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PubMed1999

Crystal structure of the complex formed between bovine beta-trypsin and MCTI-A, a trypsin inhibitor of squash family, at 1.8-A resolution.

The stoichiometric complex formed between bovine beta-trypsin and Momordica charantia, Linn. Cucurbitaceae trypsin inhibitor A (MCTI-A) was crystallized and its X-ray crystal structure was refined to a final R value of 0.179 using data of 7.0- to 1.8-A resolution. Combination with results on the complex of MCTI-A with porcine trypsin gives the sequence of MCTI-A definitely, of which 13 residues are conserved compared with other squash family trypsin inhibitors. Its spatial structure and the conformation of its primary binding segment from Cys3I (P3) to Glu7I (P3'), which contains a reactive scissile bond Arg5I C-Ile6I N, were found to be very similar to the other squash family proteinase inhibitors.

Amino Acid Sequence↗

PubMed1987

An evaluation of the two-dimensional Gabor filter model of simple receptive fields in cat striate cortex.

1. Using the two-dimensional (2D) spatial and spectral response profiles described in the previous two reports, we test Daugman's generalization of Marcelja's hypothesis that simple receptive fields belong to a class of linear spatial filters analogous to those described by Gabor and referred to here as 2D Gabor filters. 2. In the space domain, we found 2D Gabor filters that fit the 2D spatial response profile of each simple cell in the least-squared error sense (with a simplex algorithm), and we show that the residual error is devoid of spatial structure and statistically indistinguishable from random error. 3. Although a rigorous statistical approach was not possible with our spectral data, we also found a Gabor function that fit the 2D spectral response profile of each simple cell and observed that the residual errors are everywhere small and unstructured. 4. As an assay of spatial linearity in two dimensions, on which the applicability of Gabor theory is dependent, we compare the filter parameters estimated from the independent 2D spatial and spectral measurements described above. Estimates of most parameters from the two domains are highly correlated, indicating that assumptions about spatial linearity are valid. 5. Finally, we show that the functional form of the 2D Gabor filter provides a concise mathematical expression, which incorporates the important spatial characteristics of simple receptive fields demonstrated in the previous two reports. Prominent here are 1) Cartesian separable spatial response profiles, 2) spatial receptive fields with staggered subregion placement, 3) Cartesian separable spectral response profiles, 4) spectral response profiles with axes of symmetry not including the origin, and 5) the uniform distribution of spatial phase angles. 6. We conclude that the Gabor function provides a useful and reasonably accurate description of most spatial aspects of simple receptive fields. Thus it seems that an optimal strategy has evolved for sampling images simultaneously in the 2D spatial and spatial frequency domains.

Animals↗

PubMed2002

Predicting levels of stress from biological assessment data: empirical models from the Eastern Corn Belt Plains, Ohio, USA.

Interest is increasing in using biological community data to provide information on the specific types of anthropogenic influences impacting streams. We built empirical models that predict the level of six different types of stress with fish and benthic macroinvertebrate data as explanatory variables. Significant models were found for six stressor factors: stream corridor structure; siltation; total suspended solids (TSS), biochemical oxygen demand (BOD), and iron (Fe); chemical oxygen demand (COD) and BOD; zinc (Zn) and lead (Pb); and nitrate and nitrite (NOx) and phosphorus (P). Model R2 values were lowest for the siltation factor and highest for TSS, BOD, and Fe. Model R2 values increased when spatial relationships were incorporated into the model. The models generally performed well when applied to a random subset of the data. Performance was more mixed when models were applied to data collected from a previous time period, perhaps because of a change in the spatial structure of these systems. These models may provide a useful indication of the levels of different stresses impacting stream reaches in the Eastern Corn Belt Plains ecoregion of Ohio, USA. More generally, the models provide additional evidence that biological communities can serve as useful indicators of the types of anthropogenic stress impacting aquatic systems.

Animals↗

PubMedDate not supplied

[Effect of various humidity on local dynamic structure of lysozyme in a spin-labeled tetragonal crystal].

The dynamics of the side groups of amino acid residues and local conformational changes in the lysozyme molecule upon dehydration and rehydration of lysozyme crystals were studied by the methods of spin label, X-ray diffraction, and molecular dynamics. The His15 residue of lysozyme from chicken egg white was modified by spin label, and spin-labeled tetragonal crystals of the protein were grown. The spatial structure of the covalently bound spin label and its immediate surroundings in the lysozyme tetragonal crystal was determined. The conformation of a fragment of the lysozyme molecule with the spin label on His15, optimized by the method of molecular dynamics, closely agreed with X-ray data. It was found by the X-ray diffraction analysis that a decrease in relative humidity to 40% is accompanied by both a decrease in the unit cell volume by 27% and a change in the diffraction field of roentgenograms from 0.23 to 0.60 HM. The dehydration of spin-labeled lysozyme crystals leads to an anomalous widening of EPR peaks without changes in their position. The dehydration in the humidity range studied has a two-stage character. The decrease in humidity to 75% is accompanied by a sharp change in the parameters measured, and on further decrease in humidity to 40% they change insignificantly. The first stage is caused by the removal of the greater part of molecules of bulk water, and the second stage is due to the removal of the remaining bulk water and possible changes in the dynamics of weakly bound water molecules and their position. The simulation of experimental EPR spectra showed that the anomalous broadening of the spectrum upon dehydration is related to an increase in the dispersion of spin label orientations induced by changes in the network of hydrogen bonds generated by water molecules in the vicinity of the spin label and a possible turn (by no more than 5 degrees) of the entire protein molecule. After rehydration, the physical state of the lysozyme crystal did not return to the starting point.

Crystallization↗

PubMed2004

Radiation damage of biosystems mediated by secondary electrons: resonant precursors for uracil molecules.

Calculations are presented for the energy locations and spatial structures of low-energy resonant states describing transient negative ions (TNIs) of the uracil molecule in the gas phase. The resonant states are modeled using scattering calculations of low energy electrons interacting with isolated molecules in their equilibrium geometry. The interaction forces used in this model are described in detail. Examination of the spatial densities of the excess resonant electrons for the various TNIs found by the calculations allows one to associate the metastable anions with specific features of the experimentally observed fragmentation patterns.

Journal Article↗

PubMed1996

Local luminance nonlinearity and receptor aliasing in the detection of high-frequency gratings.

Contrast sensitivity for orientation discrimination is limited to spatial frequencies below 50-60 cycles per degree by neural spatial integration, and we find that contrast sensitivity, measured using an orientation-discrimination criterion, declines sharply with increasing spatial frequencies in that range. Yet interference fringe patterns pulsed at constant mean luminance can be detected at spatial frequencies far above that resolution limit [D.R. Williams, Vision Res. 25, 195 (1985)]. This is due at least in part to aliasing by the receptor mosaic, but another possible cue is provided by nonlinear distortion, which can create spatially uniform temporal transients when a pulsed fringe pattern is presented. We investigated the contribution of these spatially unstructured distortion products to grating detection by superimposing the pulsed fringe patterns on a randomly flickering uniform field. This manipulation has almost no effect on contrast sensitivity well below the resolution limit. Just above the resolution limit, however, the random luminance mask greatly elevates the fringe pattern detection threshold, suggesting that spatially unstructured cues provide the basis for detection in this range. At still higher fringe pattern frequencies, which approximately match the cone mosaic, the random luminance flicker again becomes ineffective for some observers, creating a clear secondary peak in contrast sensitivity in the flicker mask condition, which is presumably due to spatially structured cues provided by aliasing with the cone mosaic. The aliasing peak is still more clearly demarcated if the subject sets contrast thresholds for the perception of pattern as such. The contrast sensitivity function then has a notch or gap between the normal sensitivity range and the aliasing range. Apparently, in the unmasked case, spatially uniform cues (changes in overall color and brightness) bridge this gap.

Artifacts↗

PubMedDate not supplied

[The problem of archetype and current biology].

Two ideas of homology--transformational and taxic--are used in biology. The first one deals with homology of different structures from morphological point of view, the second one--with the homology of characters. The main question of taxic homology is: in what cases the same character is not identical in two different species? Transformational homologies are determined according the archaetype, taxic ones--according inheritance from the common ancestor of comparing taxa. Archaetype is an idea of an organism from the position of its components. Archaetype should be distinguished from the type character, i.e. the description of an organism combining general and special features. The main idea of archaetype is an idea of coherence of characters describing morphological organization. Archaetype was considered by Owen as mechanical construction. As a matter of fact, the organism is a dynamic system Its dynamic nature can be demonstrated by the conception of module organization of living systems. In the framework of this conception archaetype is a description of an organism from constructive position, focused on the characters of the parts reflecting ontogenetic and evolutionary autonomy. The progress in developmental genetics in understanding of genetic mechanisms of spatial structure formation during the last years opens the wide perspectives in interpretation of archaetype idea. Homeobox family of genes of Hox complex is especially interesting from this point of view. They are characterized by colinearity: spatial and temporal sequence of their expression is corresponding to their order in chromosome. As it was shown by several experiments, changes in the level and sequence of expression of Hox genes result in the changes of archaetype. The discovery of homological genes determining non homological morphological structures in non related groups is a new challenge to morphologists studying the problem of homologies. The disagreements on this subject are connected with non critical use of transformational (archaetypical) and taxic approximations. From transformational positions, eyes of vertebrates and invertebrates are homological, although they have different structure. At the same time, if we specify what type of eyes we are considered, the results will change. Thus, compound eyes of insects and bivalve mollusk Arca are not homological because they originated independently from forms without compound eyes.

Animal Population Groups↗

PubMedDate not supplied

[Cotranslational, cosecretory protein folding and its renaturation from a denatured state].

On the basis of the available experimental data on structure, biosynthesis and secretion of globular proteins it is concluded that an alpha-helix is a starting conformation at formation of the native structure of any globular protein (alpha-helical model for initiation of protein folding). The structural invariant (clusterization of hydrophobic side chains on the alpha-helix surface) in the amino acid sequences of globular proteins is found which is predicted by alpha-helical model for the initiation of protein folding. The model predicts the pyramidization of the atoms C and N of peptide groups during the formation of spatial structure of proteins and a number of other effects that can be put to the experimental test. In the work the mechanism for protein translocation across membrane lipid bilayer is also suggested.

Amino Acid Sequence↗

PubMed2000

The structure of a serpin-protease complex revealed by intramolecular distance measurements using donor-donor energy migration and mapping of interaction sites.

BACKGROUND: The inhibitors that belong to the serpin family are widely distributed regulatory molecules that include most protease inhibitors found in blood. It is generally thought that serpin inhibition involves reactive-centre cleavage, loop insertion and protease translocation, but different models of the serpin-protease complex have been proposed. In the absence of a spatial structure of a serpin-protease complex, a detailed understanding of serpin inhibition and the character of the virtually irreversible complex have remained controversial. RESULTS: We used a recently developed method for making precise distance measurements, based on donor-donor energy migration (DDEM), to accurately triangulate the position of the protease urokinase-type plasminogen activator (uPA) in complex with the serpin plasminogen activator inhibitor type 1 (PAI-1). The distances from residue 344 (P3) in the reactive-centre loop of PAI-1 to residues 185, 266, 313 and 347 (P1') were determined. Modelling of the complex using this distance information unequivocally placed residue 344 in a position at the distal end from the initial docking site with the reactive-centre loop fully inserted into beta sheet A. To validate the model, seven single cysteine substitution mutants of PAI-1 were used to map sites of protease-inhibitor interaction by fluorescence depolarisation measurements of fluorophores attached to these residues and cross-linking using a sulphydryl-specific cross-linker. CONCLUSIONS: The data clearly demonstrate that serpin inhibition involves reactive-centre cleavage followed by full-loop insertion whereby the covalently linked protease is translocated from one pole of the inhibitor to the opposite one.

Amino Acid Substitution↗

PubMedDate not supplied

Postmortem cryosectioning as an anatomic reference for human brain mapping.

This study examined the densitometric and topographic detail of high resolution 3D digital postmortem cryosectioned brain images. Anatomic image data and histology from cryosectioned human brain were compared to in vivo MRI for the ability to delineate neuroanatomic structure. 3D surface reconstructions in the Talairach and Tournoux atlas ("Co-planar stereotaxic atlas of the human brain", Thieme, New York, 1988) coordinate system enabled morphometric comparisons for a representative sample of neuroanatomic structures. Spatial resolution of cryosection images averaged 200 and 170 microns/pixel for whole head and brain, respectively, and 40 microns/pixel for isolated the brain regions. Anatomic detail was far superior to MRI, particularly in deep subcortical regions such as the basal ganglia and in mesencephalic nuclei and tracts. Digital repositioning in the Talairach coordinate system enabled efficient structure localization and morphometric comparison. Histology from collected tissue sections provided cytologic detail that could be mapped to its approximate 3D context. This approach permits comprehensive morphometric analyses necessary for an anatomic framework to a digital atlas of the human brain.

Aged↗

PubMed1993

[The studies on electronic structure and structure-activity relationships of [Leu5]-enkephalin].

The quantum chemical (INDO) calculations have been undertaken for [Leu5]-enkephalin. The electronic structure was investigated, the active site, the way of action and structure-activity relationship were discussed. It was found that the region of N(1) is the main active site for acceptance of electron, the region of O(51) and O(52) is the main active site for providing electron when interacting with the opiate receptor. [Leu5]-enkephalin was compared with morphine and R31833 in electronic and spatial structure of active site. Study of the results showed that the N(1) in [Leu5]-enkephalin corresponds to the N in morphine and the N(9) in R31833, phenyl of Tyr1 in [Leu5]-enkephalin corresponds to the phenyl in morphine and the phenyl of phenylethyl in R31833, the O(51) and O(52) in [Leu5]-enkephalin corresponds to the O(3) in morphine and the O(25) in R31833, the O(4) in [Leu5]-enkephalin corresponds to the O(29) or O(27) in R31833. On the basis of these studies, it was inferred that these compounds have common feature in pharmacophore. They not only have the same way of action but also have common site of action in the receptor when they interact with the opiate receptor.

Analgesics, Opioid↗

PubMed1996

An assessment of galactic cosmic radiation quality considering heavy ion track structures within the cellular environment.

Beyond the magnetic influence of the Earth, the flux of galactic cosmic radiation (GCR) represents a radiological concern for long-term manned space missions. Current concepts of radiation quality and equivalent dose are inadequate for accurately specifying the relative biological "efficiency" of low doses of such heavily ionising radiations, based as they are on the single parameter of Linear Energy Transfer (LET). Such methods take no account of the mechanisms, nor of the highly inhomogeneous spatial structure, of energy deposition in radiation tracks. DNA damage in the cell nucleus, which ultimately leads to the death or transformation of the cell, is usually initiated by electrons liberated from surrounding molecules by the incident projectile ion. The characteristics of these emitted "delta-rays", dependent primarily upon the charge and velocity of the ion, are considered in relation to an idealised representation of the cellular environment. Theoretically calculated delta-ray energy spectra are multiplied by a series of weighting algorithms designed to represent the potential for DNA insult in this environment, both in terms of the quantity and quality of damage. By evaluating the resulting curves, and taking into account the energy spectra of heavy ions in space, a relative measure of the biological relevance of the most abundant GCR species is obtained, behind several shielding configurations. It is hoped that this method of assessing the radiation quality of galactic cosmic rays will be of value when considering the safety of long-term manned space missions.

Algorithms↗

PubMed2005

Mining the structural knowledge of high-dimensional medical data using isomap.

The paper describes an application of a new, non-linear dimensionality reduction method, named Isomap, for mining the structural knowledge from high-dimensional medical data. The algorithm was evaluated on two publicly available medical datasets: the pathological dataset of breast cancer (241 malignant samples) and the gene expression dataset from the lung (186 tumours). It was found by Isomap that the approximate intrinsic dimensionalities of these two datasets were as low as three. The spatial structures of both datasets were presented in low-dimensional space. Isomap, as a general tool for dimensionality reduction analysis, is helpful in revealing the nonlinear structural knowledge of high-dimensional medical data.

Algorithms↗

PubMed2004

Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain.

The genetic structure of the population of Watermelon mosaic virus (WMV) in Spain was analysed by the biological and molecular characterisation of isolates sampled from its main host plant, melon. The population was a highly homogeneous one, built of a single pathotype, and comprising isolates closely related genetically. There was indication of temporal replacement of genotypes, but not of spatial structure of the population. Analyses of nucleotide sequences in three genomic regions, that is, in the cistrons for the P1, cylindrical inclusion (CI) and capsid (CP) proteins, showed lower similar values of nucleotide diversity for the P1 than for the CI or CP cistrons. The CI protein and the CP were under tighter evolutionary constraints than the P1 protein. Also, for the CI and CP cistrons, but not for the P1 cistron, two groups of sequences, defining two genetic strains, were apparent. Thus, different genomic regions of WMV show different evolutionary dynamics. Interestingly, for the CI and CP cistrons, sequences were clustered into two regions of the sequence space, defining the two strains above, and no intermediary sequences were identified. Recombinant isolates were found, accounting for at least 7% of the population. These recombinants presented two interesting features: (i) crossover points were detected between the analysed regions in the CI and CP cistrons, but not between those in the P1 and CI cistrons, (ii) crossover points were not observed within the analysed coding regions for the P1, CI or CP proteins. This indicates strong selection against isolates with recombinant proteins, even when originated from closely related strains. Hence, data indicate that genotypes of WMV, generated by mutation or recombination, outside of acceptable, discrete, regions in the evolutionary space, are eliminated from the virus population by negative selection.

Citrullus↗

PubMed2006

Texture analysis of the epidermis based on fast Fourier transformation in Sjögren-Larsson syndrome.

OBJECTIVE: To investigate whether image analysis of routine hematoxylin-eosin (H-E) skin sections using fast Fourier transformation (FFT) could detect structural alterations in patients with Sjögren-Larsson syndrome (SLS) diagnosed by molecular biology. STUDY DESIGN: Skin punch biopsies of 9 patients with SLS and 17 healthy volunteers were obtained. Digital images of routine histologic sections were taken, and their gray scale luminance was analyzed by FFT. The inertia values were determined for different ranges of the spatial frequencies in the vertical and horizontal direction. To get an estimation of anisotropy, we calculated the resultant vector of the designated frequency ranges. RESULTS: In the prickle cell layer, SLS patients showed more intense amplitudes in spatial structures with periods between 1.2 and 3.6 microm in the vertical direction, which correlated in part with accentuated nuclei and nucleoli and perinucleolar halos in the H-E sections. In a linear discriminant analysis, the variables derived from the FFT images correctly discriminated 84.6% of the patients. Texture features derived from the gray level cooccurrence matrix were not able to separate the groups. CONCLUSION: Exploratory texture analysis by FFT was able to detect discrete alterations in the prickle cell layer in routine light microscopy slides of SLS patients. The structural changes identified by FFT may be related to abnormal cellular components associated with aberrant lipid metabolism.

Eosine Yellowish-(YS)↗

PubMedDate not supplied

Spatio-temporal receptive-field structure of phasic W cells in the cat retina.

The spatio-temporal receptive-field structure of 54 phasic W cells in cat retinas has been examined using the reverse-correlation method of Jones and Palmer (1987). Within this sample, 12 cells had on-center, 16 off-center, and 26 on-off receptive fields. Three of the on-center and seven of the on-off cells were directionally selective. Forty percent of the cells in this sample had local receptive fields consisting of two or more distinct subregions. However, no correlation was observed between the number of subregions in the local receptive field and other response properties such as center sign or direction selectivity. In all cases, individual subregions, including those in on-off cells, appear to be produced by a half-wave rectification of the input signal. For 76% of the cells, these local receptive fields were contained within large suppressive fields which could be seen to extend for at least 10 deg in all directions with no apparent spatial structure. The mechanism producing the suppressive field also appears to involve a rectification of the input signal, and has a relatively high spatial resolution. Furthermore, the suppressive field itself is only responsive to moving or flickering stimuli; large, stationary gratings have no effect on the output of the local receptive-field mechanism. Thus, the overall receptive-field organization of these cells is particularly well suited for detecting local motion. The remaining 24% of cells in the sample lacked suppressive fields, and consequently responded well to large moving stimuli, but these cells were otherwise similar in their receptive-field properties to cells with suppressive fields. The significance of these properties is discussed in the context of the projections of phasic W cells to the superior colliculus and accessory optic system.

Animals↗

PubMed2002

Extending the coalescent to multilocus systems: the case of balancing selection.

Natural populations are structured spatially into local populations and genetically into diverse 'genetic backgrounds' defined by different combinations of selected alleles. If selection maintains genetic backgrounds at constant frequency then neutral diversity is enhanced. By contrast, if background frequencies fluctuate then diversity is reduced. Provided that the population size of each background is large enough, these effects can be described by the structured coalescent process. Almost all the extant results based on the coalescent deal with a single selected locus. Yet we know that very large numbers of genes are under selection and that any substantial effects are likely to be due to the cumulative effects of many loci. Here, we set up a general framework for the extension of the coalescent to multilocus scenarios and we use it to study the simplest model, where strong balancing selection acting on a set of n loci maintains 2n backgrounds at constant frequencies and at linkage equilibrium. Analytical results show that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. However, simulation results reveal that the structured coalescent approach breaks down when the number of backgrounds approaches the population size, because of stochastic fluctuations in background frequencies. A new method is needed to extend the structured coalescent to cases with large numbers of backgrounds.

Alleles↗

PubMed2000

Quantum state tomography with array detectors.

I propose a method for measuring the quantum state of an optical field that occupies a mode having a complicated spatial structure. The technique uses array detectors and a single, plane-wave local oscillator beam. The advantage of using array detectors is that the local oscillator is not mode matched to the field being measured, yet the deleterious effects of this mismatch on the effective detection efficiency are greatly reduced compared to using single detectors. Indeed, when the spatial mode of the signal field is describable by a real function, the effective mode-matching efficiency is unity.

Journal Article↗