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At least 1,405 records · Page 78Linked to original sources
PubMed1995

Detailed assessment of spatial hydrophobic and electrostatic properties of 2D NMR-derived models of neurotoxin II.

2D NMR-derived spatial structures of neurotoxin II (NtII) and several homologous toxins in solution were assessed by comparison with their own amino acid sequences using a three-dimensional (3D) profile method. 3D profiles of all the toxin models match the sequences well and, therefore, the method of 3D profile was demonstrated to work correctly for these well-resolved NMR structures in aqueous solution. At the same time, the profile window plots reveal low scores in the bottom tip of loop II (residues 22-34 in NtII) and in beta-strand of loop III (residues 49-52). Some residues in the first poor-scoring region are of functional importance being involved in binding with nicotinic acetylcholine receptor (AChR). Furthermore, the second segment participates in intermolecular hydrogen bonding upon dimerization of postsynaptic neurotoxins in solution resulting in increasing of the 3D-1D score for residues at the interface between monomers. Therefore, the 3D profile method can be useful for detection functionally-important regions in well-resolved protein structures.

Algorithms↗
PubMed1998

A new method to characterize hydrophobic organization of proteins: application to rational protein engineering of barnase.

We present a new algorithm for characterization of protein spatial structure basing on the molecular hydrophobicity potential approach. The method is illustrated by the analysis of three-dimensional structure of barnase and barnase-barstar complex. Current approach enables identification of amino acid residues situated in unfavorable environment (these residues may be "active" for binding), and to map quantitatively hydrophobic, hydrophilic and unfavorable hydrophobic-hydrophilic intra- and inter-molecular contacts involving backbone and side-chain segments of amino acid residues. Calculation of individual contributions of amino acid residues to such contacts permits identification of structurally-important residues. The contact plots obtained with molecular hydrophobicity potential calculations, provide easy rules to choose sites for mutations, which can increase a strength of intra- or inter-molecular hydrophobic interactions. The unfavorable hydrophobic-hydrophilic contact can be mutated to favorable hydrophobic, and already existing weak hydrophobic contact can be strengthen by increasing hydrophobicity of residues in contact. Basing on the analysis of the contact plots, we suggest several mutations of barnase which are supposed to increase intramolecular hydrophobic interactions, and thus might lead to increased stability of the protein. Part of these mutations was studied previously experimentally, and indeed stabilized barnase. The other of predicted mutations were not studied experimentally yet. Several new mutations of barnase and barstar are also proposed to enhance the hydrophobic interactions on their binding interface.

Algorithms↗
PubMed2002

Entropy of protein sequences: an integral approach.

Several classifications of protein spatial structures and their structural elements are known. This makes revealing of the relation between these structural elements and sequence fragments rather topical. The most important move in this direction would be the determination of positional sensitivity levels and ranges between the residues in protein sequences. In this work the Shannon-Weaver informational entropy was used as a disorder criterion for solving this problem. This entropy was computed as function of the distance between the amino acid residues in different sets of unhomological protein sequences. Similarity of this function for different sets of protein sequences was shown. Analysis of informational entropy allows detecting a long-range positional correlation (> or =30) between the amino acid residues and oscillations with periods of 3.6 and 2.9. These oscillation periods correspond to periodicity of alpha- and 3(10)-helices.

Computational Biology↗
PubMed1996

Design of an artificial hemoprotein based on human serum albumin.

For modelling cytochrome P450-catalyzed reactions, an artificial hemoprotein was designed. Upon complex formation of human serum albumin with iron protoporphyrine IX, there occurred the incorporation of heme into the protein and formation of a specific complex with the albumin to heme molar ratio 2:1. The apparent dissociation constant Kd of the complex, as determined by optical absorption spectroscopic technique, was 1.9 +/- 0.4 M-6. Based on spectral studies and molecular modelling of the complex spatial structure, it was assumed that His 31 or His 90 may be the most probable 5th ligand for the heme iron. The artificial hemoprotein was able to catalyze (in the presence of riboflavin as electron carrier) the NADH-dependent aniline hydroxylation and dimethylaniline and amidopyrine N-demethylation. The electron transfer pathway from NADH to substrate was demonstrated. Flavin appears to serve as an input center (mediator) for the rapid transfer of electrons from NADH to heme, where substrate is oxidized. The same reactions were accomplished using riboflavin photoreduction in the hemoalbumin-riboflavin system with the unfocussed laser emission at lambda = 457.9 nm. As electron donor, metallic zinc was used. The artificial hemoprotein obtained was also able to catalyze H2O2-dependent oxidase reactions.

Aminopyrine↗
PubMed1976

The role of nonclassical Fc receptor-associated, Ag-B antigens (Ia) in rat allograft enhancement.

The ability of a hyperimmune Lew anti-BN serum (HIS) to induce enhancement of (Lew/BN)F1 kidneys transplanted into Lew recipients was compared to that of the same antiserum that had been depleted of hemagglutinating anti-Ag-B antibodies by absorption with Brown-Norway (BN) RBC-absorbed sera (RAS) or platelet-absorbed sera (PAS). The RAS and PAS were as effective as the unabsorbed HIS in abrogating early rejection as assessed by renal function and promotion of long-term survival. The absorbed sera retained the capacity to block the mixed lymphocyte culture (MLC) between Lew and BN lymphocytes and to a lesser degree the MLC between Lew and BUF, WF, AUG, and ACI lymphocytes; however, strain specificity was clearly evident at high antiserum dilutions. Similarly, these absorbed sera retained the capacity to block the Fc receptor of BN lymphocytes, and this effect was completely strain specific. In contrast, hemagglutinating and cytotoxic antibodies eluted from platelets used for antiserum absorption did not react with Fc receptors as assessed by rabbit antisheep (IgG)-coated SRBC (EA) rosette formation. F(Ab')2 fragments of PAS also blocked EA rosettes. On the other hand, complement rosettes (EAC) were not inhibited by the HIS. The antibodies were therefore directed against the Fc receptor itself or a structure spatially or functionally closely related to it. Both the Fc receptors and the enhancing capacity of the antisera were strictly specific for the BN genotype. It is suggested that the anti-"Fc receptor" antibody could play an important role in the induction of enhancement by impairing host T-B collaboration as a result of its binding to graft allogeneic "Fc receptors" which appear to be analogous to the major histocompatibility complex (MHC)-coded Ia antigens of the mouse.

Animals↗
PubMed2000

A Reevaluation of Density-Dependent Population Cycles in Open Systems.

Studies motivated by consideration of barnacle populations have led to the prediction of two different dynamic states for space-limited open populations subject to density-dependent mortality. Population densities may cycle or fluctuate stochastically around a mean value. Despite the potential generality of the associated theory, there are few examples of population cycling in open systems that have been shown to be driven by density-dependent effects. This may be because settlement and growth processes are generally too slow or too variable to generate consistent cycles. An alternative explanation is examined in this article using spatially explicit simulations. Even under conditions of consistent settlement and growth, the cycles predicted in at least one previous study are shown to represent a special case. Clear population cycles are only observed when the density-dependent disturbances are constrained to reoccur in exactly the same location. In the more general case, where density-dependent disturbances respond to local variations in population density, the cycling predicted from simple models is difficult to detect. Hence, a failure to detect cycling in population density does not refute a role for density dependence. Density-dependent disturbances can create a characteristic spatial structure consisting of a mosaic of cohorts.

barnacles↗
PubMed2000

Inbreeding Depression and Genetic Rescue in a Plant Metapopulation.

While migration of individuals has been shown to increase the persistence of small isolated populations through a process known as the "rescue effect," the demographic effects that pollen-mediated gene flow may have in plant populations are not known empirically. This study investigates the role that inbreeding depression plays in newly colonized populations of a common, dioecious, weedy species, Silene alba. Experimental greenhouse studies presented here show that S. alba displays high levels of inbreeding depression (expressed as lowered germination success) in progeny produced with inbreeding coefficients of 0.125 (half-sib mated), 0.250 (full-sib mated), and 0.375 (second-generation sib mated). In addition, it is shown that the degree of inbreeding depression in 12 natural colonies varies with the degree of isolation from other established populations. Significantly, data from experimental populations showed that gene flow into patches comprised of full sibs was higher than those observed into patches comprised of unrelated individuals and may serve to mitigate the effects of inbreeding depression. It is suggested that population connectivity through pollen-mediated gene flow may have substantial effects on the persistence of isolated colonies and on the spatial structure of a metapopulation in general.

gene flow↗
PubMed1997

Variations in the 3 micron spectrum across the Orion Bar: polycyclic aromatic hydrocarbons and related molecules.

Long-slit spectra across the Orion Bar reveal significant differences in the spatial behavior of the components of the 3 microns polycyclic aromatic hydrocarbon (PAH) spectrum. The strong PAH band at 3.29 microns generally decreases exponentially with distance from the ionization front into the molecular cloud (scale height approximately 12"), although excesses appear approximately 10" and 20" behind the ionization front, close to layers of H2 and CO emission, respectively. The 3.40 microns PAH feature separates into two components with very different spatial distributions. The main component (at 3.395 microns), along with the 3.51 microns band and the PAH plateau (3.3-3.6 microns), shows excess emission approximately 10" and approximately 20" behind the ionization front, stronger than the excesses in the 3.29 microns band. The extra component of the 3.40 microns band, which peaks at approximately 3.405 microns, has a spatial distribution very similar to the H2 emission. Aromatic C-H stretches in PAHs most likely produce the 3.29 microns feature. Aliphatic C-H stretches in either attached methyl side-groups or superhydrogenated PAHs, or perhaps both, could produce the complicated spectral and spatial structure at 3.40 microns.

Astronomy↗
PubMed2000

A Chandra High-Resolution X-ray Image of Centaurus A.

We present first results from a Chandra X-Ray Observatory observation of the radio galaxy Centaurus A with the High-Resolution Camera. All previously reported major sources of X-ray emission including the bright nucleus, the jet, individual point sources, and diffuse emission are resolved or detected. The spatial resolution of this observation is better than 1&arcsec; in the center of the field of view and allows us to resolve X-ray features of this galaxy not previously seen. In particular, we resolve individual knots of emission in the inner jet and diffuse emission between the knots. All of the knots are diffuse at the 1&arcsec; level, and several exhibit complex spatial structure. We find the nucleus to be extended by a few tenths of an arcsecond. Our image also suggests the presence of an X-ray counterjet. Weak X-ray emission from the southwest radio lobe is also seen, and we detect 63 pointlike galactic sources (probably X-ray binaries and supernova remnants) above a luminosity limit of approximately 1.7x1037 ergs s-1.

Journal Article↗
PubMed2004

From individual behavior to metapopulation dynamics: unifying the patchy population and classic metapopulation models.

Spatially structured populations in patchy habitats show much variation in migration rate, from patchy populations in which individuals move repeatedly among habitat patches to classic metapopulations with infrequent migration among discrete populations. To establish a common framework for population dynamics in patchy habitats, we describe an individual-based model (IBM) involving a diffusion approximation of correlated random walk of individual movements. As an example, we apply the model to the Glanville fritillary butterfly (Melitaea cinxia) inhabiting a highly fragmented landscape. We derive stochastic patch occupancy model (SPOM) approximations for the IBMs assuming pure demographic stochasticity, uncorrelated environmental stochasticity, or completely correlated environmental stochasticity in local dynamics. Using realistic parameter values for the Glanville fritillary, we show that the SPOMs mimic the behavior of the IBMs well. The SPOMs derived from IBMs have parameters that relate directly to the life history and behavior of individuals, which is an advantage for model interpretation and parameter estimation. The modeling approach that we describe here provides a unified framework for patchy populations with much movements among habitat patches and classic metapopulations with infrequent movements.

Animal Migration↗
PubMed2006

On testing the competition-colonization trade-off in a multispecies assemblage.

The competition-colonization trade-off has long been considered an important mechanism explaining species coexistence in spatially structured environments, yet data supporting it remain ambiguous. Most competition-colonization research examines plants and the dispersal-linked traits of their seeds. However, colonization is more than just dispersal because rapid population growth is also an important component of colonization. We tested for the presence of competition-colonization trade-offs with a commonly used artificial assemblage consisting of protozoan and rotifer species, where colonization was the ability of a species to establish populations in patches. By ranking species according to their colonization abilities and their pairwise competitive interactions, we show that these species exhibit competition-colonization trade-offs. These results reveal that the competition-colonization trade-off exists within nonplant assemblages and that even in a laboratory setting, species are constrained to be either good competitors or colonizers but not both.

Animals↗
PubMed2004

Physical schemata underlying biological pattern formation-examples, issues and strategies.

Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the harnessing of pattern-forming processes of non-equilibrium physics and chemistry. For these systems, the study of biological pattern formation starts with placing a biological phenomenon of interest within the context of the proper pattern-formation schema and then focusing on the ways in which control is exerted to adapt the pattern to the needs of the organism. This approach is illustrated by several examples, notably bacterial colonies (diffusive-growth schema) and intracellular calcium waves (excitable-media schema).

Animals↗
PubMed2005

Change in spatial distribution patterns of a biennial plant between growth stages and generations in a patchy habitat.

BACKGROUND AND AIMS: The aim of the study was to evaluate factors causing change in spatial distribution patterns of plants between growth stages and generations for a monocarpic biennial plant, Lysimachia rubida. It was assumed that habitat heterogeneity was a primary factor determining spatial patterns of plants, and a randomization procedure was developed for testing the null hypothesis that only spatial association with ground surface conditions determined spatial patterns of plants. METHODS: A 5-year demographic census was conducted on an open dry habitat that was heterogeneous with regard to the ground surface conditions. KEY RESULTS: There was significant habitat association in that plants at vegetative and reproductive stages were denser in areas with smaller gravel than with larger gravel. Point process analyses rejected the null hypothesis of the spatial association with ground surface conditions. CONCLUSIONS: The results suggest that other factors, such as patchy seed dispersal, secondary dispersal of the seeds and life-history variation at various spatial scales, also affected spatial patterns of individuals in a population of L. rubida. Spatial structures and dynamics of a local population in a patchy habitat represent various performances of plants within patches and seed dispersal within a patch and beyond the patch.

Ecosystem↗
PubMed2001

STOCHSIM: modelling of stochastic biomolecular processes.

SUMMARY: STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of STOCHSIM provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neighbour interactions of molecules in a 2-D lattice can be simulated.

Algorithms↗
PubMed2006

Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model.

MOTIVATION: Comparative genomic hybridization array experiments that investigate gene copy number changes present new challenges for statistical analysis and call for methods that incorporate spatial dependence between sequences along the chromosome. For this purpose, we propose a novel method called CGHmix. It is based on a spatially structured mixture model with three states corresponding to genomic sequences that are either unmodified, deleted or amplified. Inference is performed in a Bayesian framework. From the output, posterior probabilities of belonging to each of the three states are estimated for each genomic sequence and used to classify them. RESULTS: Using simulated data, CGHmix is validated and compared with both a conventional unstructured mixture model and with a recently proposed data mining method. We demonstrate the good performance of CGHmix for classifying copy number changes. In addition, the method provides a good estimate of the false discovery rate. We also present the analysis of a cancer related dataset. SUPPLEMENTARY INFORMATION: http://www.bgx.org.uk/papers.html

Algorithms↗
PubMed2002

Pupil response components: studies in patients with Parinaud's syndrome.

In addition to light flux changes, it is well established that other stimulus attributes such as colour, spatial structure or movement can also cause a transient constriction of the pupil, even when the onset of the stimulus causes a net decrease in light flux level on the retina. Although experimental findings in human subjects with postgeniculate lesions show that the generation of such responses must involve the processing of stimulus attributes in extrastriate areas of the cortex, little is known about the site of integration of cortical signals into the pupillomotor pathway. We have investigated how visual performance and the various components of the pupil response have been affected in subjects with damage to the dorsal midbrain (Parinaud's syndrome). The results show that the probable destruction of the olivary pretectal nucleus and the nucleus of the optic tract has little or no effect on pupil grating or pupil colour responses. The light reflex response, on the other hand, is virtually abolished, with only a small residual component that is similar to the pupil grating response and may not require an afferent projection to the midbrain. These new findings suggest that the site of integration of cortical signals in relation to pupil colour and grating responses and the generation of sleepiness-induced oscillations of the pupil do not rely on the normal functioning of pretectal nuclei that are involved in the light reflex response.

Adult↗
PubMed2003

High-resolution analysis of the spatio-temporal activity patterns in rat olfactory bulb evoked by enantiomer odors.

Understanding how mammals process olfactory stimuli has motivated the development of tools and techniques which permit the simultaneous study of finely structured spatial and temporal patterns of neural activity. A technique is described that uses an array of 32 penetrating microelectrodes implanted bilaterally into the dorsal aspect of rat olfactory bulb to investigate the responses of mitral and tufted neurons to stimulation with simple enantiomer odor pairs at a number of concentrations. It is shown that stable, simultaneous recordings from up to 49 single- and multi-units can be performed for periods of up to 14 h. We show that such odors evoke unique spatial and fast-temporal activity patterns which may subserve odor discrimination. This technique is extensible to other systems neuroscience investigations of olfactory sensory processing.

Animals↗
PubMed2003

Fixation probability and time in subdivided populations.

New alleles arising in a population by mutation ultimately are either fixed or lost. Either is possible, for both beneficial and deleterious alleles, because of stochastic changes in allele frequency due to genetic drift. Spatially structured populations differ from unstructured populations in the probability of fixation and the time that this fixation takes. Previous results have generally made many assumptions: that all demes contribute to the next generation in exact proportion to their current sizes, that new mutations are beneficial, and that new alleles have additive effects. In this article these assumptions are relaxed, allowing for an arbitrary distribution among demes of reproductive success, both beneficial and deleterious effects, and arbitrary dominance. The effects of population structure can be expressed with two summary statistics: the effective population size and a variant of Wright's F(ST). In general, the probability of fixation is strongly affected by population structure, as is the expected time to fixation or loss. Population structure changes the effective size of the species, often strongly downward; smaller effective size increases the probability of fixing deleterious alleles and decreases the probability of fixing beneficial alleles. On the other hand, population structure causes an increase in the homozygosity of alleles, which increases the probability of fixing beneficial alleles but somewhat decreases the probability of fixing deleterious alleles. The probability of fixing new beneficial alleles can be simply described by 2hs(1 - F(ST))N(e)/N(tot), where hs is the change in fitness of heterozygotes relative to the ancestral homozygote, F(ST) is a weighted version of Wright's measure of population subdivision, and N(e) and N(tot) are the effective and census sizes, respectively. These results are verified by simulation for a broad range of population structures, including the island model, the stepping-stone model, and a model with extinction and recolonization.

Alleles↗