was not sufficient to produce migration of the cell population as efficiently as with fibronectin. In conclusion, our study indicates that neural crest cells express a multiplicity of fibronectin-binding integrins and suggests that dispersion of the cell population requires cooperation between distinct integrins regulating different events of cell adhesion, locomotion and, possibly, proliferation and survival.

Animals↗

PubMedDate not supplied

Viral perturbation of endocrine function: disordered cell function leads to disturbed homeostasis and disease.

Virus-induced disease occurs both through direct destruction of cells by viruses and/or secondarily through lysis of infected cells by immunological assault. We asked whether viruses could also cause injury and disease by altering the cell's normal or expected functions without destroying the cells. Here we show that a relatively noncytopathic virus can perturb endocrine functions by disordering the synthesis of a hormone needed for growth and glucose regulation, while replicating in a specialized cell making that hormone. Yet, despite viral replication and alteration in synthesis of the specialized cell's homeostatic product, the infected cell remains free from structural injury.

Animals↗

PubMed1993

Development and maintenance of a simple reflex circuit in small-patch mosaics of Drosophila: effects of altered neuronal function and developmental arrest.

A combined genetic, anatomical, and behavioral approach has been undertaken to study the developmental and functional plasticity of identified bristle mechanosensory neurons in Drosophila. A stereotyped grooming reflex in decapitated flies enabled simple but reliable assessments of the functional output of individual bristle sensory cells to correlate with their axonal projections and terminal arbors revealed by the cobalt backfill technique. Construction of small-patch mosaics that contain only a single mutant bristle allowed functional perturbation of individual neurons within an otherwise normal environment. Mutations that affect nerve excitability and membrane recycling have been used to examine their effects on neuronal pathfinding, arborization, and the initiation and maintenance of functional connections. Previous studies (Burg and Wu, 1986, J. Neurosci. 6:2968-2976; 1989, Dev. Biol. 131:505-514) have demonstrated that para(ts)nap(ts) double-mutant sensory neurons, in which action potentials are unconditionally blocked by defects in sodium currents, and eag Sh double-mutant sensory cells, in which membrane excitability is increased by alterations in potassium currents, can establish and maintain central projections that are indistinguishable from their functionally normal counterparts. Mutations of the shi(ts) gene cause a temperature-sensitive, reversible block of the membrane recycling process, resulting in arrest of neuronal growth in culture (Kim and Wu, 1987, J. Neurosci. 7:3245-3255) and depletion of synaptic vesicles that leads to transmission blockade at established synapses (Ikeda, Ozawa, and Hagiwara, 1976, Nature 259:489-491; Koenig and Ikeda, 1983, J. Neurobiol. 14:411-419; 1989, J. Neurosci. 9:3844-3860). Prolonged heat treatments (up to 16% of total development time) of small-patch shi(ts) mosaics at different pupal stages did not prevent the establishment of central projections characteristic of the various sensory cell types. However, none of the shi(ts) sensory neurons heat-pulsed during the initial or the final 16% of pupal development were able to initiate the reflex behavior, although a proportion of those treated in other periods apparently established functional contacts with appropriate targets to support the characteristic cleaning reflex. The possibility exists that the membrane recycling process blocked in shi(ts) cells provides a crucial mechanism for cell-cell interactions taking place during initial differentiation and final synaptic stabilization, and possibly competition, in the developing sensory neuron. Heat treatments of adult shi(ts) mosaics blocked the reflex initiated by the mutant (but not the surrounding normal) bristles, as expected from the effect of synaptic block.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗

PubMed2002

Functional visualization of the excretory system of adult Schistosoma mansoni by the fluorescent marker resorufin.

Excretion of metabolic wastes as well as xenobiotics is a major concern of all living organisms, and the Platyhelminthes including Schistosoma mansoni possess the protonephridial excretory system for their survival. Except for some ultra-structural and biochemical information, little is known about the protonephridium of platyhelminths due to a lack of established techniques for exploring the excretory activity. This study describes a new technique to assess the excretory activity of S. mansoni by use of the fluorescent marker resorufin, which is a potential substrate of the drug efflux pump, P-glycoprotein. After simple diffusion into the schistosome body, fluorescent resorufin was concentrated in the excretory tubules by an energy-dependent mechanism and excreted via the nephridiopore. The present technique of labelling functionally the excretory system was applicable to adult worms, but not schistosomula or cercariae. A variety of modulators known to interfere with mammalian P-glycoprotein function perturbed resorufin excretion from male adult schistosomes, including cyclosporin A, Ro11-2933, verapamil, or nifedipine. This technique of labelling the excretory system with fluorescent resorufin has enabled us to study aspects of the physiological function, hitherto unknown, of the protonephridial system of S. mansoni.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2005

Macrophage migration inhibitory factor MIF interferes with the Rb-E2F pathway.

Macrophage migration inhibitory factor (MIF) is implicated in the regulation of inflammation and cell growth. We previously showed that MIF is a potent modulator of p53- and E2F-dependent pathways that are activated in response to oncogenic signaling. Here, we characterize the functional link between MIF and E2F transcription factors. Our results demonstrate that MIF-deficient cells exhibit E2F-dependent growth alterations and reduced susceptibility to oncogenic transformation. The basis for this transformation resistance is a perturbed function of the C-terminal Rb binding region of E2F4. However, inactivation of Rb or substitution of the E2F4 C-terminal domain by the E2F1 C-terminal region rescues the transformation defect. Importantly, the involvement of E2F factors in DNA replication rather than in regulation of transcription determines their oncogenic properties in the context of MIF deficiency. A proinflammatory molecule interfering with tumor suppression and DNA replication provides a compelling molecular link for the association of chronic inflammation and tumorigenesis.

Animals↗

PubMed1998

The conserved N-terminal BH4 domain of Bcl-2 homologues is essential for inhibition of apoptosis and interaction with CED-4.

Bcl-2 and close homologues such as Bcl-xL promote cell survival, while other relatives such as Bax antagonize this function. Since only the pro-survival family members possess a conserved N-terminal region denoted BH4, we have explored the role of this amphipathic helix for their survival function and for interactions with several agonists of apoptosis, including Bax and CED-4, an essential regulator in the nematode Caenorhabditis elegans. BH4 of Bcl-2 could be replaced by that of Bcl-x without perturbing function but not by a somewhat similar region near the N-terminus of Bax. Bcl-2 cell survival activity was reduced by substitutions in two of ten conserved BH4 residues. Deletion of BH4 rendered Bcl-2 (and Bcl-xL) inactive but did not impair either Bcl-2 homodimerization or ability to bind to Bax or five other pro-apoptotic relatives (Bak, Bad, Bik, Bid or Bim). Hence, association with these death agonists is not sufficient to promote cell survival. Significantly, however, Bcl-xL lacking BH4 lost the ability both to bind CED-4 and antagonize its pro-apoptotic activity. These results favour the hypothesis that the BH4 domain of pro-survival Bcl-2 family members allows them to sequester CED-4 relatives and thereby prevent apoptosis.

Amino Acid Sequence↗