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PubMed1976

[Conformational heterogeneity of tRNA, detected in the reaction of guanine bases with ketoxal].

The study of kinetic characteristics of the reaction of tRNA guanine bases with kethoxal has shown that temperature, ionic strength and Mg2+ ions, i.e. factors directly affecting the spatial structure of tRNA, influence also on its internal modification. The modification degree under stabilized spatial tRNA structure depends also on the concentration of kethoxal and is expressed in fractional values of the number of modified guanosine residues per tRNA molecule, which indicates the heterogeneity of tRNA for the modification degree. Chromatography of tRNA1 Val preparation on BD cellulose after the exhaustive modification with kethoxal under conditions of stabilized spatial structure has revealed a fraction of molecules completely resistant to the modificator, and a fraction containing differently modified tRNA molecules. tRNA heterogeneity after the reaction with kethoxal (the presence of resistant and reactive forms) indicates conformational heterogeneity of tRNA, expressed in the simultaneous presence of at least two conformer families.

Aldehydes↗

PubMed1988

[Effect of structural changes in thyroxine-binding globulin on its biological activity and immunochemical properties].

Using spectroscopic, electrophoretic and microcalorimetric techniques, the changes in the spatial structure of human thyroxine-binding globulin (TBG) induced by exposure of protein solutions to high temperatures (45-90 degrees C) and low pH (2.5-6.0) were studied. Simultaneously the biological activity and immunoreactivity of TBG samples were measured. The structural changes were manifested at 52 degrees C or at pH 4.0 and were then aggravated with a rise in temperature or a decrease of pH. The circular dichroism spectra showed that the molecular ellipticity had a maximum decrease (by 10%) at 218-222 nm. In fluorescence spectra excitable at 280 nm the band half-width increased by 4-6 nm; their intensity decreased by 30-40%, whereas the position of the maxima did not change significantly. After addition of an equimolar amount of thyroxine to inactivated TBG the protein fluorescence was quenched by 25-40%. The electrophoregrams of treated preparations contained additional protein bands possessing no biological activity, whose mobility was less than that of native TBG. Microcalorimetric assays of native TBG revealed a thermoabsorption peak with a maximum at 62.5 degrees C and a half-width of 7.1 degrees C. The thermodynamic parameters of melting of TBG spatial structure were consistent with a model of a two-domain structure of the molecule. The biological activity and immunoreactivity of TBG showed a coordinated decrease with a rise in the degree of protein denaturation, However, the formation of TBG complex with antibodies did not screen the thyroxine-binding center of TBG and did not alter its affinity. Possible mechanisms of structural transition of TBG and its effect on the biological properties of TBG are discussed.

Binding Sites, Antibody↗

PubMed1998

Adaptive radiation in a heterogeneous environment.

Successive adaptive radiations have played a pivotal role in the evolution of biological diversity. The effects of adaptive radiation are often seen, but the underlying causes are difficult to disentangle and remain unclear. Here we examine directly the role of ecological opportunity and competition in driving genetic diversification. We use the common aerobic bacterium Pseudomonas fluorescens, which evolves rapidly under novel environmental conditions to generate a large repertoire of mutants. When provided with ecological opportunity (afforded by spatial structure), identical populations diversify morphologically, but when ecological opportunity is restricted there is no such divergence. In spatially structured environments, the evolution of variant morphs follows a predictable sequence and we show that competition among the newly evolved niche-specialists maintains this variation. These results demonstrate that the elementary processes of mutation and selection alone are sufficient to promote rapid proliferation of new designs and support the theory that trade-offs in competitive ability drive adaptive radiation.

Adaptation, Physiological↗

PubMed2004

The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens.

The evolution of ecological specialization is expected to carry a cost, due to either antagonistic pleiotropy or mutation accumulation. In general, it has been difficult to distinguish between these two possibilities. Here, we demonstrate that the experimental evolution of niche-specialist genotypes of the bacterium Pseudomonas fluorescens that colonize the air-broth interface of spatially structured microcosms is accompanied by pleiotropic fitness costs in terms of reduced carbon catabolism. Prolonged selection in spatially structured microcosms caused the cost of specialization to decline without loss of the benefits associated with specialization. The decline in the cost of specialization can be explained by either compensatory adaptation within specialist lineages or clonal competition among specialist lineages. These results provide a possible explanation of conflicting accounts for the cost of specialization.

Adaptation, Physiological↗

PubMed1981

Extrageniculostriate vision in the monkey. VIII. Critical structures for spatial localization.

Eight monkeys (Macaca mulatta) were trained on a spatial localization task before and after either total ablation of the striate cortices with partial damage to circumstriate cortices, complete colliculus removals, or combined ablations. The lesions were histologically verified. The task, given under normal room illumination, required the animals to reach for a target randomly placed in one of eight equal segments of a while disk located at arm's length. An apple cube, affixed to the center of the target, served as the reward for accurate reaching. A correct response consisted of an initial contact with either the target or the apple cube directly. The animal was trained sequentially to a criterion level of performance set at 90% correct responses over four 56-trial consecutive sessions using black disks of decreasing diameter (i.e., 90 mm, 55 mm, 35 mm, and 15 mm). Finally, only the apple cube, about 10 mm on a side, was presented. Four animals with complete or almost complete bilateral superior colliculus removals were unimpaired in their performances. The other four subjects with total striate cortex removals could be trained to reach accurately for all targets, but with marked deficits on the first and last tests, i.e., the 90 mm disk and the apple cube. When the striate cortex was ablated in the colliculectomized animals, they failed to attain a criterion level of performance in almost 6,000 trials. These results indicate that the superior colliculus is at least one structure that is critical for spatial localization in the absence of striate cortex, but it is not crucial for this capacity in the otherwise intact animal. In addition, the findings confirmed previous studies which showed that monkeys with total bilateral striatectomies could require the ability to execute accurate visually guided reaches. The present and earlier studies emphasize the primary importance of the geniculostriate system for the function explored and do not support a sharp dichotomy between two independent visual systems in the monkey.

Animals↗

PubMed1986

A study of systematic visual perseveration involving central mechanisms.

The subject of this investigation experiences vivid after-images which persist for tens of seconds following stimulation by light insufficiently intense to produce after-images in normal subjects. The after-images occur at all points in the visual field, and have spatial structure closely similar to that of the stimuli which elicit them, the only distortion being the absence of high (greater than or equal to 10 cycles X deg-1) spatial frequencies. The duration of the after image is dependent on the spatial structure and spectral content of the eliciting stimulus, being maximum for low, nonzero spatial frequencies (1-2 cycles X deg-1) and yellow or green wavelengths. The after-images appear 'khaki' or 'mustard-green' in colour, regardless of the spectral composition of the light stimulus, and those produced by flickering or moving targets do not themselves exhibit temporal fluctuations, although movement produces a streak along the path described by the moving object. After six weeks of treatment with the anticonvulsant drug, carbamazepine, the duration of the after-images fell by about 30%, but no further reduction occurred over the following three months. In spite of the prolonged after-images, the subject has normal sensitivity for detection of flicker and movement, but that for detection of a single flash is raised abnormally at low background illumination. Neither CT nor MRI brain scans revealed any abnormality. These responses are discussed in relation to those found in other subjects suffering visual perseveration or palinopsia, and we examine their possible causes.

Adult↗

PubMed2006

Pair-level approximations to the spatio-temporal dynamics of epidemics on asymmetric contact networks.

The process of infection during an epidemic can be envisaged as being transmitted via a network of routes represented by a contact network. Most differential equation models of epidemics are mean-field models. These contain none of the underlying spatial structure of the contact network. By extending the mean-field models to pair-level, some of the spatial structure can be contained in the model. Some networks of transmission such as river or transportation networks are clearly asymmetric, whereas others such as airborne infection can be regarded as symmetric. Pair-level models have been developed to describe symmetric contact networks. Here we report on work to develop a pair-level model that is also applicable to asymmetric contact networks. The procedure for closing the model at the level of pairs is discussed in detail. The model is compared against stochastic simulations of epidemics on asymmetric contact networks and against the predictions of the symmetric model on the same networks.

Communicable Diseases↗

PubMed1984

A simple method for the calculation of low energy packings of alpha-helices--a threshold approximation. I. The use of the method to estimate the effects of amino acid substitutions, deletions and insertions in globins.

A simple method is developed for computing low energy packings in alpha-helical proteins. This method is based on a simplified representation of a protein molecule in which the backbone of the alpha-helix is represented by a cylinder and the side chains of the amino acids by hard spheres. The energy function includes hydrophobic, electrostatic and Van der Waals' interactions. This method is used to compute low energy packings of an assembly of the alpha-helices of a globin molecule. The effect of mutations, deletions and insertions of a single amino acid resulting in drastic distortion of the spatial structure of sperm whale myoglobin was studied. The results demonstrated that these events can produce a breakdown of the spatial structure of the protein molecule.

Amino Acids↗

PubMed1989

The role of stimulus structure in spatial hyperacuity.

In spatial hyperacuity the subjects discriminate a stimulus feature relative to a reference, with an accuracy significantly better than the grain of the retinal mosaic. We show that the normalized thresholds have a dichotomous behavior; they are either insensitive to the spatial parameter in the experiment or increase very steeply with it. This behavior is explained by the involvement in the processing of pixel (receptor) accuracy information about the structure of the stimulus. A computational model employing optimal filtering reproduces the experimental data and suggests that processing of spatial hyperacuity tasks in the human visual system is optimal.

Computer Simulation↗

PubMedDate not supplied

[NMR spectroscopy for studying structure and intramolecular dynamics of modified analogs of steroid hormones].

Special features of the use of homo- and heteronuclear correlation methods of NMR in one and two dimensions for studying the spatial structure and intramolecular dynamics of modified analogues of steroid hormones (MASH) are considered. The application of these methods to the assignment of resonances in the high-field 1H NMR region and to the determination of the most stereospecifically important parameters, such as the vicinal constants of spin-spin coupling (3JH-H) and nuclear Overhauser effects (NOE), are discussed using the example of NMR studies of some estrogens and androgens at 300 MHz and on the basis of literature data. The most efficient combination of the methods and the necessary modification of each of them may be chosen considering the spectral and relaxation parameters of MASH in liquid medium, including the anisotropy of the overall diffusive motion. The characteristics of MASH are the wide use of correlations through long-range couplings (COSY-45 and DQF-COSY), the application of the 4,5JH-H constants for the determination of spatial structure, and the advantage of heteronuclear HSQC methods with and without 13C decoupling over the corresponding HMQC methods in both resolution and sensitivity. In the conformationally rigid MASH molecules, the anisotropy of the MASH diffusive motion in liquid adversely affects the determination of interproton distances by the calibrating processing method for the NOE difference and NOESY spectra: it results in both overestimated and underestimated distance values depending on the polar angle ratios of the reference and the determined distances. Under certain conditions, conformationally mobile MASH demonstrate the additional contribution of the scalar relaxation mechanism between the indirectly (scalarly) bound protons. This mechanism is responsible for the underestimated values of NOE and the corresponding errors in the distance determination.

Androgens↗

PubMed2003

Representation and constraints: the inverse problem and the structure of visual space.

Visual space can be distinguished from physical space. The first is found in visual experience, while the second is defined independently of perception. Theorists have wondered about the relation between the two. Some investigators have concluded that visual space is non-Euclidean, and that it does not have a single metric structure. Here it is argued (1) that visual space exhibits contraction in all three dimensions with increasing distance from the observer, (2) that experienced features of this contraction (including the apparent convergence of lines in visual experience that are produced from physically parallel stimuli in ordinary viewing conditions) are not the same as would be the experience of a perspective projection onto a frontoparallel plane, and (3) that such contraction is consistent with size constancy. These properties of visual space are different from those that would be predicted if spatial perception resulted from the successful solution of the inverse problem. They are consistent with the notion that optical constraints have been internalized. More generally, they are also consistent with the notion that visual spatial structures bear a resemblance relation to physical spatial structures. This notion supports a type of representational relation that is distinct from mere causal correspondence. The reticence of some philosophers and psychologists to discuss the structure of phenomenal space is diagnosed in terms of the simple materialism and the functionalism of the 1970s and 1980s.

Humans↗

PubMed2003

[Application of geostatistical analysis in study of macrophytes community's pattern].

In this paper, the Log-log semivariogram and theoretical models of Geostatistics and fractal theory were applied to study the mosaic spatial pattern of macrophytes community and its different characters on different scales in littoral zone of the Baoan Lake, Hubei Province. The macrophytes in the littoral zone with a square area of 25,600 m2, which was divided in to 1,024 grids, were investigated, and the macrophytes species in every grid were recorded. If the species was discovered in the grid, the variable of the grid had a value of 1, otherwise, it was 0. The community had a value of the total species discovered in the grid. By the method, the sampling results of Vallisneria spiralis, Ceratophyllum oryzetorum, Myriophyllum spicatum and the community were made into four worksheets. With help of the software GS+ for Windows to treat these worksheets, we got their log-log semivariogram, isotropic model, anisotropic model, isotropic fractal dimension and anisotropic fractal dimension. According to the results of isotropic models, the exponential models of Vallisneria spiralis and Myriophyllum spicatum indicated their contagious distribution with a high proportion of spatial structure, which indicated that their distribution changed lesser at microscale. In their range of 48.6 m and 34.2 m respectively, they had a spatial autocorrelation. Isotropic models of Ceratophyllum oryzetorum and the community were linear, and their proportions of spatial structure were low, indicating their great change at microscale and their moderate contagious distribution. The isotropic fractal dimension and anisotropic fractal dimension results indicated the dominant pattern of Vallisneria spiralis in the direction of NE-SW, the dominant patterns of Myriophyllum spicatum and Ceratophyllum oryzetorum in the direction of N-S, and the community's dominant pattern in the direction of NW-SE. Compared with other analysis tools, the method had advantages in deciding whether the community components had a spatial autocorrelation and in quantitatively classifying the aggregation density. It provides us a new way to quantitatively describe the pattern of the macrophytes community.

Fresh Water↗

PubMedDate not supplied

[Evolutionary conservatism of the molecular structure of gamma-crystallins of vertebrates].

Homology of 18 amino acid sequences of lens gamma-crystallins of several vertebrates: frog, mouse, rat, calf and human being--has been considered. Pair sequence homology varies in the range from 57 to 100%, the mean value is equal to 74%. The spatial structures have been determined only for two calf gamma-crystallins. The protein molecule consists of four-fold repeated "motifs" (patterns) which are joint in two domains. After comparison of 18 gamma-crystallin sequences it was found that "motifs" domains and whole protein molecules have about 10, 30 and 58% conservative residues, respectively, that seem to be related to the evolution of these structural units. Structure analysis shows that almost all the conservative residues have an important structural meaning and play a basic role in the domain and molecular structure organization. This result allows us to make a conclusion about the homology of spatial structures of all considered gamma-crystallins of vertebrates.

Amino Acid Sequence↗

PubMed2005

The impact of diffusion and stirring on the dynamics of interacting populations.

We investigate the combined effects of diffusion and stirring on the dynamics of interacting populations which have spatial structure. Specifically we consider the marine phytoplankton and zooplankton populations, and model them as an excitable medium. The results are applicable to other biological and chemical systems. Under certain conditions the combination of diffusion and stirring is found to enhance the excitability, and hence population growth of the system. Diffusion is found to play an important role: too much and initial perturbations are smoothed away, too little and insufficient mixing takes place before the reaction is over. A key time-scale is the mix-down time, the time it takes for the spatial scale of a population to be reduced to that of a diffusively controlled filament. If the mix-down time is short compared to the reaction time-scale, then excitation of the system is suppressed. For intermediate values of the mix-down time the peak population can attain values many times that of a population without spatial structure. We highlight the importance of the spatial scale of the initial disturbance to the system.

Animals↗

PubMed2000

The properties of the motion-detecting mechanisms mediating perceived direction in stochastic displays.

Previous studies [e.g. Baker & Hess, 1998. Vision Research, 38, 1211-1222] have shown that perceived direction in displays composed of multiple, limited-lifetime, Gabor micropatterns (G) is influenced by movement both at the fine spatial scale of the internal luminance modulation (first-order motion) and the coarse spatial scale of the Gaussian, contrast window (second-order motion). However it is presently indeterminate as to whether this pattern of results is indicative of the processes by which first-order and second-order motion signals interact within the visual system per se or those by which motion information, irrespective of how it is defined, is utilised across different spatial scales. To address this issue, and more generally the properties of the mechanisms that analyse motion in such displays, we employed stochastic motion sequences composed of either G, G added to a static carrier (G + C) or G multiplied with a carrier (G*C). Crucially G*C, unlike both G and G + C, micropatterns contain no net first-order motion and second-order motion only at the scale of the internal contrast modulation. For small displacements perceived direction in all cases showed a dependence on the internal sinusoidal spatial structure of the micropatterns and characteristic oscillations were typically observed, consistent with models in which first-order motion and second-order motion are encoded on the basis of similar low-level mechanisms. Importantly for larger displacements, and also when the internal spatial structure was randomised on successive exposures (so that motion at this spatial scale was unreliable), performance tended to be veridical for all types of micropattern, even though under these conditions displacements of the G*C micropatterns should have been invisible to current, low-level, motion-detecting schemes. This suggests that both low-level motion sensors and mechanisms utilising a different motion-detecting strategy such as high-level, attentive, feature-tracking may mediate perceptual judgements in stochastic displays.

Humans↗

PubMed2003

[Structures and spatial distribution patterns of dominant populations in Sycopsis sinensis community in Houhe Nature Reserve].

Based on the investigation data of 2 quadrats (1,600 m2 and 2,400 m2) in Houhe Nature Reserve, tree size class method was applied to analyze the structures of the dominant populations, and t-test of v/m ratio, mean crowing index, negative binomial parameter, patchiness index and Morisita index were applied to analyze the spatial distribution patterns of two dominant populations. The clumping degrees were also evaluated according to their size classes in different quadrats. The results showed that Sycopsis sinensis population was a declining population, dominated by IV trees and difficult to regenerate. In the population, the individual percentage of IV trees accounted for 79.4% in Q1 and 87.4% in Q2, and those of I trees and II trees were few. However, the population of Cyclobalanopsis axyodon was an growing one, and the individual percentages declined with the increasing size classes. The spatial distribution patterns of the two dominant populations distributed in clumps, but the clumping degrees existed diversity. With the increase of the size classes, the clumping degree of the population of Sycopsis sinensis intensified from random to clumping distribution, while that of the population of Cyclobalanopsis axyodon weakened from clumping to random distribution.

Conservation of Natural Resources↗

PubMed1993

Studies on fibronectin and its domains. II. Secondary structure and spatial configuration of fibronectin and of its domains.

Fibronectin (FN) from human plasma, as well as recombinant proteins derived from two of its major domains, the N-terminal fibrin-binding domain (FBD) and the cell-binding domain (CBD), were studied by circular dichroism (CD), Fourier transform infrared (FTIR), and fluorescence spectroscopies. Secondary structure estimations derived from both FTIR spectra and far uv CD indicate significant differences between FBD and CBD proteins. Thus, the CBD 33-kDa protein contains 80% beta-sheet and 20% beta-turns, whereas the three refolded FBD recombinant proteins studied, the 12-, 18.5-, and r31-kDa proteins, as well as the plasma-derived p31-kDa protein, all contain some percentage of aperiodic structure, ranging from 14 to 23% for both 31-kDa proteins, and between 33 and 46% for the smaller 12- and 18.5-kDa proteins. The amount of aperiodic structure increases drastically (from 23 to 67%) in a misfolded recombinant 31 kDa, the scrambled 31 kDa. Both native FN and a chimeric 45-kDa protein, consisting of both the FBD 12-kDa and the CBD 33-kDa proteins, were found to resemble the CBD 33-kDa protein itself, i.e., consisting only of beta-sheet and beta-turns and being free of aperiodic structure. These differences between two types of conformation are corroborated by the differences in the environment and spatial configuration of the aromatic amino acids of these proteins, as evidenced from near uv CD and intrinsic fluorescence spectroscopies. Thus, in the near uv CD the typical CBD proteins, i.e., the 33- and 45-kDa proteins display a maximum at 294 nm, whereas the FBD proteins, except for the scrambled 31-kDa protein, all have a characteristic strong negative peak at 300 nm. Similarly, the lambda max of the emission spectra of the whole FN and the 33- and 45-kDa proteins are characteristically blue-shifted (317-326 nm) and with high normalized intensity, when compared with the relatively red-shifted lambda max (338-340 nm) and low intensities of the folded FBD proteins. The scrambled 31-kDa protein again takes exception, having a relatively high normalized intensity due to misfolding. The two major conclusions from this work, attained by a combination of four spectroscopic methods, are: (a) functionally different FN domains, i.e., the FBD and CBD adopt totally different conformations, with the CBD having an almost exclusive beta structure; (b) the functional specificity of the various domains of FN may depend on subtle differences in the flexibility in their protein backbones, with the FBD being more flexible than the CBD.

Circular Dichroism↗

PubMed2004

Benthic diatom community response to environmental variables and metal concentrations in a contaminated bay adjacent to Casey Station, Antarctica.

This study examined the effects of anthropogenic contaminants and environmental variables on the composition of benthic diatom communities within a contaminated bay adjacent to an abandoned waste disposal site in Antarctica. The combination of geographical, environmental and chemical data included in the study explained all of the variation observed within the diatom communities. The chemical data, particularly metal concentrations, explained 45.9% of variation in the diatom communities, once the effects of grain-size and spatial structure had been excluded. Of the metals, tin explained the greatest proportion of variation in the diatom communities (28%). Tin was very highly correlated (R2>0.95) with several other variables (copper, iron, lead, and sum of metals), all of which explained similarly high proportions of total variation. Grain-size data explained 23% of variation once the effects of spatial structure and the chemical data had been excluded. The pure spatial component explained only 1.8% of the total variance. The study demonstrates that much of the compositional variability observed in the bay can be explained by concentrations of metal contaminants.

Antarctic Regions↗