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PubMed2003

Evolution of RNA virus in spatially structured heterogeneous environments.

A hallmark of the infectious cycle for many RNA viruses parasitizing multicellular hosts is the need to invade and successfully replicate in tissues that comprise a variety of cell types. Thus, multicellular hosts represent a heterogeneous environment to evolving viral populations. To understand viral adaptation to multicellular hosts, we took a double approach. First, we developed a mathematical model that served to make predictions concerning the dynamics of viral populations evolving in heterogeneous environments. Second, the predictions were tested by evolving vesicular stomatitis virus in vitro on a spatially structured environment formed by three different cell types. In the absence of gene flow, adaptation was tissue-specific, but fitness in all tissues decreased with migration rate. The performance in a given tissue was negatively correlated with its distance to the tissue hosting the population. This correlation decreased with migration rate.

Adaptation, Biological↗

PubMed2005

Highwire function at the Drosophila neuromuscular junction: spatial, structural, and temporal requirements.

Highwire is a huge, evolutionarily conserved protein that is required to restrain synaptic growth and promote synaptic transmission at the Drosophila neuromuscular junction. Current models of highwire function suggest that it may act as a ubiquitin ligase to regulate synaptic development. However, it is not known in which cells highwire functions, whether its putative ligase domain is required for function, or whether highwire regulates the synapse during development or alternatively sets cell fate in the embryo. We performed a series of transgenic rescue experiments to test the spatial, structural, and temporal requirements for highwire function. We find that presynaptic activity of highwire is both necessary and sufficient to regulate both synapse morphology and physiology. The Highwire RING domain, which is postulated to function as an E3 ubiquitin ligase, is required for highwire function. In addition, highwire acts throughout larval development to regulate synaptic morphology and function. Finally, we show that the morphological and physiological phenotypes of highwire mutants have different dosage and temporal requirements for highwire, demonstrating that highwire may independently regulate the molecular pathways controlling synaptic growth and function.

Animals↗

PubMed1992

[Intracomplex alkylation of octanucleotide pd(TGTTTGGC) by a 5'-(4-N-methyl-N-(2-chloroethyl)-amino)benzylphosphamide derivative of heptanucleotide pd(CCAAACA). Preparation of a covalent adduct and study of its spatial structure in an aqueous solution by two-dimensional (1)H-NMR spectroscopy].

Covalent adduct--the product of intracomplex alkylation at N-3-position of dC-8-nucleoside residue of target octanucleotide pd[TGTTTGGC] was completely synthesized by means of 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5'-phosphamido derivative of heptanucleotide pd[CCAAACA]. Its melting temperature was shown to be 70 degrees C. Tm did not depend on covalent adduct concentration and was by 40 degrees C higher than that for unmodified duplex pd[TGTTTGGC].pd[CCAAACA] at concentration of 0.5 x 10(-4) M. The spatial structure of the covalent adduct in aqueous solution was investigated by two-dimensional 3H-NMR spectroscopy. The assignment of oligonucleotide protons as well as protons of a modifying group was carried out using COSY, COSY-DQF and NOESY experiments. Conformational analysis of proton-proton coupling constants for H1', H2'a, H2'b and H3' protons showed the sugar residues to be in 2'-endo conformation. Analysis of NOE connectivities observed between the protons of the alkylating group and oligonucleotide protons yielded conclusion, regarding the 4-[N-methyl-N-(2-chloroethyl)amino]benzylamido 5'-residue being localized in the region of the lacked nucleoside residue of the heptanucleotide chain about 5 A apart from the dC-1 residue and from cytosine base of the alkylated dC-8 residue.

Alkylation↗

PubMed1998

Spatial structure of the M3 transmembrane segment of the nicotinic acetylcholine receptor alpha subunit.

The three-dimensional structure of a synthetic peptide corresponding to the putative transmembrane segment M3 (amino acid residues 277-301) of the alpha subunit of the nicotinic acetylcholine receptor from Torpedo californica has been studied by means of two-dimensional 1H-NMR spectroscopy in a chloroform/methanol (1:1) mixture containing 0.1 M LiClO4. Complete resonance assignment has been performed using double-quantum-filtered COSY (DQF-COSY), TOCSY and NOESY spectra. The spatial structure has been calculated using the Diana program on the basis of integrated intensities of NOESY spectra. HN-C(alpha)H and HC(alpha)-C(beta)H spin-spin coupling constants. Residues 279-297 of M3 form a right-handed helix (root mean square deviation is 0.032 nm for backbone atoms and 0.088 nm for all heavy atoms). The conformations of the 17 side chains have been unambiguously determined. The obtained structure is in accord with the photolabeling pattern of the membrane nicotinic acetylcholine receptor (nAChR) which suggests alpha-helical structure of M3 in the labeled portion [Blanton, M. P. & Cohen, J. B. (1994) Biochemistry 33, 2859-2872].

Amino Acid Sequence↗

PubMed2006

Colloidal aggregation phenomena: Spatial structuring of TEOS-derived silica aerogels.

In this contribution, the homogeneity of silica aerogels made from tetraethyl orthosilicate (TEOS) was studied by means of Fourier transform infrared (FTIR) and 29Si nuclear magnetic resonance (NMR) spectroscopies. FTIR spectra show a slight difference in the asymmetric Si-O-Si stretching vibration frequency in the outer and inner part of the aerogels. According to the 29Si NMR data, a higher relation Q4/Q3 was obtained in the inner parts of the gels compared with their outer parts, proving the difference in the cross linkage of the silica network. The obtained results are interpreted in terms of the specific spatial structuring of the colloidal suspensions due to the presence of gravity.

Journal Article↗

PubMed2006

Patchy propagators, brain dynamics, and the generation of spatially structured gamma oscillations.

Propagator theory of brain dynamics is generalized to incorporate a new class of patchy propagators that enable treatment of approximately periodic structures such as are seen in the visual cortex. Complex response fields are also incorporated to allow for features such as orientation preference and wave-number selectivity. The results are applied to the corticothalamic system associated with the primary visual cortex. It is found that this system can generate gamma ( > or = 30 Hz) oscillations during stimulation, whose properties are consistent with experimental findings on gamma frequency and bandwidth, and existence of fine-scale spatial structure. It is found that a potential resonance is associated with each reciprocal lattice vector corresponding to periodic modulations of the propagators. It is found that the lowest resonances are the most likely to give rise to noticeable spectral peaks and increases of correlation amplitude, length, and time, and that these aspects are prominent only if the system is close to marginal stability, in accord with previous measurements and discussions of cortical stability. These features also enable gamma resonances to be stimulus-evoked, with substantial resonance sharpening for relatively small changes in mean neural firing rate. The results also imply dependence of gamma frequency on stimulus features.

Action Potentials↗

PubMed2006

Biased representations of the spatial structure of navigable environments.

Recent studies (e.g., Shelton & McNamara in Cognitive Psychology, 43(4), 274-310, 2001; Valiquette, McNamara, & Smith in Memory and Cognition, 31(3), 479-489, 2003) have demonstrated that judgments of relative direction (JRD) access a single enduring orientation-dependent allocentric representation of the layout of objects in an environment, regardless of whether the space is viewed from one or multiple vantage points. Two experiments tested the limits of this phenomenon. In both experiments participants learned the locations of objects in a large room from two views: one view was aligned with salient environmental frames of reference (edges of the mat on which objects were placed and walls of the enclosing room) and expected to be preserved in long-term memory; the other view was misaligned and not expected to be preserved in long-term memory. The first experiment demonstrated that performing JRD between studying the misaligned view and studying the aligned view did not result in the misaligned view being maintained in long-term memory. The second experiment demonstrated that after studying the layout extensively from the misaligned view, 30 s of exposure to the aligned view (with no instructions to learn the layout from that view) resulted in the aligned but not the misaligned view being preserved in long-term memory. These findings indicate that the human spatial memory and navigation system is strongly biased to represent the spatial structure of navigable environments with reference directions or axes that are aligned with salient environmental frames of reference.

Bias↗

PubMed1985

[Study of the spatial structure of a cyclic analog of bradykinin in solution by two-dimensional NMR spectroscopy].

H NMR resonances of [cyclo (9----18) Lys1, Gly6]bradykinin (CBK) in (CD3)2SO and H2O solution have been assigned by combined analysis of two-dimensional COSY and NOESY spectra. The presence of two slowly interchangeable conformers of CBK in (CD3)2SO is established, the minor conformer not exceeding 15% in the population. The minor conformer is absent from the aqueous solution, chemical shifts of the CBK and bradykinin NH and C alpha H protons differ insignificantly. The major CBK conformer contains at least two X-Pro trans-peptide groups and three amide protons NH Phe5, NH Arg9 and N zeta H Lys1 protected from solvent. A system of cross-peaks from the NOESY spectra of CBK in (CD3)2SO has been analysed and the maximum distance between backbone protons and neighbouring amino acid residues evaluated. The experimental data agree well with the assumed type II beta-bend in the sequence Pro2-Pro3-Gly4-Phe5. Spatial structure models for the backbone fragment 6-9 of CBK containing two intramolecular hydrogen bonds that involve the NH Arg9 and N zeta H Lys1 protons and the carbonyl groups of Phe5 and Gly4 are proposed.

Amino Acid Sequence↗

PubMed1984

[NMR study of the spatial structure of the Naja naja siamensis toxin 3].

The 300 and 500 MHz 1H NMR spectra of a long-chain neurotoxin, toxin 3 Naja naja siamensis (S-T3), its derivatives and close homolog, toxin 3 Naja naja naja (N-T3), have been analyzed. A combination of double resonance, difference spectroscopy and usage of a series of toxin S-T3 derivatives acetylated or trifluoroacetylated at lysine residues allowed to assign the signals from all aromatic protons and a number of signals in the aliphatic region, and to elucidate the microenvironment of certain functionally important residues. Analysis of chemical shifts pH-dependences in the 1H and 19F NMR spectra of toxin S-T3 and its trifluoroacetylated congeners delineated a considerable region of the neurotoxin molecule affected by the conformational transition, with the midpoint at pH 5,4, between two states. This conformational transition is induced by protonation of His22 and is accompanied by a change in the accessibility of its imidazole ring for the solvent, along with the alteration of the distance between the side chains of functionally important Lys27 and Lys53 residues. According to EPR data (-196 degrees) for the respective S-T3 derivative having spin labels at Lys27 and Lys53 epsilon-amino groups, the inter-label distance increases from 18 A at pH 7,5 to 23 A at pH 3,5. Notwithstanding this conformational change, the totality of the obtained results evidences in favor of considerable similarity of the toxin S-T3 spatial structure in the solution and crystalline state.

Acetylation↗

PubMed1996

Structural characterization of extracellular ribonuclease of Bacillus polymyxa: amino acid sequence determination and spatial structure prediction.

The primary structure of extracellular Bacillus polymyxa ribonuclease (RNase Bpo) was established by mass spectroscopy analysis and automatic Edman degradation of the individual peptides obtained from protein digestion with Glu-specific protease V8. RNase Bpo consists of 111 amino acid residues, with a relative molecular weight of 12 607. RNase Bpo is a close structural homolog of RNases of B. amyloliquefaciens (RNase Ba) and B. intermedius (RNase Bi), the similarity of their primary structures being 68%. Molecular modelling of the structure of the complex of RNase Bpo with substrate analog d(CGAC) was performed and a spatial model based on the known crystal structure of RNase Ba complex with the corresponding nucleotide was constructed using the methods of interactive computer graphics and energy minimization. The differences in the primary and tertiary structures of the enzymes were analyzed in order to understand the substrate specificity of Bacillus RNases.

Amino Acid Sequence↗

PubMed2005

Generalized spatial structural equation models.

It is common in public health research to have high-dimensional, multivariate, spatially referenced data representing summaries of geographic regions. Often, it is desirable to examine relationships among these variables both within and across regions. An existing modeling technique called spatial factor analysis has been used and assumes that a common spatial factor underlies all the variables and causes them to be related to one another. An extension of this technique considers that there may be more than one underlying factor, and that relationships among the underlying latent variables are of primary interest. However, due to the complicated nature of the covariance structure of this type of data, existing methods are not satisfactory. We thus propose a generalized spatial structural equation model. In the first level of the model, we assume that the observed variables are related to particular underlying factors. In the second level of the model, we use the structural equation method to model the relationship among the underlying factors and use parametric spatial distributions on the covariance structure of the underlying factors. We apply the model to county-level cancer mortality and census summary data for Minnesota, including socioeconomic status and access to public utilities.

Bayes Theorem↗

PubMed1992

Hierarchical geometric constraint networks as a representation for spatial structural knowledge.

A representation is proposed for capturing generic spatial knowledge about classes of objects in a structural hierarchy of biology. The basic premise is that spatial properties such as shape and relative relationships can be expressed as networks of interacting constraints. The representation is defined, partial implementations that demonstrate practical utility are described for model based organ and protein structure determination, and research issues are presented that must be solved before the representation can be implemented in its entirety. As these issues are resolved the representation will find increasing utility as the foundation for a spatial knowledge base of structural biology.

Computer Simulation↗

PubMedDate not supplied

[The functional organization of the spatial structures of the neuronal receptive fields in field 21 of the cat cerebral cortex].

In result study of structural organization of neural receptive fields (RFs) and their different zones on the prestriate cortex level was shown that neural RFs in this area have hypercomplex structure and consist of some spatial different excitatory zones. Orientation and velocity selectivity and spatial-frequency characteristics of the excitatory zones of the same RF may differ between zones. The number of zones in RFs correlate with RF sizes: the more RF size the more zones number in them (r = 0.05, P < 0.02). About 66% of zones in RFs have approximately identical sizes (12-16 deg) and sizes those zones an dependence as from their number in RFs (r = 0.03, P > 0.05) as from the eccentricity (r = 0.3, P > 0.05). Zones in RF were distributed so that distance their centres was between 56-65 degrees (an average across all 60 degrees). If two or three zones were tested simultaneously the neuron changed own frequency and orientation tuning. Consequently the functional organization of neural RFs of prestriate cortex depend upon number simultaneously tested zones in spatial information processing. Was shown that important properties of prestriate cortex neurons is their ability to integrate and complex processing of spatial information across wide area of the visual field; in the prestriate cortex thus violate of straight retinotopical representation principle of visual field, characteristics of all investigated areas of visual system. The results represented in this review allow suppose that the structural and functional unit of cortex which make integration of spatial information from different compose this information is prestriate cortex neurons and not is no striate cortex modules. Consequently combined of neurons which make images description from different parts of visual field out of dependence of cortical area in turn integrate in neuron networks. Is known that neurons of any level have characteristics different of (from) characteristics of other levels visual system. The interaction of different elements of visual system form ultrastructure of RFs and their different zones in prestriate cortex, and ensure function of networks. So just on prestriate cortex neurons level appear whole system of surrounding world universe system of connections from different cortical areas which is morphological and functional base in process of spatial information integration RFs which have the central and peripheral representation.

Animals↗

PubMedDate not supplied

[From determination of amino acid residue conformation to reconstruction of the spatial structure of proteins (from the data of nuclear Overhauser enhancement spectroscopy].

A new approach to the calculation of the spatial protein structure based on the joint utilization of the theoretical conformational analysis method and nuclear Overhauser enhancement (NOE) spectroscopy data is proposed and verified. The quality in determining various molecule structural parameters is estimated in terms of the expected NOE spectral parameters derived from the X-ray analysis data of the avian pancreatic polypeptide. The proposed approach is shown to correctly determine such structural parameters of protein molecules as local amino acid residue conformations, reciprocal spatial orientation of the C alpha atoms neighbouring along amino acid sequence and reapproached segments of the polypeptide chain. Spatially remote molecule fragments are mainly responsible for the error in determining structural parameters.

Amino Acids↗

PubMed1988

Mathematical modelling of intercellular regulation causing the formation of spatial structures in bacterial colonies.

Bacterial colonies may grow forming stable spatial, particularly circular, structures. For instance, motile bacteria Proteus vulgaris or Escherichia coli grown on agar under certain conditions may form concentric rings with the centre in the inoculation point (Rüss-Münzer, 1935, Bact. Parasit Kde (Abt 1) 7, 214; Budriené, 1985, Dokl. Acad. Nauk SSR, 283, 470). A similar picture can be observed in a different situation, i.e. when a lawn of non-motile Salmonella typhimurium bacteria is cultivated on a solid agar with the locally introduced substrate (Hoppensteadt & Jäger, 1980, Lecture Notes in Biomath. 38, 68). This paper describes a mechanism of bacterial interactions through a hypothetical mediator released by the organisms. A mathematical model has been built. Its analysis has shown that the selected laws of secretion and reception of the mediator can adequately account for the formation of circular structures in the case of both motile and non-motile bacteria.

Animals↗

PubMed2005

A spatially structured metapopulation model with patch dynamics.

Metapopulation models that incorporate both spatial and temporal structure are studied in this paper. The existence and stability of equilibria are provided, and an extinction threshold condition is derived which depends on patch dynamics (patch destruction and creation) and metapopulation dynamics (patch colonization and extinction). These results refine threshold conditions given by previous metapopulation models. By comparing landscapes with different spatial heterogeneities with respect to weighted long-term patch occupancies, we conclude that the pattern of a landscape is of overwhelming importance in determining metapopulation persistence and patch occupancy. We show that the same conclusion holds when a rescue effect is considered. We also derive a stochastic differential equations (SDE) model of the Itô type based on our deterministic model. Our simulations reveal good agreement between the deterministic model and the SDE model.

Animals↗

PubMed2005

Genetic spatial structure of European common hamsters (Cricetus cricetus)--a result of repeated range expansion and demographic bottlenecks.

The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15,000-10,000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85,000-147,000 bp. Expansion times fall during the last glaciation (115,000-10,000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50,000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains--core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.

Animals↗

PubMed1984

[Dominant and reciprocal relationships in the organization of the spatial structure of the biopotential correlations of the brain].

The factor analysis of correlation coefficients of brain potentials spatial-temporal structure revealed the "leading constellations" of neural centers in the coordination system for activity of the human brain hemispheres in resting as well as in functional loads; the reciprocity in organization of potential oscillations in the frontal and occipital brain areas, the reciprocal interrelationships being more obvious in the dominant hemisphere. This factor was shown to depend on the level of activation of the subjects even in a functional state unaltered in respect to other EEG indices. When expecting stimuli demanding a left-hand response, a rearrangement of spontaneous dominant interrelationships to the advantage of the right hemisphere occurs in the EEG.

Adult↗