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Results for “functional network connectivity”

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PubMed2007

Functional imaging reveals respiratory network activity during hypoxic and opioid challenge in the neonate rat tilted sagittal slab preparation.

In mammals, respiration-modulated networks are distributed rostrocaudally in the ventrolateral quadrant of the medulla. Recent studies have established that in neonate rodents, two spatially separate networks along this column-the parafacial respiratory group (pFRG) and the pre-Bötzinger complex (preBötC)-are hypothesized to be sufficient for respiratory rhythm generation, but little is known about the connectivity within or between these networks. To be able to observe how these networks interact, we have developed a neonate rat medullary tilted sagittal slab, which exposes one column of respiration-modulated neurons on its surface, permitting functional imaging with cellular resolution. Here we examined how respiratory networks responded to hypoxic challenge and opioid-induced depression. At the systems level, the sagittal slab was congruent with more intact preparations: hypoxic challenge led to a significant increase in respiratory period and inspiratory burst amplitude, consistent with gasping. At opioid concentrations sufficient to slow respiration, we observed periods at integer multiples of control, matching quantal slowing. Consistent with single-unit recordings in more intact preparations, respiratory networks were distributed bimodally along the rostrocaudal axis, with respiratory neurons concentrated at the caudal pole of the facial nucleus, and 350 microns caudally, at the level of the pFRG and the preBötC, respectively. Within these regions neurons active during hypoxia- and/or opioid-induced depression were ubiquitous and interdigitated. In particular, contrary to earlier reports, opiate-insensitive neurons were found at the level of the preBötC.

Analgesics, Opioid↗

PubMed2007

Dynamic scaling of polymer gels comprising nanoparticles.

We present dynamic light scattering (DLS) measurements of soft poly(methyl-methacrylate) (PMMA) and polyacrylamide (PA) polymer gels prepared with trapped bodies (latex spheres or magnetic nanoparticles). We show that the anomalous diffusivity of the trapped particles can be analyzed in terms of a fractal Gaussian network gel model for the entire time range probed by DLS technique. This model is a generalization of the Rouse model for linear chains extended for structures with power law network connectivity scaling, which includes both percolating and uniform bulk gel limits. For a dilute dispersion of strongly scattering particles trapped in a gel, the scattered electric field correlation function at small wavevector ideally probes self-diffusion of gel portions imprisoning the particles. Our results show that the time-dependent diffusion coefficients calculated from the correlation functions change from a free diffusion regime at short times to an anomalous subdiffusive regime at long times (increasingly arrested displacement). The characteristic time of transition between these regimes depends on scattering vector as approximately q(-2), while the time decay power exponent tends to the value expected for a bulk network at small q. The diffusion curves for all scattering vectors and all samples were scaled to a single master curve.

Acrylic Resins↗

PubMed2006

Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach.

Large, complex data sets that are generated from microarray experiments, create a need for systematic analysis techniques to unravel the underlying connectivity of gene regulatory networks. A modular approach, previously proposed by Kholodenko and co-workers, helps to scale down the network complexity into more computationally manageable entities called modules. A functional module includes a gene's mRNA, promoter and resulting products, thus encompassing a large set of interacting states. The essential elements of this approach are described in detail for a three-gene model network and later extended to a ten-gene model network, demonstrating scalability. The network architecture is identified by analysing in silico steady-state changes in the activities of only the module outputs, communicating intermediates, that result from specific perturbations applied to the network modules one at a time. These steady-state changes form the system response matrix, which is used to compute the network connectivity or network interaction map. By employing a known biochemical network, the accuracy of the modular approach and its sensitivity to key assumptions are evaluated.

Algorithms↗

PubMedDate not supplied

A connectionist model of left-right sound discrimination by the Mauthner system.

Artificial neural networks were used to explore the auditory function of the Mauthner system, the brainstem circuit in teleost fishes that initiates fast-start escape responses. The artificial neural networks were trained with backpropagation to assign connectivity and receptive fields in an architecture consistent with the known anatomy of the Mauthner system. Our first goal was to develop neurally specific hypotheses for how the Mauthner system discriminates right from left in the onset of a sound. Our model was consistent with the phase model for directional hearing underwater, the prevalent theory for sound source localization by fishes. Our second goal was to demonstrate how the neural mechanisms that permit sound localization according to the phase model can coexist with the mechanisms that permit the Mauthner system to discriminate between stimuli based on amplitude. Our results indicate possible computational roles for elements of the Mauthner system, which has provided us a theoretical context within which to consider past and future experiments on the cellular physiology. Thus, these findings demonstrate the potential significance of this approach in generating experimentally testable hypotheses for small systems of identified cells.

Acoustic Stimulation↗

PubMedDate not supplied

Changes in impairment and disability from the third to the sixth month after stroke and its relationship evaluated by an artificial neural network.

Functional recovery in a rather late stage after stroke was examined in 70 stroke patients using the Stroke Impairment Assessment Set (SIAS) and the Functional Independence Measure (FIM). The SIAS and the FIM were administered at three and six months after the onset of stroke. Motor items and the abdominal manual muscle testing item improved in more than 30 percent of patients. The motor subscore of the FIM changed from 60.8 to 73.4, and the cognitive subscore changed from 28.4 to 30.4. The relationship between impairment and disability was evaluated using the neural network method with the software, Skiltran. The change of the FIM motor subscore from three months to six months was used as an output variable, and the change in the SIAS items and the FIM motor subscore were included as input variables. As a result of the connection weight obtained from this network, the change in the fifth motor item (one of the tone items, abdominal manual muscle testing) and the unaffected side grip as well as the FIM at three months had a strong connection to the change of the FIM. It is compatible with ordinary experience that function of both the affected and unaffected side influences the level of disability. Contribution of the impairment to the disability indicates the importance of taking into consideration the impairment for predicting prognosis and selecting adequate treatment when we carry out stroke rehabilitation. In conclusion, we described the relationship between the SIAS and the FIM using the neural network in stroke patients and proved the importance of the impairment to predict the outcome of disability.

Activities of Daily Living↗

PubMed2026

ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.

MOTIVATION: The accelerating crisis of antimicrobial resistance among the critical so-called ESKAPE pathogens demands the urgent identification of novel molecular targets. However, a substantial fraction of ESKAPE proteomes remains functionally uncharacterized, with many genes annotated as encoding hypothetical proteins. These protein sequences often lack significant similarity to known protein families when conventional homology-based annotation methods are used and thus remain "dark". This limits our ability to explore their roles in pathogenicity, and it is thus crucial to bridge this substantial gap in pathogen biology by developing new strategies to illuminate these "dark" regions of the ESKAPE pan-proteome. RESULTS: We introduce ECLIPSE (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration), a network-based computational framework that systematically identifies and prioritizes functionally dark protein families in ESKAPE pan-proteomes. ECLIPSE embeds target ESKAPE pathogen proteomes within the global sequence similarity network of the Protein Universe Atlas. It detects connected components composed entirely of unannotated proteins, called the "dark proteome." As a case study, we applied ECLIPSE to a pan-proteome of 3 460 657 protein sequences from 635 strains of Pseudomonas aeruginosa (PA). ECLIPSE identified 120 985 proteins (4%) residing in completely dark connected components. Furthermore, we have performed a taxonomic diversity analysis using normalized Shannon indices to characterize each dark component by its enrichment in ESKAPE pathogens. The analysis utilized the evenness (E) value (see Methods 2.1), which distinguishes Pseudomonas-specific (target-specific) from ESKAPE-enriched dark components. We then developed the Dark Proteome Prioritization Score (DPPS), a composite multidimensional scoring framework (see Methods 2.5). It ranks these dark components by biological relevance across four orthogonal axes: (i) functional darkness, (ii) P. aeruginosa proportion in the Atlas, (iii) AMR-clade taxonomic restriction, and (iv) conservation across the 635 P. aeruginosa strains. This framework outputs a robust four-tier scoring system; the prioritized Tier I components were validated by weight sensitivity analysis and remained stable across 500 Monte Carlo weight perturbations. Structural characterization of one of the top-ranked ESKAPE-enriched dark components revealed that it belongs to the beta-barrel fold DUF1302 (PF06980) family, for which no experimentally solved three-dimensional structure exists in the PDB. The genomic context analysis indicates that it is co-localized with a LuxR-type transcriptional regulator. Collectively, ECLIPSE identifies evolutionarily conserved, structurally defined, and functionally dark proteins enriched across ESKAPE pathogens; these dark proteins can further be utilized as alternative antimicrobial targets for experimental characterization. AVAILABILITY AND IMPLEMENTATION: The source code and dataset are available for free at: Github: https://github.com/surabhilata/ECLIPSE.git, Zenodo: DOI: 10.5281/zenodo.21064323.

Proteome↗

PubMed1995

Luigi Rolando and his pioneering efforts to relate structure to function in the nervous system.

The fissure separating the motor from the sensory cortex and the substantia gelatinosa capping the posterior horn of the spinal cord are still known by the name of the Italian anatomist Rolando, Luigi Rolando was born in Turin, Italy, in 1773 and died in 1831. His life was not easy, the first of his problems being the death of his father when Rolando was still very young. Three people were to be influential in his life and career: Father Maffei, his maternal uncle who raised him; Dr. Cigna, the anatomy professor who discovered his talent; and Dr. Anformi, a general practitioner who introduced him to the practice of medicine and to the best circles of the city. Forced to leave Turin by the Napoleonic invasion of the country, Rolando first stopped in Florence, where he learned about anatomical dissection, drawing, and engraving and studied the appearance of nervous tissue under the microscope. Later he went to Sardinia where, although cut off from European cultural circles, he developed his major theories. Rolando pioneered the idea that brain functions could be differentiated and located in specific areas and discovered the fixed pattern of cerebral convolutions, highlighting motor and sensory gyri. He demonstrated the complexity of the central gray matter of the spinal cord, describing the "substantia gelatinosa," and he deduced that nervous structures are connected in a network of nervous fibers linked by electrical impulses. Rolando had to struggle for recognition, however, as the priority of his discoveries was challenged by the almost contemporaneous work of Gall and Spurzheim on cerebral localization and of Flourens on cerebellar function. Nevertheless, his efforts contributed greatly to the clarification of brain function. His observations on nervous anatomy have been especially accurate, as shown by the nomenclature "fissure of Rolando."

History, 19th Century↗

PubMed2002

Cardiac tissue engineering.

Recent progress in implantations of differentiated cardiac and non-cardiac cells as well as adult stem cells into the heart suggests that the irreversible loss of viable cardiac myocytes that occurs during myocardial infarction can be at least partly substituted. We evaluated an alternative approach by reconstituting cardiac tissue grafts in vitro and implanting them as spontaneously and coherently contracting tissues. For this purpose we have optimized a method to generate ring-shaped three-dimensional engineered heart tissue (EHT) in vitro from neonatal rat cardiac myocytes. When subjected to isometric force measurements in organ baths, electrically stimulated EHTs exhibit a Frank-Starling behavior, a positive inotropic response to increases in extracellular calcium, a positive inotropic and lusitropic response to isoprenaline, and a negative inotropic response to the muscarinic agonist carbachol ('accentuated antagonism'). Twitch tension under maximal calcium amounts to 1-2 mN/ mm2. Importantly, passive (resting) tension is low, yielding a ratio of active/passive tension of approximately 1.5 under basal and 14 under maximal calcium. Morphologically, EHTs represent a highly interconnected three-dimensional network of cardiac myocytes resembling loose cardiac tissue with a high fraction of binucleated cardiac myocytes, strong eosin staining and elongated centrally located nuclei. Electron microscopy demonstrated well developed sarcomeric structures, T-tubules, SR vesicles, T-tubule-SR-junctions, all types of intercellular connective structures, and a basement membrane. Thus, EHTs comprise functional and morphological properties of intact, ventricular myocardium. First implantation experiments of EHTs in the peritoneum of Fischer 344 rats showed that EHTs survived for at least 14 days, maintained a network of differentiated cardiac myocytes, and were strongly vascularized. Thus, EHTs may serve as material for a novel tissue replacement approach.

Animals↗

PubMed2005

Secrets of a double agent: CDK7 in cell-cycle control and transcription.

In metazoans, cyclin-dependent kinase 7 (CDK7) has essential roles in both the cell-division cycle and transcription, as a CDK-activating kinase (CAK) and as a component of the general transcription factor TFIIH, respectively. Controversy over its double duty has been resolved, but questions remain. First, how does CDK7 achieve the dual substrate specificity necessary to perform both roles? Second, is there a deeper connection implied by the dichotomy of CDK7 function, for example similar mechanisms controlling cell division and gene expression, and/or actual coordination of the two processes? Enzymological studies have revealed solutions to the unusual substrate recognition problem, and there is evidence that the distinct functions of CDK7 can be regulated independently. Finally, despite divergence in their wiring, the CAK-CDK networks of budding yeast, fission yeast and metazoans all link transcriptional regulation with operation of the cell-cycle machinery. This connection might help to ensure that mRNAs encoding effectors of cell division are expressed at the right time in the cycle.

Animals↗

PubMed2000

Interaction between metabolism and flow in tendon and muscle.

Blood vessels supplying the musculotendinous region of tendons, including interfibrillar connective tissue, represent a parallel vascular network to that supplying muscle fibers. Reciprocal control by vasomodulators and neural input determines relative flow in each network, and therefore relative supply of nutrients and hormones. Vessels supplying the tendon support fat cells and may function as a non-nutritive network within muscle groups to regulate resting muscle energy metabolism and to act as a flow reservoir for nutrient delivery in exercise.

Animals↗

PubMed2006

Weaker top-down modulation from the left inferior frontal gyrus in children.

Previous studies have shown that developmental changes in the structure and function of prefrontal regions can continue throughout childhood and adolescence. Our recent results suggested a role for the left inferior frontal cortex in modulating task-dependent shifts in effective connectivity when adults focus on orthographic versus phonological aspects of presented words. Specifically, the top-down influence of the inferior frontal cortex determined whether incoming word-form information from the fusiform gyrus would have a greater impact on the parietal areas involved in orthographic processing or temporal areas involved in phonological processing (Bitan, T., Booth, J.R., Choy, J., Burman, D.D., Gitelman, D.R. and Mesulam, M.-M., 2005. Shifts of Effective Connectivity within a Language Network during Rhyming and Spelling. J. Neurosci. 25, 5397-5403.). In the current study, we find that children displayed an identical pattern of task-dependent functional activations within this network. In comparison to adults, however, children had significantly weaker top-down modulatory influences emanating from the inferior frontal area. Adult language processing may thus involve greater top-down cognitive control compared to children, resulting in less interference from task-irrelevant information.

Adult↗

PubMed2004

Clathrin adaptor epsinR is required for retrograde sorting on early endosomal membranes.

Retrograde transport links early/recycling endosomes to the trans-Golgi network (TGN), thereby connecting the endocytic and the biosynthetic/secretory pathways. To determine how internalized molecules are targeted to the retrograde route, we have interfered with the function of clathrin and that of two proteins that interact with it, AP1 and epsinR. We found that the glycosphingolipid binding bacterial Shiga toxin entered cells efficiently when clathrin expression was inhibited. However, retrograde transport of Shiga toxin to the TGN was strongly inhibited. This allowed us to show that for Shiga toxin, retrograde sorting on early/recycling endosomes depends on clathrin and epsinR, but not AP1. EpsinR was also involved in retrograde transport of two endogenous proteins, TGN38/46 and mannose 6-phosphate receptor. In conclusion, our work reveals the existence of clathrin-independent and -dependent transport steps in the retrograde route, and establishes a function for clathrin and epsinR at the endosome-TGN interface.

Adaptor Proteins, Vesicular Transport↗

PubMed2005

The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.

Dihydrodipicolinate synthase (DHDPS) mediates the key first reaction common to the biosynthesis of (S)-lysine and meso-diaminopimelate. The activity of DHDPS is allosterically regulated by the feedback inhibitor (S)-lysine. The crystal structure of DHDPS from Escherichia coli has previously been published, but to only a resolution of 2.5 A, and the structure of the lysine-bound adduct was known to only 2.94 A resolution. Here, the crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from E. coli are presented to 1.9 and 2.0 A, respectively, resolutions that allow, in particular, more accurate definition of the protein structure. The general architecture of the active site is found to be consistent with previously determined structures, but with some important differences. Arg138, which is situated at the entrance of the active site and is thought to be involved in substrate binding, has an altered conformation and is connected via a water molecule to Tyr133 of the active-site catalytic triad. This suggests a hitherto unknown function for Arg138 in the DHDPS mechanism. Additionally, a re-evaluation of the dimer-dimer interface reveals a more extensive network of interactions than first thought. Of particular interest is the higher resolution structure of DHDPS with (S)-lysine bound at the allosteric site, which is remote to the active site, although connected to it by a chain of conserved water molecules. (S)-Lysine has a slightly altered conformation from that originally determined and does not appear to alter the DHDPS structure as others have reported.

Allosteric Site↗

PubMed1995

Cooperative effects of neuronal ensembles.

Electrophysiological properties of neurons as the basic cellular elements of the central nervous system and their synaptic connections are well characterized down to a molecular level. However, the behavior of complex noisy networks formed by these constituents usually cannot simply be derived from the knowledge of its microscopic parameters. As a consequence, cooperative phenomena based on the interaction of neurons were postulated. This is a report on a study of global network spike activity as a function of synaptic interaction. We performed experiments in dissociated cultured hippocampal neurons and, for comparison, simulations of a mathematical model closely related to electrophysiology. Numeric analyses revealed that at a critical level of synaptic connectivity the firing behavior undergoes a phase transition. This cooperative effect depends crucially on the interaction of numerous cells and cannot be attributed to the spike threshold of individual neurons. In the experiment a drastic increase in the firing level was observed upon increase of synaptic efficacy by lowering of the extracellular magnesium concentration, which is compatible with our theoretical predictions. This "on-off" phenomenon demonstrates that even in small neuronal ensembles collective behavior can emerge which is not explained by the characteristics of single neurons.

Animals↗

PubMed2005

The meaning of mammalian adult neurogenesis and the function of newly added neurons: the "small-world" network.

Adult neurogenesis has been observed in mammalian brain including human but a question remains: how do new neurons become functional in the adult brain? We propose that the random addition of only a few new neurons functions as a maintenance system for the brain's "small-world" networks. In popular parlance, the small-world network phenomenon is described by the concept of "six degrees of separation", which postulates that everyone in the world is connected to everyone else through a chain of at most six mutual acquaintances. Randomly added to an orderly network, new links enhance signal propagation speed and synchronizability. Newly generated neurons are ideally suited to become such links: they are immature, form more new connections compared to mature ones, and their number but not their precise location may be maintained by continuous proliferation and dying off. Similarly, we envisage that the treatment of brain pathologies by cell transplantation would also create new random links in small-world networks and that even a small number of successfully incorporated new neurons may be functionally important.

Adult↗

PubMed1997

Steroid hormones and excitability in the mammalian brain.

Adrenocortical and gonadal steroid hormones can pass the blood-brain barrier and bind to intracellular receptors in the brain. In addition to steroid hormones binding to intracellular steroid receptors, metabolites of these steroids and steroid hormones produced in the brain (neurosteroids) are thought to bind to membrane recognition sites. Actions mediated by the intracellular receptors are generally delayed in onset and are of prolonged duration, whereas the hormones binding to membrane recognition sites induce fast effects. Both fast and delayed actions by steroid hormones potentially alter the electrical properties of neuronal membranes and thus the firing patterns of neurons carrying receptors for the hormones. We here review the fast and delayed actions by steroid hormones on single cell electrical properties in the mammalian nervous system. In general, fast effects by corticosteroids-presumably mediated by membrane receptors-induce inhibitory effects on cellular firing, although regional differences seem to exist. Delayed effects by corticosteroid hormones via mineralocorticoid receptors serve to maintain or enhance fast transmission in the brain, while modulatory inputs are suppressed. By contrast, corticosteroids acting through glucocorticoid receptors suppress transmission carried by amino acids, particularly when the activity is elevated in comparison to resting level; modulatory inputs are enhanced. Prolonged activation of glucocorticoid receptors can implicate the integrity of neuronal circuits by allowing considerable influx of calcium ions during depolarization. Of the gonadal hormones, estradiol mainly exerts excitatory actions, in both a rapid and a delayed mode. Progesterone on the other hand is predominantly inhibitory, usually with a short delay in onset. The effect of androgens on neuronal excitability has not yet been studied in great detail. Finally, neurosteroids and A-ring reduced steroids in general induce rapid effects on firing patterns, probably by acting on ligand gated ion channels. The diverse actions of steroid hormones on single cell activity have consequences for the excitability in local circuits in which these cells participate. This is illustrated in this review for two processes that depend on circuit rather than single cell function, i.e., long term potentiation and epilepsy. The diverging character of steroid hormones with regard to the time frame, space, and nature of their effects is also reflected in the functional processes that are linked to the activity of the networks responding to steroids. In this way steroid hormones add an essentially new aspect to the regulation of functional processes in the brain, during physiological conditions but also when networks are implicated during diseases and disorders. Future research on steroid modulation of cellular excitability will gain considerably from attempts to either link the changed excitability to the underlying molecular events or study the effects on cellular activity in close connection with behavioral functions.

Animals↗

PubMed1999

Matrilin-2, a large, oligomeric matrix protein, is expressed by a great variety of cells and forms fibrillar networks.

Matrilin-2 is a member of the protein superfamily with von Willebrand factor type A-like modules. Mouse matrilin-2 cDNA fragments were expressed in 293-EBNA cells, and the protein was purified, characterized, and used to immunize rabbits. The affinity-purified antiserum detects matrilin-2 in dense and loose connective tissue structures, subepithelial connective tissue of the skin and digestive tract, specialized cartilages, and blood vessel walls. In situ hybridization of 35S-labeled riboprobes localizes the matrilin-2 mRNA to fibroblasts of dermis, tendon, ligaments, perichondrium, and periosteum; connective tissue elements in the heart; smooth muscle cells; and epithelia and loose connective tissue cells of the alimentary canal and respiratory tract. RNA blot hybridization and immunoblotting revealed both matrilin-2 mRNA and protein in cultures of a variety of cell types, confirming the tissue distribution. Alternative splicing affects a module unique for matrilin-2 in all of the above RNA sources. SDS-polyacrylamide gel electrophoresis and electron microscopy reveals matrilin-2 from tissue extracts and cell line cultures as a mixture of mono-, di-, tri-, and tetramers. Matrilin-2 is substituted with N-linked oligosaccharides but not with glycosaminoglycans. Because of other, yet unidentified, cell-type dependent posttranslational modifications, the monomer is heterogeneous in size. Immunofluorescence showed that matrilin-2 functions by forming an extracellular, filamentous network.

Animals↗

PubMed2005

The self-trapping attractor neural network--part II: properties of a sparsely connected model storing multiple memories.

In a previous paper, the self-trapping network (STN) was introduced as more biologically realistic than attractor neural networks (ANNs) based on the Ising model. This paper extends the previous analysis of a one-dimensional (1-D) STN storing a single memory to a model that stores multiple memories and that possesses generalized sparse connnectivity. The energy, Lyapunov function, and partition function derived for the 1-D model are generalized to the case of an attractor network with only near-neighbor synapses, coupled to a system that computes memory overlaps. Simulations reveal that 1) the STN dramatically reduces intra-ANN connectivity without severly affecting the size of basins of attraction, with fast self-trapping able to sustain attractors even in the absence of intra-ANN synapses; 2) the basins of attraction can be controlled by a single free parameter, providing natural attention-like effects; 3) the same parameter determines the memory capacity of the network, and the latter is much less dependent than a standard ANN on the noise level of the system; 4) the STN serves as a useful memory for some correlated memory patterns for which the standard ANN totally fails; 5) the STN can store a large number of sparse patterns; and 6) a Monte Carlo procedure, a competitive neural network, and binary neurons with thresholds can be used to induce self-trapping.

Algorithms↗