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PubMed1989

Circumvention of adriamycin resistance by dipyridamole analogues: a structure-activity relationship study.

Dipyridamole restores sensitivity to Adriamycin (ADR) in drug-resistant cells. In an effort to elucidate the relationship between activity and chemical structure of dipyridamole, the ability to enhance the growth inhibitory effect of ADR, in multidrug-resistant (MDR) P388 murine leukemia cells, was determined for 43 derivatives and related compounds. Since both substituted pyrimidopyrimidines and pteridines enhanced the growth-inhibitory effect of ADR in drug resistant cells, the core skeleton may not be directly involved and rather serve as a carrier for the substituents connected with this activity. The exact positions of the active substituents on the core skeleton did not seem to be critical for exertion of the activity. Activity was dependent on the presence of 3 tertiary amine groups. However, not all tertiary amines showed the same potency which might be related to the degree of basicity and/or the spatial structure of these groups. The most active derivatives carried piperidine and pyrrolidine groups while derivatives with thiomorpholine, 3-hydroxypiperidine or dimethylamine groups had low activity. Activity was also dependent on the presence of a substituent with partial electronegative charges as found in a diethanolamine group. However, this function could be carried out, with even higher efficiency, by a substituent containing 6 pi electrons.

Animals↗

PubMed1983

Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes.

The experimental observations described in this article indicated that a distribution of many different fluctuations is present in a globular protein. These fluctuations were characterized by observation of many natural internal probes such as the labile peptide protons and the aromatic side chains. The conditions which are necessary to get reactions of the internal probes have been discussed in detail. The structural interpretation of the data was facilitated by the development and the use of new NMR techniques which provided the identification of the resonances of all the labile peptide protons. With NOE measurements a distinction between correlated and uncorrelated exchange events was obtained. This enabled us to elucidate the exchange mechanism over a wide range of p2H and temperature and to classify different subsets of fluctuations with respect to their lifetimes. It was further demonstrated that a change of external conditions such as temperature, p2H or pressure can change the distribution of fluctuations in the protein. The mechanisms responsible for rotation of internal aromatic side chains were also found to change with temperature, and mechanistic aspects of these fluctuations were discussed. This demonstration of a manifold of spatial fluctuations in a small protein provides an impression on the kind of fluctuations which have to be expected for larger proteins. When studying protein reactions one should therefore consider the presence of a large number of different, transiently formed, spatial structures available for the partner in the reaction, which may pick out only that structure which will optimally perform a particular reaction with the highest efficiency.

Magnetic Resonance Spectroscopy↗

PubMed2005

Causes and consequences of animal dispersal strategies: relating individual behaviour to spatial dynamics.

Knowledge of the ecological and evolutionary causes of dispersal can be crucial in understanding the behaviour of spatially structured populations, and predicting how species respond to environmental change. Despite the focus of much theoretical research, simplistic assumptions regarding the dispersal process are still made. Dispersal is usually regarded as an unconditional process although in many cases fitness gains of dispersal are dependent on environmental factors and individual state. Condition-dependent dispersal strategies will often be superior to unconditional, fixed strategies. In addition, dispersal is often collapsed into a single parameter, despite it being a process composed of three interdependent stages: emigration, inter-patch movement and immigration, each of which may display different condition dependencies. Empirical studies have investigated correlates of these stages, emigration in particular, providing evidence for the prevalence of conditional dispersal strategies. Ill-defined use of the term 'dispersal', for movement across many different spatial scales, further hinders making general conclusions and relating movement correlates to consequences at the population level. Logistical difficulties preclude a detailed study of dispersal for many species, however incorporating unrealistic dispersal assumptions in spatial population models may yield inaccurate and costly predictions. Further studies are necessary to explore the importance of incorporating specific condition-dependent dispersal strategies for evolutionary and population dynamic predictions.

Animals↗

PubMed2002

Spatial arrangement of branches in relation to slope and neighbourhood competition.

To gain a better understanding of the effects of spatial structure on patterns of neighbourhood competition among hardwood trees, the three-dimensional extension of primary branches was surveyed for ten community-grown Castanea crenata (Fagaceae) trees with respect to the positioning of neighbouring branches and the slope of the forest floor. There were significantly more branches extending towards the lower side of the slope than towards the upper side, but structural properties such as branch length and vertical angle were not affected by slope. When horizontal extension of a branch towards its neighbour was compared for a C. crenata branch and a neighbouring heterospecific, the former was significantly narrower than the latter when the inter-branch distance (horizontal distance between the base positions of two neighbouring branches) was short (< approx. 5 m). Castanea crenata branches tended to extend in a direction avoiding neighbouring branches of heterospecifics when the inter-branch distance was short. Furthermore, for an inter-branch distance <3 m, the horizontal extension of a C. crenata branch was less when it was neighbouring a heterospecific branch than when neighbouring a conspecific branch. These results suggest that horizontal extension of C. crenata branches is more prone to spatial invasion by nearby neighbouring branches of heterospecifics, and that the invasion can be lessened when C. crenata trees are spatially aggregated. The reason why such an arrangement occurs is discussed in relation to the later leaf-flush of C. crenata compared with that of other species in the forest.

Computer Simulation↗

PubMed2006

Geostatistical analysis of data on air temperature and plant phenology from Baden-Württemberg (Germany) as a basis for regional scaled models of climate change.

The rise of the air temperature is assured to be part of the global climatic change, but there is still a lack of knowledge about its effects at a regional scale. The article tackles the correlation of air temperature with the phenology of selected plants by the example of Baden-Württemberg to provide a spatial valid data base for regional climate change models. To this end, the data on air temperature and plant phenology, gathered from measurement sites without congruent coverage, were correlated after performing geostatistical analysis and estimation. In addition, geostatistics are used to analyze and cartographically depict the spatial structure of the phenology of plants in spring and in summer. The statistical analysis reveals a significant relationship between the rising air temperature and the earlier beginning of phenological phases like blooming or fruit maturation: From 1991 to 1999 spring time, as indicated by plant phenology, has begun up to 15 days earlier than from 1961 to 1990. As shown by geostatistics, this holds true for the whole territory of Baden-Württemberg. The effects of the rise of air temperature should be investigated not only by monitoring biological individuals, as for example plants, but on an ecosystem level as well. In Germany, the environmental monitoring should be supplemented by the study of the effects of the climatic change in ecosystems. Because air temperature and humidity have a great influence on the temporal and spatial distribution of pathogen carriers (vectors) and pathogens, mapping of the environmental determinants of vector and pathogen distribution in space and time should be performed in order to identify hot spots for risk assessment and further detailed epidemiological studies.

Air↗

PubMed2001

Spatial distribution of vital and dead microorganisms in dental biofilms.

To examine the spatial structure of dental biofilms a vital fluorescence technique was combined with optical analysis of sections in a confocal laser scanning microscope (CLSM). Enamel slaps were worn in intraoral splints by three volunteers for five days to accumulate smooth-surface plaque. After vital staining with fluorescein diacetate and ethidium bromide the specimens were processed for CLSM examination. Optical sections 1 microm apart were analysed in the z-axis of these dental biofilms. One of the films was 15 microm high, sparse and showed low vitality, i.e. <16%, while the others were taller (25 and 31 microm) and more vital, i.e. up to 30 and 69%, respectively. In all instances the bacterial vitality increased from the enamel surface to the central part of the plaque and decreased again in the outer parts of the biofilm. The spatial arrangement of the microorganisms in the biofilm showed voids outlined by layers of vital bacteria, which themselves were packed in layers of dead material.

Biofilms↗

PubMed2004

Urea effect on Cu(2+)-induced DNA structural transitions in solution.

Cu(2+) ion interaction with DNA in aqueous solutions containing urea (0-5 M) was studied by IR spectroscopy. It was shown that upon the Cu(2+) ion binding DNA transition into a compact form occurs. This transition is of positive cooperativity. We suppose that the mechanism of Cu(2+)-induced DNA compaction in solutions containing urea is not completely electrostatic. Urea addition to the DNA solution decreases the Cu(2+) ion concentration required to induce DNA compaction. As the urea content in solution rises, the binding constant of Cu(2+) ions interacting with DNA increases, going through the maximum in the case of 2 M solution; further increase of the urea content in solutions leads to decrease of the binding constant. DNA transition into the compact form under the Cu(2+) ion action is determined not only by the effects of the solution dielectric permeability but by the solvation effects; when changes of the dielectric permeability are small the solvation effects may prevail. Urea addition to the DNA solution also decreases cooperativity of the DNA compaction process. Perhaps, cooperativity of the DNA transition into the compact state depends on the ordered spatial structure of water adjacent to the macromolecule and decreases on the structure destruction.

Animals↗

PubMed2001

Population genetic analysis of Colombian Trypanosoma cruzi isolates revealed by enzyme electrophoretic profiles.

Although Colombia presents an enormous biological diversity, few studies have been conducted on the population genetics of Trypanosoma cruzi. This study was carried out with 23 Colombian stocks of this protozoa analyzed for 13 isoenzymatic loci. The Hardy-Weinberg equilibrium, the genetic diversity and heterogeneity, the genetic relationships and the possible spatial structure of these 23 Colombian stocks of T. cruzi were estimated. The majority of results obtained are in agreement with a clonal population structure. Nevertheless, two aspects expected in a clonal structure were not discovered in the Colombian T. cruzi stocks. There was an absence of given zymodemes over-represented from a geographical point of view and the presumed temporal stabilizing selective phenomena was not observed either in the Colombian stocks sampled several times through the years of the study. Some hypotheses are discussed in order to explain the results found.

Adult↗

PubMed1982

Carp insulin: amino acid sequence, biological activity and structural properties.

The amino acid sequence of insulin of carp (Cyprinus carpio) has been determined and correlated with its biological activity in a fat-cell test and its structural properties as measured by circular dichroism and sedimentation analysis. The amino acid sequence of carp insulin displays some unusual features: the B chain is longer at the N terminus by two residues as compared with mammalian insulins and there are substitutions of the charged residues, found in most insulins at positions B21 and B22, by proline and threonine respectively. On the other hand, all amino acid residues essential for biological activity and for the association of insulin monomers are the same in carp insulin. Accordingly, the half-maximal response in a fat-cell test is reached with carp insulin at concentrations which are only three times higher than with porcine insulin and the maximal response is the same. The circular dichroism spectrum of carp insulin resembles greatly that of bovine insulin indicating that it has a similar spatial structure. Despite amino acid substitutions in the dimer-dimer contact region, carp insulin is able to form hexamers.

Adipose Tissue↗

PubMed1982

[Stereospecificity of active centers of acylcholinesterases].

The stereospecificity of the active center of acetylcholinesterase from human erythrocytes (AChE) and butyrylcholinesterase from horse blood serum (BuChE) in reactions with enantiomers of irreversible organophosphorus inhibitors (OPI) with asymmetrical central phosphorus atom and different structure of the leaving moiety: C2H5O(CH3)P(O)SR, where R = C2H7; C6H13: C4H4SC2H5; C2H4SC2H5 and C2H4S(CH3)C2H5, was studied. The strongest inhibiting effect with respect to cholinesterases was exerted by (-)-isomers of the OPI tested. The differences in the inhibiting activity of (-) and (+)-isomers were especially well-pronounced for OPI with R = C3H7 and C4H4SC2H5. The differences in the inhibiting activity of the enantiomers suggest that the stereospecificity of the active center of AChE was the highest and that of BuChE was considerably lower. After treatment by N,N-dimethyl-2-phenylaziridinium ions which specifically and irreversibly modify the anionic groups on the active surface of AChE, the stereospecificity of the latter is decreased and is approximated to that of BuChE. The differences in stereospecificity of AChE and BuChE are probably due to the considerable differences in the spatial structure of the enzyme active centers.

Acetylcholinesterase↗

PubMed2003

From connectivity to isolation: genetic consequences of population fragmentation in capercaillie across Europe.

The capercaillie inhabits a continuous range in large parts of the Palearctic boreal forest, but is patchily distributed in temperate Europe. An ongoing population decline, largely related to human land use changes, has been most pronounced in central and western Europe, where some local populations have become extinct. In this study, we document the genetic differentiation of capercaillie populations at different stages along a gradient of spatial structuring from high connectivity (continuous range in the boreal forest) to a metapopulation systems (Alps) and recent (central Europe) and historic (Pyrenees) isolation. Four hundred and sixty individuals from 14 sample sites were genotyped at 10 polymorphic microsatellite loci to assess genetic structure and variation of capercaillie populations across its European range. As expected, differentiation was least pronounced within the continuous range in the boreal forest. Within the metapopulation system of the Alps, differentiation was less than among the isolated populations of central Europe (Black Forest, Fichtelgebirge, Thuringia, Vosges). In the long-isolated population of the Pyrenees, and the recently isolated populations of central Europe, genetic diversity was significantly reduced compared with the Alps and boreal forest. Our results agree with the concept of a gradual increase in genetic differentiation from connectivity to isolation, and from recent to historic isolation. Anthropogenic habitat deterioration and fragmentation thus not only leads to range contractions and extinctions, but may also have significant genetic and evolutionary consequences for surviving populations. To maintain high levels of genetic variation in species in fragmented habitats, conservation should aim at securing connectivity between spatially distinct populations.

Animals↗

PubMed2003

Catalytic properties of mutant 23 S ribosomes resistant to oxazolidinones.

Kinetic analysis of ribosomal peptidyltransferase activity in a methanolic puromycin reaction with wild type and drug-resistant 23 S RNA mutants was used to probe the structural basis of catalysis and mechanism of resistance to antibiotics. 23 S RNA mutants G2032A and G2447A are resistant to oxazolidinones both in vitro and in vivo with the latter displaying a 5-fold increase in the value of Km for initiator tRNA and a 100-fold decrease in Vmax in puromycin reaction. Comparison of the Ki values for oxazolidinones, chloramphenicol, and sparsomycin revealed partial cross-resistance between oxazolidinones and chloramphenicol; no cross-resistance was observed with sparsomycin, a known inhibitor of the peptidyltransferase A-site. Inhibition of the mutants using a truncated CCA-Phe-X-Biotin fragment as a P-site substrate is similar to that observed with the intact initiator tRNA, indicating that the inhibition is substrate-independent and that the peptidyltransferase itself is the oxazolidinone target. Mapping of all known mutations that confer resistance to these drugs onto the spatial structure of the 50 S ribosomal subunit allows for docking of an oxazolidinone into a proposed binding pocket. The model suggests that oxazolidinones bind between the P- and A-loops, partially overlapping with the peptidyltransferase P-site. Thus, kinetic, mutagenesis, and structural data suggest that oxazolidinones interfere with initiator fMet-tRNA binding to the P-site of the ribosomal peptidyltransferase center.

Antibiotics, Antineoplastic↗

PubMed2003

Representation of two geometric features of the environment in the domestic chick ( Gallus gallus).

We report experiments based on a novel test in domestic chicks ( Gallus gallus), designed to examine the encoding of two different geometric features of an enclosed environment: relative lengths of the walls and amplitude of the corners. Chicks were trained to search for a food reward located in one corner of a parallelogram-shaped enclosure. Between trials, chicks were passively disoriented and the enclosure was rotated, making reorientation possible only on the basis of the internal spatial structure of the enclosure. In order to reorient, chicks could rely on two sources of information: the relative lengths of the walls of the enclosure (associated to their left-right sense order) and the angles subtended by walls at corners. Chicks learned the task choosing equally often the reinforced corner and its rotational equivalent. Results of tests carried out in novel enclosures, the shapes of which were chosen ad hoc (1) to induce reorientation based only on the ratio of walls lengths plus sense (rectangular enclosure), or (2) to induce reorientation based only on corner angles (rhombus-shaped enclosure), suggested that chicks encoded both features of the environment. In a third test, in which chicks faced a conflict between these geometric features (mirror parallelogram-shaped enclosure), reorientation seemed to depend on the salience of corner angles. These results shed light on the elements of the environmental geometry which control spatial reorientation, and broaden the knowledge on the geometric representation of space in animals.

Animals↗

PubMed2000

The spatial spread of altruism versus the evolutionary response of egoists.

Several recent models have shown that altruism can spread in viscous populations, i.e. in spatially structured populations within which individuals interact only with their immediate neighbours and disperse only over short distances. I first confirm this result with an individual-based model of a viscous population, where an individual can vary its level of investment into a behaviour that is beneficial to its neighbours but costly to itself. Two distinct classes of individuals emerge: egoists with no or very little investment into altruism, and altruists with a high level of investment; intermediate levels of altruism are not maintained. I then extend the model to investigate the consequences of letting interaction and dispersal distances evolve along with altruism. Altruists maintain short distances, while the egoists respond to the spread of altruism by increasing their interaction and dispersal distances. This allows the egoistic individuals to be maintained in the population at a high frequency. Furthermore, the coevolution of investment into altruism and interaction distance can lead to a stable spatial pattern, where stripes of altruists (with local interactions) alternate with stripes of egoists (with far-reaching interactions). Perhaps most importantly, this approach shows that the ease with which altruism spreads in viscous populations is maintained despite countermeasures evolved by egoists.

Altruism↗

PubMed1999

Modelling regional migration in China: estimation and decomposition.

"In this paper I consider the issue of identifying the effects of spatial structure and the origin and destination attributes on interregional migration. A decomposition approach is developed based on migration models. The interprovincial migration data in China over the period 1985-1990 are used to estimate a gravity migration model, an extended gravity model, a Poisson gravity model, and a multilevel Poisson model, which are then used to decompose the various effects on migration in China."

Asia↗

PubMed2006

Characterization of metallothioneins (MT-I and MT-II) in the yak.

The cDNA-encoding sequences for yak metallothionein isoforms I (MT-I) and II (MT-II) were amplified and cloned by reverse-transcription PCR to characterize the nucleotide sequence and protein structure of metallothionein in the yak. The cDNA sequences of MT-I and MT-II were subjected to BLAST searching at the National Center for Biotechnology Information, and the results indicated that the nucleotide sequences of yak MT-I and MT-II, when compared among different species of mammals, are highly conserved. The yak open reading frames have a length of 183 nucleotides, which encode for yak MT-I and MT-II proteins of 61 AA, respectively. Analysis of hydrophobicity, trans-membrane region, and signal peptides suggested that metallothioneins of the yak are nonsecretory proteins. There were several conserved tripeptide sequences, such as C-X-C, C-C-X-C-C, and C-X-X-C (X designates AA excluding cysteine in MT-I and MT-II), and they are highly conserved in their evolution. By homologous comparative modeling, we predicted the molecular spatial structures of yak MT-I and MT-II, which are composed of alpha- and beta-domains that are linked by the conserved tripeptide Lys(30)-Lys(31)-Ser(32) (KKS).

Amino Acid Sequence↗

PubMed1995

Coordinate system matching for neuromagnetic and morphological reconstruction overlay.

The overlay of functional and morphological images is an essential tool for advanced and improved functional diagnosis showing the correlation between spatial structures or lesions and functional areas. We present an improved coordinate system matching technique. The well known method of three orthogonal coils combined in one coilset for an angular-independent measure is validated for the use of first- or higher order gradiometers instead of magnetometers. The coilset localization procedure was modified with lock-in detection and current feedback for better long range sensitivity. Real measurements with the 31-channel Philips-MEG system have been carried out. A very good localization accuracy below the measuring area with deviations below 2 mm was found. For coordinate system matching, a 3-D cursor with surface images from segmented MR-data was implemented and an optimized, weighted least squares fit transformation algorithm between functional and morphological systems was developed. The resulting transformations consist of weighted shifts and best-fit rotations and lead to deviations of marker positions in the mm range, depending mainly on the spatial accuracy of the marker fixation.

Algorithms↗

PubMed2004

Ordering of agarose near the macroscopic gelation point.

Gel formation and spatial structure is an important area of study in polymer physics and in macromolecular and cellular biophysics. Agarose has a sufficiently complex gelation mechanism to make it an interesting prototype for many other gelling systems, including those involved in amyloid fibrillogenesis. Static (over a scattering vector range of 0.1-30 microm(-1)) and dynamic light scattering and rheology methods were used to follow the gelation kinetics of agarose at 0.5% in water or in the presence of 25 mM NaCl and quenched to temperatures of 20-43 degrees C. Light scattering results on gelling samples are fully described by a fractal aggregate model with four physically meaningful parameters. In all cases aggregates, with fractal dimensions at or near 3, form more rapidly and are smaller in characteristic size at lower quench temperatures. A region three to four times larger than the aggregate becomes depleted of agarose as the gelation proceeds. Below about 30 degrees C the aggregation process freezes spatial ordering rapidly, resulting in fragile macroscopic gels as determined by rheology. Salt effects are seen to be minimal and not important in the fundamental aggregation mechanism.

Journal Article↗