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A discrete map for the dynamics of recurrent excitatory neural networks in the presence of noise.

We investigate the effect of the neuron characteristics on the behavior of a recurrent excitatory neural network model. First, we present the different types of dynamics obtained with simulations of a network of coupled excitatory spike-response neuron models placed under the influence of noise. Then, we derive a discrete map describing the dynamics of large fully connected networks. By studying the bifurcation structure of this map, we can determine for which ranges of the neuron model parameters the network will display collective oscillations or other types of dynamics.

Action Potentials↗

PubMed2000

Two-dimensional pulsed TRIPLE at 95 GHz

The one-dimensional (1D) pulsed TRIPLE resonance experiment, introduced by Mehring et al. (M. Mehring, P. Hofer, and A. Grupp, Ber. Bunseges. Phys. Chem. 91, 1132-1137 (1987)) is a modification of the standard Davies ENDOR experiment where an additional RF pi-pulse is applied during the mixing time. While the first RF pulse is set to one of the ENDOR transitions, the frequency of the second RF pulse is scanned to generate the TRIPLE spectrum. The difference between this spectrum and the ENDOR spectrum yields the difference TRIPLE spectrum, which exhibits only ENDOR lines that belong to the same M(S) manifold as the one selected by the first RF pulse. We have extended this experiment in two dimensions (2D) by sweeping the frequencies of both RF pulses. This experiment is particularly useful when the spectrum is congested and consists of signals originating from different paramagnetic centers. The connectivities between the peaks in the 2D spectrum enable a straightforward assignment of the signals to their respective centers and M(S) manifolds, thus providing the relative signs of hyperfine couplings. Carrying out the experiment at high fields has the additional advantage that nuclei with different nuclear gyromagnetic ratios are well separated. This is particularly true for protons which appear at significantly higher frequencies than other nuclei. The feasibility and effectiveness of the experiment is demonstrated at W-band (94.9 GHz) on a crystal of Cu(2+)-doped l-histidine. Homonuclear (1)H-(1)H, (14)N/(35)Cl-(14)N/(35)Cl and heteronuclear (1)H-(14)N/(35)Cl 2D TRIPLE spectra were measured and from the various connectivities in the 2D map the (1)H, (14)N, and (35)Cl signals that belong to two different Cu(2+) centers were identified and grouped according to their M(S) manifolds. Copyright 2000 Academic Press.

Journal Article↗

PubMed2000

Human PRRX1 and PRRX2 genes: cloning, expression, genomic localization, and exclusion as disease genes for Nager syndrome.

In this study, we extend our examination of the function of the Prrx1 (a.k.a Mhox, Prx1, K-2, and Pmx1) as well as Prrx2 (a.k.a. S8 and Prx2) genes by characterizing the expression of the human orthologs and their potential for causing specific human malformations. The expression pattern of PRRX2 and its close relative, PRRX1, were analyzed in human tissue by RT-PCR. Although the expression of these human genes is similar to their mouse orthologs, there are notable differences in expression. PRRX2 was detected in the human kidney and lung, whereas in mice and chickens neither of these tissues has been reported to express Prrx2. For PRRX1 the expression pattern was quite similar to other vertebrates, but the ratio of the two isoforms was reversed. To begin the search for the gene-disease connection, both genes were mapped to human chromosomes by FISH. The PRRX1 locus maps to 1q23, whereas the PRRX2 locus maps to 9q34.1. This localization, along with the recently described phenotypes of the gene-targeted Prrx1, Prrx2 and double mutant mice, enabled us to search the human disease databases for similar malformations. This examination suggested that mutations at the PRRX1 and/or PRRX2 loci could result in Nager Acrofacial Dysostosis (NAFD) syndrome. We obtained DNA samples from eight patients with NAFD, as well as two patients with Miller syndrome, and analyzed them for mutations in the PRRX1 and PRRX2 genes. The data excludes mutations in the presumed coding sequences of these genes from causing NAFD.

Abnormalities, Multiple↗

PubMed1985

Hand and hemispace effects in tactual tasks in children.

In Experiment I, 3-and 5-yr-old dextrals matched textures better by either hand when it operated in left hemispace. Girls and 3-yr olds were the more disadvantaged by non-alignment of hand and hemispace. In Experiment II, 8-yr-olds reproduced finger sequences; dextrals demonstrated a right-hand and sinistrals a right-hemispace superiority. In Experiment III, both a left-hand and a left-hemispace superiority appeared when 5-yr-old dextrals reproduced a static configuration of finger spacing. Asymmetries were generally stronger for the side of presentation than for the side of response. Our findings are consistent with the operation of two semi-independent systems, one involving hand-hemisphere connections, and the other mapping of extracorporeal space by the hemispheres.

Age Factors↗

PubMed2004

Quantitative methods for ecological network analysis.

The analysis of networks of ecological trophic transfers is a useful complement to simulation modeling in the quest for understanding whole-ecosystem dynamics. Trophic networks can be studied in quantitative and systematic fashion at several levels. Indirect relationships between any two individual taxa in an ecosystem, which often differ in either nature or magnitude from their direct influences, can be assayed using techniques from linear algebra. The same mathematics can also be employed to ascertain where along the trophic continuum any individual taxon is operating, or to map the web of connections into a virtual linear chain that summarizes trophodynamic performance by the system. Backtracking algorithms with pruning have been written which identify pathways for the recycle of materials and energy within the system. The pattern of such cycling often reveals modes of control or types of functions exhibited by various groups of taxa. The performance of the system as a whole at processing material and energy can be quantified using information theory. In particular, the complexity of process interactions can be parsed into separate terms that distinguish organized, efficient performance from the capacity for further development and recovery from disturbance. Finally, the sensitivities of the information-theoretic system indices appear to identify the dynamical bottlenecks in ecosystem functioning.

Animals↗

PubMed2004

Modeling of submicrometer aerosol penetration through sintered granular membrane filters.

We present a deep-bed aerosol filtration model that can be used to estimate the efficiency of sintered granular membrane filters in the region of the most penetrating particle size. In this region the capture of submicrometer aerosols, much smaller than the filter pore size, takes place mainly via Brownian diffusion and direct interception acting in synergy. By modeling the disordered sintered grain packing of such filters as a simple cubic lattice, and mapping the corresponding 3D connected pore volume onto a discrete cylindrical pore network, the efficiency of a granular filter can be estimated, using new analytical results for the efficiency of cylindrical pores. This model for aerosol penetration in sintered granular filters includes flow slip and the kinetics of particle capture by the pore surface. With a unique choice for two parameters, namely the structural tortuosity and effective kinetic coefficient of particle adsorption, this semiempirical model can account for the experimental efficiency of a new class of "high-efficiency particulate air" ceramic membrane filters as a function of particle size over a wide range of filter thickness and texture (pore size and porosity) and operating conditions (face velocity).

Journal Article↗

PubMed2004

Assessment of lichen diversity by index of atmospheric purity (IAP), index of human impact (IHI) and other environmental factors in an urban area (Grenoble, southeast France).

An assessment of air quality in the Grenoble area was made using the index of atmospheric purity (IAP). The survey area was divided into 198 units (0.7 x 1 km), in which 345 average lichen relevés were analyzed according to the Braun-Blanquet method. Each relevé station was characterized in the field by a subjective index of human impact (IHI) calculated according to four local environmental parameters influencing the epiphytic lichen flora: urbanization (urban, suburban or rural area), road traffic (low or high), local developments (stations located within crop fields, green areas, housing sites or car parks), and exposure (trees isolated, in rows or grouped). Eighty-three epiphytic lichen species and two algae were recorded and grouped into three ecological categories defined according to bark type and nutrient needs: nitrophytic, neutrophytic and acidophytic species. IAP values, varying from 5.9 to 71.7, were clustered into five categories in order to produce an air-quality map. The geographical pattern of the IAP map showed no clear connection with local sources of pollution, such as the vicinity of a road or an industrial plant, and was not correlated with annual mean values of SO(2), NO(2) and NO for the years 1994-1997. IAP appeared to be influenced by environmental artificiality as shown by a polynomial trend observed between IAP and IHI, even if IAP values were broadly scattered. Multivariate analysis (canonical correspondence) showed that high IAP values could be observed in stations of "natural" environments at high elevations and in stations of "artificial" environments at low elevations. It was also shown that IAP varied in relation to the relative proportion of ecological groups of lichen relevés: although a majority of neutrophytic species (>50%) with a much lower percentage of nitrophytic species generally characterized high IAP, a predominance of acidophytic or nitrophytic species led to a decrease in the IAP. A correlation between nitrophytic species and artificiality of the environment was also shown. Furthermore, IAP, initially created to characterize atmospheric pollution or atmospheric purity by means of the lichen flora, is shown to be influenced by other parameters such as environmental and landscape factors.

Air Pollutants↗

PubMed2005

The RNA of turnip yellow mosaic virus exhibits icosahedral order.

Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses.

Crystallization↗

PubMed2001

Nucleus accumbens, entorhinal cortex and latent inhibition: a neural network model.

A neural network model of classical conditioning (Schmajuk, Lam, and Gray, J. Exp. Psychol.: Anim. Behav. Process, 22, 1996, 321-349) is applied to the description of the neural substrates of latent inhibition. Experimental data suggest that latent inhibition might be controlled by a circuit that involves the hippocampus, the entorhinal cortex, the nucleus accumbens, and the mesolimbic dopaminergic projection from the ventral tegmental area to the accumbens. By mapping different nodes and connections in the model onto this brain circuit, computer simulations demonstrate that, in most cases, the model provides a good quantitative description of: (1) the impairment of latent inhibition by lesions of the shell of the nucleus accumbens; (2) the restoration of latent inhibition by haloperidol following lesions of the shell; (3) the preservation of latent inhibition by lesions of the core of the nucleus accumbens; (4) the facilitation of latent inhibition by combined shell core lesions and by core lesions with extended conditioning; (5) the impairment of latent inhibition following lesions of the entorhinal cortex or the hippocampus; and (6) the restoration of latent inhibition by haloperidol following lesions of the entorhinal cortex and ventral subiculum. In addition, the model is able to describe neural activity in the nucleus accumbens.

Animals↗

PubMed1995

Mapping light-dependent structural changes in the cytoplasmic loop connecting helices C and D in rhodopsin: a site-directed spin labeling study.

All 20 single cysteine substitution mutants in the sequence Y136-M155 of bovine rhodopsin have been prepared and modified with a sulfhydryl-specific nitroxide reagent. This sequence contains the C-D interhelical loop, a transducin interaction site. The accessibilities of the attached nitroxides to collisions with paramagnetic probes in solution were determined, and the electron paramagnetic resonance spectra were analyzed, both in the dark and after photoexcitation. Accessibility data show that the rhodopsin polypeptide crosses an aqueous/hydrophobic boundary near V138 and H152. The nitroxide mobilities inferred from the spectra are consistent with a model where the C helix extends to at least residue C140, with much of the helix surface in contact with protein rather than lipid near the cytoplasmic surface of the membrane. Upon photoexcitation, electron paramagnetic resonance spectral changes are observed at sites on the putative C helix surface that are in contact with the protein and at specific sites in the C-D interhelical loop. A simple interpretation of these results is that photoexcitation involves a rigid body movement of the C helix relative to the others in the helix bundle.

Amino Acid Sequence↗

PubMed2002

The role of the specificity-determining loop of the integrin beta subunit I-like domain in autonomous expression, association with the alpha subunit, and ligand binding.

Integrin beta subunits contain a highly conserved I-like domain that is known to be important for ligand binding. Unlike integrin I domains, the I-like domain requires integrin alpha and beta subunit association for optimal folding. Pactolus is a novel gene product that is highly homologous to integrin beta subunits but lacks associating alpha subunits [Chen, Y., Garrison, S., Weis, J. J., and Weis, J. H. (1998) J. Biol. Chem. 273, 8711-8718] and a approximately 30 amino acid segment corresponding to the specificity-determining loop (SDL) in the I-like domain. We find that the SDL is responsible for the defects in integrin beta subunit expression and folding in the absence of alpha subunits. When transfected in the absence of alpha subunits into cells, extracellular domains of mutant beta subunits lacking SDL, but not wild-type beta subunits, were well secreted and contained immunoreactive I-like domains. The purified recombinant soluble beta1 subunit with the SDL deletion showed an elongated shape in electron microscopy, consistent with its structure in alphabeta complexes. The SDL segment is not required for formation of alpha5beta1, alpha4beta1, alphaVbeta3, and alpha6beta4 heterodimers, but is essential for fomation of alpha6beta1, alphaVbeta1, and alphaLbeta2 heterodimers, suggesting that usage of subunit interface residues is variable among integrins. The beta1 SDL is required for ligand binding and for the formation of the epitope for the alpha5 monoclonal antibody 16 that maps to loop segments connecting blades 2 and 3 of beta-propeller domain of alpha5, but is not essential for nearby beta-propeller epitopes.

Amino Acid Sequence↗

PubMed2004

Doing without schema hierarchies: a recurrent connectionist approach to normal and impaired routine sequential action.

In everyday tasks, selecting actions in the proper sequence requires a continuously updated representation of temporal context. Previous models have addressed this problem by positing a hierarchy of processing units, mirroring the roughly hierarchical structure of naturalistic tasks themselves. The present study considers an alternative framework, in which the representation of context depends on recurrent connections within a network mapping from environmental inputs to actions. The ability of this approach to account for human performance was evaluated by applying it, through simulation, to a specific everyday task. The resulting model learned to deal flexibly with a complex set of sequencing constraints, encoding contextual information at multiple time scales within a single, distributed internal representation. Degrading this representation led to errors resembling those observed both in everyday behavior and in apraxia. Analysis of the model's function yielded numerous predictions relevant to both normal and apraxic performance.

Cognition↗

PubMed2006

Using mating designs to uncover QTL and the genetic architecture of complex traits.

Analysis of quantitative trait loci (QTL) affecting complex traits is often pursued in single-cross experiments. For most purposes, including breeding, some assessment is desired of the generalizability of the QTL findings and of the overall genetic architecture of the trait. Single-cross experiments provide a poor basis for these purposes, as comparison across experiments is hampered by segregation of different allelic combinations among different parents and by context-dependent effects of QTL. To overcome this problem, we combined the benefits of QTL analysis (to identify genomic regions affecting trait variation) and classic diallel analysis (to obtain insight into the general inheritance of the trait) by analyzing multiple mapping families that are connected via shared parents. We first provide a theoretical derivation of main (general combining ability (GCA)) and interaction (specific combining ability (SCA)) effects on F(2) family means relative to variance components in a randomly mating reference population. Then, using computer simulations to generate F(2) families derived from 10 inbred parents in different partial-diallel designs, we show that QTL can be detected and that the residual among-family variance can be analyzed. Standard diallel analysis methods are applied in order to reveal the presence and mode of action (in terms of GCA and SCA) of undetected polygenes. Given a fixed experiment size (total number of individuals), we demonstrate that QTL detection and estimation of the genetic architecture of polygenic effects are competing goals, which should be explicitly accounted for in the experimental design. Our approach provides a general strategy for exploring the genetic architecture, as well as the QTL underlying variation in quantitative traits.

Animals↗

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↗

PubMed1996

A pathogen-specific epitope inserted into recombinant secretory immunoglobulin A is immunogenic by the oral route.

Oral administration of rabbit secretory IgA (sIgA) to adult BALB/c mice induced IgA+, IgM+, and IgG+ lymphoblasts in the Peyer's patches, whose fusion with myeloma cells resulted in hybridomas producing IgA, IgM, and IgG1 antibodies to the secretory component (SC). This suggests that SC could serve as a vector to target protective epitopes into mucosal lymphoid tissue and elicit an immune response. We tested this concept by inserting a Shigella flexneri invasin B epitope into SC, which, following reassociation with IgA, was delivered orally to mice. To identify potential insertion sites at the surface of SC, we constructed a molecular model of the first and second Ig-like domains of rabbit SC. A surface epitope recognized by an SC-specific antibody was mapped to the loop connecting the E and F beta strands of domain I. This 8-amino acid sequence was replaced by a 9-amino acid linear epitope from S. flexneri invasin B. We found that cellular trafficking of recombinant SC produced in mammalian CV-1 cells was drastically altered and resulted in a 50-fold lower rate of secretion. However, purification of chimeric SC could be achieved by Ni2+-chelate affinity chromatoraphy. Both wild-type and chimeric SC bound to dimeric IgA, but not to monomeric IgA. Reconstituted sIgA carrying the invasin B epitope within the SC moiety triggers the appearance of seric and salivary invasin B-specific antibodies. Thus, neo-antigenized sIgA can serve as a mucosal vaccine delivery system inducing systemic and mucosal immune responses.

Administration, Oral↗

PubMed1998

Cholesterol depletion of caveolae causes hyperactivation of extracellular signal-related kinase (ERK).

Previously we showed that activation of Erk in quiescent cells occurs in the caveolae fraction isolated from fibroblasts. Since the structure and function of caveolae is sensitive to the amount of cholesterol in the membrane, it might be that a direct link exists between the concentration of membrane cholesterol and mitogen-activated protein (MAP) kinase activation. We acutely lowered the cholesterol level of the caveolae fraction by incubating Rat-1 cells in the presence of either cyclodextrin or progesterone. Cholesterol-depleted caveolae had a reduced amount of several key protein components of the MAP kinase complex, including Ras, Grb2, Erk2, and Src. Incubation of these cells in the presence of epidermal growth factor (EGF) caused a rapid loss of EGF receptor from the caveolae fraction, but the usual recruitment of c-Raf was markedly inhibited. Despite the reduced amount of c-Raf and Erk2 in the cholesterol-depleted caveolae fraction, EGF caused a hyperactivation of the remaining caveolae Erk isoenzymes. This was followed by an increase in the amount of active Erk in the cytoplasm. The increased amount of activated Erk produced under these conditions was linked to a 2-fold higher level of EGF-stimulated DNA synthesis. Even cholesterol depletion by itself stimulated Erk activation and DNA synthesis. These results suggest that the MAP kinase pathway can connect the cholesterol level of caveolae membrane to the control of cell division.

Animals↗

PubMed2000

A novel topology model of the human Na(+)/H(+) exchanger isoform 1.

The membrane topology of the human Na(+)/H(+) exchanger isoform 1 (NHE1) was assessed by substituted cysteine accessibility analysis. Eighty-three cysteine residues were individually introduced into a functional cysteineless NHE1, and these mutants were expressed in the exchanger-deficient PS120 cells. The topological disposition of introduced cysteines was determined by labeling with a biotinylated maleimide in the presence or absence of preincubation with the membrane-impermeable sulfhydryl reagent, 2-trimethylammoniumethyl-methanethiosulfonate in streptolysin O-permeabilized or nonpermeabilized cells. We proposed a new model for the topology of NHE1 that is significantly different from the model derived from hydropathy analysis. In this model, NHE1 is composed of 12 transmembrane segments (TMs) with the N and C termini located in the cytosol. The large, last extracellular loop in the membrane domain of the original model was suggested to comprise an intracellular loop, a new transmembrane segment (TM11), and an extracellular loop in the new model. Interestingly, cysteines at 183 and 184 and at 324 and 325 mapped to intracellular loops connecting TMs 4 and 5 (IL2) and TMs 8 and 9 (IL4), respectively, were accessible to sulfhydryl reagents from the outside. Furthermore, exchange activities of two mutants, R180C and Q181C, within IL2 were markedly inhibited by external MTSET. These data suggest that part of IL2 or IL4 may be located in a pore-lining region that is accessible from either side of the membrane and involved in ion transport.

Amino Acid Sequence↗

PubMed1976

A guide to the synaptic analysis of the neuropil.

A morphological analysis of the organization of the gray matter in the central nervous system depends on the discovery of consistent repetitive patterns. Without these, the gray matter remains a chaotic jungle. An hypothesis derived from the study of a few simple regions has been developed to serve as a guide in finding these patterns. It states that all nerve fibers and terminals arising from a particular group of nerve cells, or, more precisely, a particular nerve cell type, display similar axoplasmic configurations despite variations in size and shape of the terminations. This hypothesis is reminiscent of the so-called Dale's principle that a nerve cell makes use of the same transmitter at all of its branches or terminations. These apparent rules of uniformity or congruity merely reflect the functional integrity of the nerve cell and the role of its parts in the nervous system. But as an hypothesis, it needs to be tested, and it needs to be tested anew in each region, since exceptions to the assumed rule can be expected. It is therefore proposed as the first working hypothesis in each new region. If it should prove to be true in general, it will facilitate and rationalize the analysis of the gray matter, as it has already done in the cerebellar cortex and the deep cerebellar nuclei. If it should prove to be false in a few regions, the analysis will become more difficult, and additional modes of marking nerve endings will have to be used. Experimental methods for identifying nerve terminals can be translated from the light microscopic to the electron microscopic level, but there are significant drawbacks at both levels: lack of precision, destruction of fibers of passage, and rapid evolution of the degenerative process may greatly restrict their usefulness. Labeling with tritiated amino acids or transmitters, or with horseradish peroxidase, provide new methods for tracing interneuronal connections at the electron microscopic level. These have the advantages of high specificity, nondestructiveness and a physiological mode of selective marking. However, they do not offer a solution to the problem of short-range connections. For these, careful reconstructions of serial sections may prove necessary, as Sjöstrand (1974) has demonstrated in a remarkable paper on the retina. The aim of all these methods is to discover patterns of synaptic connectivity in order to map the cellular organization of the nervous system. In the foregoing, nothing was said about synapses other than those articulating axons with somata or dendrites and their appendages. Clearly the same principles of recognition apply to axo-axonal and dendro-dendritic synapses. Although the synapses that have been considered here are chemical synapses, the same questions regarding the identity of the partners in electrotonic junctions must be asked as well.

Amino Acids↗