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Results for “spatial structure”

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PubMed1994

Spatial and temporal response properties of residual vision in a case of hemianopia.

Residual vision in subjects with damage of the primary visual cortex (striate cortex) has been demonstrated in many previous studies and is taken to reflect the properties of known subcortical and extrastriate visual pathways. In this report we describe psychophysical experiments carried out on a subject clinically blind in half of his visual field (i.e. homonymous hemianopia) caused by striate cortex damage. They reveal the existence of two distinct channels mediating such vision. One channel responds to spatial structure and the other to light flux changes. The spatially tuned channel has a peak response at about 1.2 cycles per degree and shows rapid loss of sensitivity at both high and low spatial frequencies. This channel does not respond to diffuse illumination. The light flux channel, however, responds only to sudden increments in light flux levels on the retina and shows extensive spatial summation. Both channels require transient inputs, with a peak sensitivity at about 10 cycles per second and show virtually complete attenuation at temporal frequencies below 2 cycles per second. The spatiotemporal characteristics of these two channels account for much of the reported limits of visual performance attributed to subcortical or extrastriate pathways in some patients, and especially for their relatively good sensitivity for the detection of abrupt, transient stimuli or fast-moving targets. A new method is also applied to the measurement of the amount of light scatter in the eye. The measurements show that light scatter into the sighted hemifield could not account for the results obtained with the stimuli used to characterized the residual vision of this subject.

Accidents, Traffic↗

PubMed2002

Harmonic forcing of an extended oscillatory system: homogeneous and periodic solutions.

In this paper we study the effect of external harmonic forcing on a one-dimensional oscillatory system described by the complex Ginzburg-Landau equation (CGLE). For a sufficiently large forcing amplitude, a homogeneous state with no spatial structure is observed. The state becomes unstable to a spatially periodic "stripe" state via a supercritical bifurcation as the forcing amplitude decreases. An approximate phase equation is derived, and an analytic solution for the stripe state is obtained, through which the asymmetric behavior of the stability border of the state is explained. The phase equation, in particular the analytic solution, is found to be very useful in understanding the stability borders of the homogeneous and stripe states of the forced CGLE.

Journal Article↗

PubMed2005

The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases.

Peptidases are classical objects of enzymology and structural studies. However, a few protein families with experimentally characterized proteolytic activity, but unknown catalytic mechanism and three-dimensional structures, still exist. Using comparative sequence analysis, we deduce spatial structure for one of such families, namely, U40, which contains just one P5 protein from bacteriophage phi-6. We show that this singleton sequence possesses conserved sequence motifs characteristic of lysozymes and is a distant homolog of lytic transglycosylases that cleave bacterial peptidoglycan. The structure of the P5 protein is therefore predicted to adopt the lysozyme-like fold shared by T4, lambda, C-type, G-type lysozymes, and lytic transglycosylases. Since previous biochemical experiments with P5 of phi-6 have indicated that the purified enzyme possesses endopeptidase activity and not glycosidase activity, our results point to the possibility of a newly evolved molecular function and call for further experimental characterization of this unusual P5 protein.

Amino Acid Sequence↗

PubMed1992

[Conformational aspects of the biological effect of functional fragments of the p21ras oncoprotein family. 2. Fragment 1-16, various sequences].

The conformational analysis data on active ([Val12-Gly13], [Asp12-Gly13] and [Gly12-Asp13]) and passive ([Gly12-Gly13] and [Pro12-Gly13]) modifications of the p21ras family oncoproteins are presented. The activating amino acid substitutions are shown to be accompanied by essential changes in the secondary structure, resulted in the 9-16 fragment spiralization. The spatial structure of the 1-9 fragment does not vary for all the predominant forms of the active and passive analogues. The results of the conformational analysis have been used for studying the structural-functional relationships.

Amino Acids↗

PubMed1996

Cytonuclear genetic structure of a hybrid zone in lizards of the Sceloporus grammicus complex (Sauria, Phrynosomatidae).

Lizards of the Sceloporus grammicus complex are comprised of multiple chromosome races that form several zones of parapatric hybridization in central Mexico. We scored diagnostic mitochondrial DNA (mtDNA) haplotypes and autosomal chromosome markers in a sample of 342 lizards from one well-defined zone between 2n = 34 and 2n = 46 races. A two-part analysis was performed on this data set in an attempt to infer the predominant evolutionary forces shaping the cytonuclear structure of this zone. The complications posed by its spatial structure were addressed by analysing a hierarchical series of smaller subsamples chosen to approximate single mating units. Two critical conclusions were drawn from this first-stage analysis. First and foremost, the three chromosomes have largely concordant cytonuclear disequilibrium patterns within each subsample with adequate numbers of individuals for detecting nonrandom cytonuclear associations. This suggests that the cytonuclear structure of this zone is predominantly a result of deterministic genome-wide forces rather than genetic drift of deterministic forces specific to individual chromosomes or loci. Second, the fit of a series of migration models to the data shows that the cytonuclear structure of the subsamples is well accounted for by continued gene flow from the two parental races alone, with random mating with respect to cytonuclear genotype and no other evolutionary forces. These results motivate several further empirical and theoretical investigations to refine our understanding of the relative roles of migration and other potentially important forces such as natural selection and genetic drift, in this and other hybrid zones.

Animals↗

PubMed1991

[Structure-functional studies of polymyxins. (1)-NMR analysis of polymyxin B and M conformation].

Spatial structures of two polymyxin antibiotics are compared by means of one- and two-dimensional 1H NMR spectroscopy. Cyclic parts of polymyxins B and M contain a system of hydrogen bonds including two beta-turns, however, the analysis of coupling constants 3JHN-C alpha H demonstrated that torsional angles phi of peptide bonds of the residues forming beta-turns in polymyxin M depend on the type of the anion. An increase in lability of the polymyxin M cyclic part in comparison with polymyxin B correlated with the selective cleavage of the peptide bond Dab8-Dab9 of this antibiotic with subtilisin. A similar correlation was found for a short analogue of polymyxin B, a cycloheptapeptide.

Magnetic Resonance Spectroscopy↗

PubMedDate not supplied

[Cytosol aspartate aminotransferase from the chicken heart: three-dimensional structure at 2.8 angstroms resolution and the characteristic conformation of various enzyme forms].

The spatial structure of cytosolic chicken aspartate aminotransferase (AAT) has been determined by X-ray crystallographic analysis at 2.8 A resolution. AAT consists of two chemically identical subunits. Each subunit can be subdivided into the large pyridoxal phosphate (PLP) binding domain and the small domain. The two active sites of AAT are situated in deep clefts at the subunit interface. The binding of PLP and 2-oxoglutarate is described. Conformations of the following enzyme forms have been compared by difference Fourier syntheses: the nonliganded PLP-form in phosphate and acetate buffers; the non-liganded pyridoxamine phosphate (PMP) form; complexes of the PLP-form with glutarate and 2-oxoglutarate. Lattice-induced dynamic asymmetry of the dimeric AAT molecules was revealed. In one subunit the small domain is mobile and shifted either toward the active site ("closed" conformation) or in the opposite direction ("open" conformation). The closed conformation is induced by the binding of dicarboxylate anions. In the second subunit the small domain is immobile and shifted toward the active site in all enzyme forms or complexes studied. In this subunit, there occurs a rotation of the PLP ring by approximately 20 degrees toward the substrate site. The rotation is observed when crystals are soaked in 0.6 saturated (NH4)2SO4 solution buffered with 0.3 M potassium phosphate, pH 7.5; it was explained by formation of an external aldimine between PLP and NH3. This aldimine is not formed in the presence of dicarboxylates or acetate. It was inferred that dicarboxylate or acetate anions stabilize the internal PLP-lysine aldimine and prevent its reaction with ammonia. Conversion of AAT from the PLP- to PMP-form is accompanied by rotation of the coenzyme ring by approximately 20 degrees; the rotation occurs in both subunits.

Animals↗

PubMed2001

AL2CO: calculation of positional conservation in a protein sequence alignment.

MOTIVATION: Amino acid sequence alignments are widely used in the analysis of protein structure, function and evolutionary relationships. Proteins within a superfamily usually share the same fold and possess related functions. These structural and functional constraints are reflected in the alignment conservation patterns. Positions of functional and/or structural importance tend to be more conserved. Conserved positions are usually clustered in distinct motifs surrounded by sequence segments of low conservation. Poorly conserved regions might also arise from the imperfections in multiple alignment algorithms and thus indicate possible alignment errors. Quantification of conservation by attributing a conservation index to each aligned position makes motif detection more convenient. Mapping these conservation indices onto a protein spatial structure helps to visualize spatial conservation features of the molecule and to predict functionally and/or structurally important sites. Analysis of conservation indices could be a useful tool in detection of potentially misaligned regions and will aid in improvement of multiple alignments. RESULTS: We developed a program to calculate a conservation index at each position in a multiple sequence alignment using several methods. Namely, amino acid frequencies at each position are estimated and the conservation index is calculated from these frequencies. We utilize both unweighted frequencies and frequencies weighted using two different strategies. Three conceptually different approaches (entropy-based, variance-based and matrix score-based) are implemented in the algorithm to define the conservation index. Calculating conservation indices for 35522 positions in 284 alignments from SMART database we demonstrate that different methods result in highly correlated (correlation coefficient more than 0.85) conservation indices. Conservation indices show statistically significant correlation between sequentially adjacent positions i and i + j, where j < 13, and averaging of the indices over the window of three positions is optimal for motif detection. Positions with gaps display substantially lower conservation properties. We compare conservation properties of the SMART alignments or FSSP structural alignments to those of the ClustalW alignments. The results suggest that conservation indices should be a valuable tool of alignment quality assessment and might be used as an objective function for refinement of multiple alignments. AVAILABILITY: The C code of the AL2CO program and its pre-compiled versions for several platforms as well as the details of the analysis are freely available at ftp://iole.swmed.edu/pub/al2co/.

Algorithms↗

PubMed1978

Studies on the structure of rat-liver polysomes by small-angle X-ray scattering.

The spatial structure of rat liver polysomes in dilute solution has been studied by the small-angle X-ray scattering technique. The distance between the mass centres of neighbouring ribosomes on the mRNA molecule is 35 nm, and the distance from next-but-one neighbour, about 55 nm. The spatial arrangement of the ribosomes on the polysome is compact; stretched configurations can be ruled out. The best model is a solenoid with six ribosomes per turn and a pitch of about 33 nm. The greatest diameter of a polysome with eight ribosomes is 130 nm, the radius of gyration 34 nm.

Animals↗

PubMed2003

Spatial mechanisms for coexistence of species sharing a common natural enemy.

We examine the conditions under which spatial structure can mediate coexistence of apparent competitors. We use a spatially explicit, host-parasitoid metapopulation model incorporating local dynamics of Nicholson-Bailey type and global dispersal. Depending on the model parameters, the resulting system displays a plethora of asynchronous dynamical behaviors for which permanent or transient coexistence is observed. We identify a number of spatially mediated tradeoffs which apparent competitors can utilize and demonstrate that the dynamics of spatial coexistence can typically be understood from consideration of two and three patch systems. The phase relationships of species abundances are different for our model than for some other mechanisms of spatial coexistence. We discuss the implications of our findings relative to issues of community organization and biological conservation.

Animals↗

PubMedDate not supplied

Immunological activity of new heterocyclic amides of 5-amino-3-methylisoxazole-4-carboxylic acid.

In the present study, some new amides of 5-amino-3-methylisoxazole-4-carboxylic acid were obtained. All new structures possessed markedly different groups of electron acceptor character, different spatial structure and they contained nitrogen heteroatom, enabling formation of salts and, at the same time, higher biological availability. They were examined for immunomodulating activity in comparison with cyclosporine A (CsA). We investigated effects of the compounds on the lipopolysaccharide (LPS)-induced production of tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) by human peripheral blood cells. Some compounds exhibited suppressory action which corresponded with increasing electronoacceptor nature of the amide substituent. Two compounds, characterized by flat aromatic rings, demonstrated quite different properties. Much higher activity was expressed by compounds which contained -NH group, the group which conditioned immunostimulatory activity in other compounds described previously.

Adjuvants, Immunologic↗

PubMed1987

The use of rotating checkerboard patterns in the treatment of amblyopia.

Sixty-four amblyopic children (mean age 7.5 years, age range 4-12 years) were subjected to treatment using slowly rotating patterns of different spatial frequencies. In 20 amblyopes square-wave gratings (spatial frequencies 0.26-16.84 c/deg), in 44 checkerboard-patterned structures (spatial frequencies 0.04-5.2 c/deg) were used for stimulation. The mean improvement of the distance visual acuity was significantly higher in the checkerboard-stimulated group (3.59 equidistant optotype lines) than in the grating-stimulated group (2.71). As the highest spatial frequency of the checkerboards was substantially lower than of gratings, the results cannot be explained in terms of optical qualities of the stimulating patterns. Other factors, such as short-term occlusion, accomplishment of demanding visuomotor tasks and the quality of cooperation and attentiveness of the patients are considered to be more important for the success of treatment.

Amblyopia↗

PubMedDate not supplied

Outline of chronohygiene.

Since chronotherapy already manipulates rhythmical functions, it is the important task of chronohygiene to outline the object of therapy i.e. health, from chronobiological points of view. Only on such a basis can chronohygiene be extended to the preventive provisions of health care and health education in regard to the biological time structure. Health can be characterized as an optimal state of harmonious time structure and its integration into the temporal orders of the environment. The circannual variations of an organism establish a seasonal risk cycle changing the inner preconditions of therapy as well. Moreover, chronohygiene must raise the question of whether the biological circannual rhythm is an integrating component of the human time organization, or if it may be levelled by civilization. Circadian variations of the organism not only modify the preconditions of therapy, but in particular those of activity and efficiency. The nocturnal maximum of functional economy normally is protected against exploitation by a simultaneous minimum of vigilance, which provides the nightly recovery. Therefore the destruction of this phase relationship by night-work must worsen recovery conditions. The disturbance of the time structure in the organism by night-work not only affects the circadian system, but faster rhythms as well. The phase position of the circadian rhythms is closely related to the individual responsiveness of the autonomous system as well as to the pulse-respiration-ratio. The latter can serve as a chronobiological criterion for evaluating suitability or risk of night- and shift-work. The effort of chronohygiene is based on the fact that disturbances of the time structure represent just a complementary aspect to disturbances of the spatial structure of the organism.

Biological Clocks↗

PubMed2005

Near-field nonuniformities in angularly multiplexed KrF fusion lasers with induced spatial incoherence.

Induced spatial incoherence (ISI) has been proposed for KrF laser drivers to achieve the high degree of spatial beam uniformity required for direct-drive inertial confinement fusion. Although ISI provides ultrasmooth illumination at the far field of the laser, where the target is located, it can still allow the beams in the quasi-near field to develop a time-averaged spatial structure. This speckle, which arises primarily from random-phase aberration, builds up as the laser beams propagate away from the pupil plane located at the final amplifier stage; it is distinct from any structure imposed by gain nonuniformities in the amplifiers. Because of the spatial incoherence, the speckle is significantly smaller than that experienced by coherent beams. Nevertheless, it remains a damage issue, especially for the long beam delay paths required in angularly multiplexed KrF lasers. We develop a novel algorithm for calculating the time-integrated intensities; compare simulations and measurements of the near-field speckle in the Nike KrF laser; and explore options, such as aberration reduction and optical relaying, for controlling the problem in future angularly multiplexed KrF drivers.

Journal Article↗

PubMedDate not supplied

Structural polymorphism of gramicidin A channels: ion conductivity and spectral studies.

The relation between the various spatial structures of the gramicidin A channels and their ionic conductance has been studied. For this aim, various conformations of the peptide were pre-formed in liposomal bilayer and after subsequent fusion of liposomes with planar lipid bilayer the measured channel conductance was correlated with gramicidin structures established in liposomes. To form the single-stranded pi 6.3 pi 6.3 helix the peptide and lipid were co-dissolved in TFE prior to liposome preparation. THF and other solvents were used to form parallel and antiparallel double helices. Conformation of gramicidin in liposomes made by various phosphatidylcholines was monitored by CD spectroscopy, and computer analysis of the spectra obtained was performed. After fusion of gramicidin containing liposomes with planar bilayer membranes from asolectin, the histograms of single-channel conductance were obtained. The histograms had one or three distinct peaks depending on the liposome preparation. Assignment of the structure of the channel to conductance levels was made by correlation of CD data with conductance histograms. The channel-forming analogue, des(Trp-Leu)2-gramicidin A, has been studied by the same protocol. The channel conductances of gramicidin A and the shortened analogue increase in the following order: antiparallel < parallel < pi 6.3 pi 6.3. Single-channels formed by double helices have higher dispersity of conductance than the pi 6.3 pi 6.3 helical channel. Lifetimes of the double helical and the pi 6.3 pi 6.3 helical channels are very close to each other. The data obtained were compared with theoretically predicted properties of double helices [1].

Amino Acid Sequence↗

PubMed1990

[Three-dimensional structure of the lipotropic active fragment of sea whale somatotropin].

Using semiempirical conformational analysis method, the spatial structure and conformational properties of the sea-whale somatotropin lipotropic action were investigated. The calculations were based on the fragmental analysis using non-valent, electrostatic interactions, torsional barriers and hydrogen bonds. The computer data suggest that this molecule can exist only in several low energy conformational states. The experimental results can be used for the analysis of structural-and-functional relationships.

Amino Acid Sequence↗

PubMed2001

Pattern formation and spatial self-entrainment in bistable chemical systems.

We describe the formation of spatial structures generated by diffusive instabilities in bistable systems. The coupling between the different spatial modes emanating from the two homogeneous steady states can then give rise to self-parametric instabilities favoring the occurrence of resonant rhombic or quasiperiodic structures such as superlattices or quasicrystalline patterns.

Journal Article↗

PubMed2006

Radial structure of Alfvén eigenmodes in the DIII-D tokamak through electron-cyclotron-emission measurements.

The spatial structure of toroidal Alfvén eigenmodes and reversed shear Alfvén eigenmodes in DIII-D is obtained from electron-cyclotron-emission measurements. Peak measured temperature perturbations are of similar magnitude for both toroidal Alfvén eigenmodes and reversed shear Alfvén eigenmodes and found to be deltaT(e)/T(e) approximately equal to 0.5%. Simultaneous measurements of density fluctuations using beam-emission spectroscopy indicate deltan(e)/n(e) approximately equal to 0.25%. Predictions of the measured temperature and density perturbation profiles as well as deltaT(e)/deltan(e) from the ideal magnetohydrodynamic code NOVA are in close agreement with experiment.

Journal Article↗