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PubMed2006

Community structure, abundance, and in situ activity of nitrifying bacteria in river sediments as determined by the combined use of molecular techniques and microelectrodes.

The community structure, spatial distributions, and in situ activity of ammonia-oxidizing bacteria (AOB) representing the Betaproteobacteria and nitrite-oxidizing bacteria (NOB) representing the genus Nitrospira in three different river sediments with different pollution sources and levels along the Niida River, Hachinohe, Japan, were investigated by the combined use of 16S rRNA gene-cloning analysis, real-time quantitative polymerase chain reaction (RTQ-PCR) assays, and microelectrodes. The goal of this research was to evaluate the contribution of nitrifying activity in the sediment to the overall nitrogen elimination rate in this river. The 16S rRNA gene-cloning analysis revealed that the community structures of AOB and Nitrospira-like NOB are present in three sediments. On the basis of the results of 16S rRNA gene-cloning analysis, the RTQ-PCR assay using a TaqMan probe was developed and optimized for the quantification of the Nitrospira-like NOB. In the sediments, AOB specific 16S rRNA genes were detected in the range of 10(6) to 10(7) copies/cm3 and evenly distributed over the sampled sediment depth (0-5 mm), whereas the Nitrospira-like NOB 16S rRNA gene copy numbers per cm3 were 1-2 orders of magnitude higher than the AOB copy numbers. Under light conditions, intensive oxygenic photosynthesis occurred in the surface and increased the maximal O2 concentration and O2 penetration depth in all sediments. This concomitantly stimulated nitrifying bacteria present in diurnally anoxic deeper zones and expanded nitrification zones, which consequently increased the total NH4+ consumption rate in the sediment (i.e., total NH4+ flux into the sediment). The results suggested that the in situ nitrifying activity was restricted mainly to the surface 2 mm of the sediment and linked with photosynthetic activity, which obviously plays an important role in nitrogen elimination in this river.

Ammonia↗

PubMed1998

Molecular and genetic ecotoxicologic approaches to aquatic environmental bioreporting.

Molecular and population genetic ecotoxicologic approaches are being developed for the utilization of arthropods as bioreporters of heavy metal mixtures in the environment. The explosion of knowledge in molecular biology, molecular genetics, and biotechnology provides an unparalleled opportunity to use arthropods as bioreporter organisms. Interspecific differences in aquatic arthropod populations have been previously demonstrated in response to heavy metal insult in the Arkansas River (AR) California Gulch Superfund site (CGSS). Population genetic analyses were conducted on the mayfly Baetis tricaudatus. Genetic polymorphisms were detected in polymerase chain reaction amplified 16S mitochondrial rDNA (a selectively neutral gene) of B tricaudatus using single-strand conformation polymorphism analysis. Genetic differences may have resulted from impediments to gene flow in the population caused by mortality arising from exposure to heavy metal mixture pollution. In laboratory studies a candidate metal-responsive mucinlike gene, which is metal and dose specific, has been identified in Chironomus tentans and other potential AR-CGSS bioreporter species. Population genetic analyses using the mucinlike gene may provide insight into the role of this selectable gene in determining the breeding structure of B. tricaudatus in the AR-CGSS and may provide mechanistic insight into determinants of aquatic arthropod response to heavy metal insult. Metal-responsive (MR) genes and regulatory sequences are being isolated, characterized, and assayed for differential gene expression in response to heavy metal mixture pollution in the AR-CGSS. Identified promoter sequences can then be engineered into previously developed MR constructs to provide sensitive in vitro assays for environmental bioreporting of heavy metal mixtures. The results of the population genetic studies are being entered into an AR geographic information system that contains substantial biological, chemical, and geophysical information. Integrated spatial, structural, and temporal analyses of these parameters will provide invaluable information concerning environmental determinants that restrict or promote gene flow in bioreporter populations.

Aedes↗

PubMed2000

Low-pass filtering, a new method of fractal analysis: application to PET images of pulmonary blood flow.

The pattern of a spatial structure that repeats itself independently of the scale of magnification or resolution is often characterized by a fractal dimension (D). Two-dimensional low-pass filtering, which may serve as a method to assess D, was applied to functional images of pulmonary perfusion measured by positron emission tomography. The corner frequency of a low-pass filter is inversely proportional to the resolution scale. The method was applied to three types of images: random noise images, synthetic fractal images, and positron emission tomographic images of pulmonary perfusion. Images were processed with two-dimensional low-pass filters of decreasing corner frequencies, and a spatial heterogeneity index, the coefficient of variation, was calculated for each low-pass-filtered image. The natural logarithm of the coefficient of variation scaled linearly with the natural logarithm of the resolution scale for the PET images studied (average R(2) = 0.99). D ranged from 1.25 to 1.36 for the residual distribution of pulmonary perfusion after vertical gradients were removed by linear regression. D of the same data without removal of vertical gradients ranged from 1.11 to 1.14, but the fractal plots had systematic deviations from linearity and a lower linear correlation coefficient (R(2) = 0. 96). The method includes all data in the lung field and is insensitive to the effects of misregistration. We conclude that low-pass filtering offers new insights into the interpretation of D of two-dimensional functional images as a measure of the frequency content of spatial heterogeneity.

Fractals↗

PubMed2002

Intrinsic frames of reference in spatial memory.

Three experiments investigated the frames of reference used in memory to represent the spatial structure of the environment. Participants learned the locations of objects in a room according to an intrinsic axis of the configuration; the axis was different from or the same as their viewing perspective. Judgments of relative direction using memory were most accurate for imagined headings parallel to the intrinsic axis, even when it differed from the viewing perspective, and there was no cost to learning the layout according to a nonegocentric axis. When the shape of the layout was bilaterally symmetric relative to the intrinsic axis of learning, novel headings orthogonal to that axis were retrieved more accurately than were other novel headings. These results indicate that spatial memories are defined with respect to intrinsic frames of reference, which are selected on the basis of egocentric experience and environmental cues.

Adult↗

PubMed2003

Sand stirred by chaotic advection.

We study the spatial structure of a granular material, N particles subject to inelastic mutual collisions, when it is stirred by a bidimensional smooth chaotic flow. A simple dynamical model is introduced where four different time scales are explicitly considered: (i) the Stokes time, accounting for the inertia of the particles, (ii) the mean collision time among the grains, (iii) the typical time scale of the flow, and (iv) the inverse of the Lyapunov exponent of the chaotic flow, which gives a typical time for the separation of two initially close parcels of fluid. Depending on the relative values of these different times, a complex scenario appears for the long-time steady spatial distribution of particles, where clusters of particles may or may not appear.

Journal Article↗

PubMed2001

Purification and structure of the major product obtained by reaction of NADPH and NMNH with the myeloperoxidase/hydrogen peroxide/chloride system.

The first spectrophotometric study of the reaction of the myeloperoxidase/H2O2/Cl- system with NADPH and NMNH showed that the reaction products were not the corresponding oxidized nucleotides and that modifications would take place on the nicotinamide part of the molecule [Auchère, F. & Capeillère-Blandin, C. (1999) Biochem. J. 343, 603-613]. In this report, in order to obtain more precise information on the structural modifications and mechanism of the reaction, we focus on the purification and isolation of products derived from NADPH and NMNH by RP-HPLC. Electrospray ionization mass spectra indicated that the relative height of the peaks reflected that of the natural isotopic abundance of 35Cl and 37Cl, providing evidence that the products derived from NADPH and NMNH were monochlorinated. Moreover, calculated masses revealed the 1 : 1 addition of HOCl to the molecule. Various 1D and 2D NMR experiments provided data for the assignments of the chemical shifts of protons and carbons and the coupling constants of the protons of the chlorinated nucleotides. Further NOESY experiments allowed the characterization of the spatial structure of the chlorinated product and showed that trans HOCl addition occurred at the C5=C6 carbon double bond of the nicotinamide ring, leading to a chlorohydrin.

Carbon↗

PubMedDate not supplied

[Modeling of monoamine oxidase B active site by computer moulding].

Using previously developed approach for active site modelling of enzymes with unknown spatial structure (Veselovsky et al., Biochemistry (Moscow), 65, 1072-1079) substrate/inhibitor binding site of monoamine oxidase B was designed by means of computer moulding. This mould corresponds to the shape and volume size of selective substrates and inhibitors of this enzyme. Active site moulds of monoamine oxidases A and B exhibit significant differences in these parameters. The correctness of the resultant model of monoamine oxiadse B active site was validated by using three compounds which were not employed in the training sets. Weak inhibitors were not accommodated in the mould whereas their "flexible" analogues exhibitng rather potent inhibition are readily accommodated in this mould. This suggests that our mould reflects some important spatial features of monoamine oxidase B active site. This mould can be employed for screening of new perspective inhibitior of monoamine oxidase B and pilot evaluation of their monoamine oxidase B inhibitory activity.

Binding Sites↗

PubMed1985

A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA.

We have inserted the 509-bp-long fragment of sea urchin P. miliaris histone gene spacer region into plasmid pUC19. The fragment contains the 60-bp-long homopurine-homopyrimidine tract that is known to be hypersensitive to the S1 endonuclease. Using two-dimensional gel electrophoresis we have observed a sharp structural transition in the insert with increasing DNA superhelicity. As in the cases of cruciform and Z form formation, the observed transition partly relaxes the superhelical stress. In contrast with the other two well documented transitions, the observed transition strongly depends on pH. At pH7 and above the transition occurs at negative superhelicities exceeding the physiological range (- sigma greater than 0.08). For pH6 the transition occurs at -sigma = 0.055, whereas for pH4.3 it takes place at -sigma = 0.001. A comprehensive analysis of the obtained data has made it possible to define the nature of the observed transition. We conclude that under superhelical stress or/and at low pH homopurinehomopyrimidine tracts adopt a novel spatial structure called the H form.

Animals↗

PubMed2001

Two-generation analysis of pollen flow across a landscape. I. Male gamete heterogeneity among females.

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processess and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model's elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model's effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by phiFT, a male gametic analogue of Wright's F(ST) and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that phiFT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

Genetic Variation↗

PubMed2006

The influence of depth segmentation on colour constancy.

In real scenes, surfaces in different depth planes often differ in the luminance and chromatic content of their illumination. Scene segmentation is therefore an important issue when considering the compensation of illumination changes in our visual perception (lightness and colour constancy). Chromatic adaptation is an important sensory component of colour constancy and has been shown to be linked to the two-dimensional spatial structure of a scene (Werner, 2003 Vision Research 43 1611 - 1623). Here, the question is posed whether this cooperation also extends to the organisation of a scene in depth. The influence of depth on colour constancy was tested by introducing stereo disparity, whereby the test patch and background were perceived in either the same or one of five different depth planes (1.9-57 min of arc). There were no additional cues to depth such as shadows or specular highlights. For consistent illumination changes, colour constancy was reduced when the test patch and background were separated in depth, indicating a reduction of contextual influences. An interaction was found between the influences of stereo depth and spatial frequency on colour constancy. In the case of an inconsistent illumination change, colour constancy was reduced if the test patch and background were in the same depth plane (2-D condition), but not if they were separated in depth (3-D condition). Furthermore, colour constancy was slightly better in the 3-D inconsistent condition than in the 2-D inconsistent condition. It is concluded that depth segmentation supports colour constancy in scenes with inconsistent illumination changes. Processes of depth segmentation are implemented at an early sensory stage of colour constancy, and they define visual regions within which the effects of illuminant changes are discounted for separately. The results support recent models that posit such implementation of scene segmentation in colour constancy.

Adaptation, Ocular↗

PubMed1985

The complete primary structure of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus.

The amino acid sequences of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus have been completely determined. This has been achieved by sequence analyses of peptides derived from enzymatic digestions of the proteins with trypsin, chymotrypsin, pepsin, Staphylococcus aureus protease, and Armillaria mellea protease as well as by chemical cleavage with hydroxylamine and cyanogen bromide. Based on the primary structures of the six proteins, their secondary structures were predicted using four different computer prediction programs. A comparison of the amino acid sequences of the studied proteins from B. stearothermophilus with the homologous proteins from Escherichia coli revealed that in four proteins (L1, L15, L24 and L29) between 40-50% of the residue in the sequences are identical, whereas this value is significantly higher (69%) for L14 and lower (28%) for L23. The distribution of those amino acid residues which are identical in the corresponding proteins from the two bacteria is not random along the protein chain: some regions are highly conserved whereas others are not. This finding indicates that the regions which are conserved during evolution are important for the spatial structure and/or function of the protein.

Amino Acid Sequence↗

PubMed2004

An interacting particle system modelling aggregation behavior: from individuals to populations.

In this paper we investigate the stochastic modelling of a spatially structured biological population subject to social interaction. The biological motivation comes from the analysis of field experiments on a species of ants which exhibits a clear tendency to aggregate, still avoiding overcrowding. The model we propose here provides an explanation of this experimental behavior in terms of "long-ranged" aggregation and "short-ranged" repulsion mechanisms among individuals, in addition to an individual random dispersal described by a Brownian motion. Further, based on a "law of large numbers", we discuss the convergence, for large N, of a system of stochastic differential equations describing the evolution of N individuals (Lagrangian approach) to a deterministic integro-differential equation describing the evolution of the mean-field spatial density of the population (Eulerian approach).

Animals↗

PubMed2005

The effect of migration on local adaptation in a coevolving host-parasite system.

Antagonistic coevolution between hosts and parasites in spatially structured populations can result in local adaptation of parasites; that is, the greater infectivity of local parasites than foreign parasites on local hosts. Such parasite specialization on local hosts has implications for human health and agriculture. By contrast with classic single-species population-genetic models, theory indicates that parasite migration between subpopulations might increase parasite local adaptation, as long as migration does not completely homogenize populations. To test this hypothesis we developed a system-specific mathematical model and then coevolved replicate populations of the bacterium Pseudomonas fluorescens and a parasitic bacteriophage with parasite only, with host only or with no migration. Here we show that patterns of local adaptation have considerable temporal and spatial variation and that, in the absence of migration, parasites tend to be locally maladapted. However, in accord with our model, parasite migration results in parasite local adaptation, but host migration alone has no significant effect.

Adaptation, Physiological↗

PubMed2006

Video compression using spatiotemporal regularity flow.

We propose a new framework in wavelet video coding to improve the compression rate by exploiting the spatiotemporal regularity of the data. A sequence of images creates a spatiotemporal volume. This volume is said to be regular along the directions in which the pixels vary the least, hence the entropy is the lowest. The wavelet decomposition of regularized data results in a fewer number of significant coefficients, thus yielding a higher compression rate. The directions of regularity of an image sequence depend on both its motion content and spatial structure. We propose the representation of these directions by a 3-D vector field, which we refer to as the spatiotemporal regularity flow (SPREF). SPREF uses splines to approximate the directions of regularity. The compactness of the spline representation results in a low storage overhead for SPREF, which is a desired property in compression applications. Once SPREF directions are known, they can be converted into actual paths along which the data is regular. Directional decomposition of the data along these paths can be further improved by using a special class of wavelet basis called the 3-D orthonormal bandelet basis. SPREF -based video compression not only removes the temporal redundancy, but it also compensates for the spatial redundancy. Our experiments on several standard video sequences demonstrate that the proposed method results in higher compression rates as compared to the standard wavelet based compression.

Algorithms↗

PubMed2004

Electrical neuroimaging based on biophysical constraints.

This paper proposes and implements biophysical constraints to select a unique solution to the bioelectromagnetic inverse problem. It first shows that the brain's electric fields and potentials are predominantly due to ohmic currents. This serves to reformulate the inverse problem in terms of a restricted source model permitting noninvasive estimations of Local Field Potentials (LFPs) in depth from scalp-recorded data. Uniqueness in the solution is achieved by a physically derived regularization strategy that imposes a spatial structure on the solution based upon the physical laws that describe electromagnetic fields in biological media. The regularization strategy and the source model emulate the properties of brain activity's actual generators. This added information is independent of both the recorded data and head model and suffices for obtaining a unique solution compatible with and aimed at analyzing experimental data. The inverse solution's features are evaluated with event-related potentials (ERPs) from a healthy subject performing a visuo-motor task. Two aspects are addressed: the concordance between available neurophysiological evidence and inverse solution results, and the functional localization provided by fMRI data from the same subject under identical experimental conditions. The localization results are spatially and temporally concordant with experimental evidence, and the areas detected as functionally activated in both imaging modalities are similar, providing indices of localization accuracy. We conclude that biophysically driven inverse solutions offer a novel and reliable possibility for studying brain function with the temporal resolution required to advance our understanding of the brain's functional networks.

Biophysics↗

PubMed2001

Structural features of a snake venom thrombin-like enzyme: thrombin and trypsin on a single catalytic platform?

The Lachesis muta thrombin-like enzyme (LM-TL) is a single chain serine protease that shares 38% sequence identity with the serine protease domain of thrombin and also displays similar fibrinogen-clotting activity. In addition, the 228 amino acid residue LM-TL is 52% identical to trypsin, and cleaves chromogenic substrates with similar specificity. Herein we report a three-dimensional (3D) model validated experimentally for LM-TL based on these two homologous proteins of known 3D structure. Spatial modeling of LM-TL reveals a serine protease with a chymotrypsin fold presenting a hydrophobic pocket on its surface, involved in substrate recognition, and an important 90's loop, involved in restricting the LM-TL catalytic site cleft. Docking analysis showed that LM-TL would not form a stable complex with basic pancreatic trypsin inhibitor and wild-type ecotin since its 90's loop would restrict the access to the catalytic site. LM-TL formed acceptable interactions with fibrinopeptide A and a variant of ecotin; ecotin-TSRR/R in which both the primary and secondary binding sites are mutated Val81Thr, Thr83Ser, Met84Arg, Met85Arg and Asp70Arg. Furthermore, analysis of the primary structures of LM-TL and of the seven snake venom thrombin-like enzymes (SVTLEs) family reveals a subgroup formed by LM-TL, crotalase, and bilineobin, both closely related to thrombin. Therefore, LM-TL provides an initial point to compare SVTLEs with their counterparts, e.g. the mammalian serine proteases, and a basis for the localization of important residues within the little known SVTLEs family.

Amino Acid Sequence↗

PubMedDate not supplied

[Structure of leghemoglobin].

The structure of the high spin complex of lupin leghemoglobin with acetate is refined at 2.0 A resolution using Diamond and Jack-Levitt technique (R=19%). The 0.05 A displacement of the iron atom from porphyrin plane to the distal side and the weakening of iron-nitrogen bond to the proximal histidine (2.37 A) give an explanation of the high affinity of the leghemoglobin for molecular oxygen. The ruffling of the porphyrin core may also favour it. Binding of nicotinate is accompanied by small conformational movements. Swinging out of the distal histidine from the heme pocket is the most prominent feature of this complex. The known amino acid sequences of leghemoglobin are analysed in view of the spatial structure of lupin hemoglobin.

Amino Acid Sequence↗

PubMed2000

Stabilization of proteins by enhancement of inter-residue hydrophobic contacts: lessons of T4 lysozyme and barnase.

Although the hydrophobic interactions are considered as the main contributors to the protein stability, not much examples of protein stabilization by rational increasing of this type of interactions still can be found in literature. This is partly due to the lack of proper theoretical "measure" of hydrophobic interactions and their changes upon mutations. In the present paper the molecular hydrophobicity potential approach is used to assess how the changes in type and the strength of inter-residue contacts upon single amino acid mutations are correlated with the changes in thermodynamic stability of T4 lysozyme and barnase mutants, and which factors affect these correlations. Mutations changing unfavorable hydrophilic-to-hydrophobic contacts into favorable hydrophobic were found to enhance the thermodynamic stability in more than 81 % of cases, if these mutations do not create steric bumps and do not involve proline residues and hydrogen-bonded side-chains. Mutations increasing hydrophobic contributions (according to molecular hydrophobicity potential formalism) lead to increase of thermodynamic stability in more than 94% of cases for certain type of mutations (i.e., mutations not involving charged residues, Pro and residues with side-chain hydrogen bonds, when these mutations do not introduce steric bumps and do not involve strongly exposed residues and residues situated at helix N- and C-cap positions). For this type of mutations the correlation was found between the change in hydrophobic contributions of mutated residues deltaCphob and thermodynamic parameters deltaTm (change in melting temperature) and deltadeltaG (change in free energy of unfolding). Although the correlation coefficients were larger if the experimental structures of mutants were used for the calculations (correlation coefficients r(exp) deltaC,deltaT = .85 and r(exp) deltaC,deltadeltaG = 0.87) than if the modeled structures were used instead (r(mod) deltaC,deltaT = 0.74 and r(mod)deltaC,deltadeltaG = 0.76), the modelled structures of mutants in the vast majority of cases can be used for qualitative predictition of the protein stabilization. Basing on the analysis of mutations increasing hydrophobic contributions in T4 lysozyme the substitution matrix was derived, which can be used to decide which new residue should be put instead the old one to increase the stability of protein. The estimation shows that the number of potential mutation sites for enhancement of hydrophobic interactions in T4 lysozyme is quite large, and only approximately 10 per cent of them were studied thus far. Basing on the current analysis of T4 lysozyme and barnase mutations the algorithm for increasing of protein stability via increasing of hydrophobic interactions for the proteins with known spatial structure is proposed.

Algorithms↗