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At least 847 records · Page 47Linked to original sources
PubMed1992

[Study of the structure of the duplex (Phn-NH(CH2)2NH)pd(CCAAACA) .pd(TGTTTGGC) with covalently bound 10-(2-hydroxyethyl)phenazine in an aqueous solution by 2D-1H-NMR spectroscopy].

The spatial structure of duplex (Phn-NH(CH2)2NH)pd(CCAAACA).pd(TGTTTGGC) having a N-(2-oxyethyl)-phenazinium residue covalently linked with the 5'-terminal phosphate of the heptanucleotide was studied by means of one- and two-dimensional 1H-NMR spectroscopy. The resonances of phenazinium protons, ethylenediamine linker protons, as well as, oligonucleotide H5/H6/H8/CH3 base protons and H1',H2'a, H2'b, H3', H4' deoxyribose protons have been assigned by means of 1H-COSY, 1H-NOESY and 1H-13C-COSY. The presence of the phenazine residue in duplex causes an additional imino proton signal of the terminal (G-7).(C-1) base pair, suggesting a higher stability of the duplex (Phn-NH(CH2)2NH)pd(CCAAACA).pd(TGTTTGGC) as compared to the unmodified duplex pd(CCAAACA).pd(TGTTTGGC). Analysis of NOE interactions between protons of the dye and the oligonucleotides show the phenazinium polycyclic system to intercalate between G-7 and C-8 residues of the octanucleotide.

Indicators and Reagents↗
PubMed2005

Pair statistics clarify percolation properties of spatially explicit simulations.

Dispersal is a fundamental control on the spatial structure of a population. We investigate the precise mechanism by which a mixed strategy of short- and long-distance dispersal affects spatial patterning. Using techniques from pair approximation and percolation theory, we demonstrate that dispersal controls the extent to which a population is completely connected by modulating the proportion of neighboring sites which are simultaneously occupied. We show that near the percolation threshold this pair statistic, rather than other metrics proposed earlier, best explains clustering, and we suggest more general circumstances under which this may hold.

Cluster Analysis↗
PubMed2003

Spatial models of prebiotic evolution: soup before pizza?

The problem of information integration and resistance to the invasion of parasitic mutants in prebiotic replicator systems is a notorious issue of research on the origin of life. Almost all theoretical studies published so far have demonstrated that some kind of spatial structure is indispensable for the persistence and/or the parasite resistance of any feasible replicator system. Based on a detailed critical survey of spatial models on prebiotic information integration, we suggest a possible scenario for replicator system evolution leading to the emergence of the first protocells capable of independent life. We show that even the spatial versions of the hypercycle model are vulnerable to selfish parasites in heterogeneous habitats. Contrary, the metabolic system remains persistent and coexistent with its parasites both on heterogeneous surfaces and in chaotically mixing flowing media. Persistent metabolic parasites can be converted to metabolic cooperators, or they can gradually obtain replicase activity. Our simulations show that, once replicase activity emerged, a gradual and simultaneous evolutionary improvement of replicase functionality (speed and fidelity) and template efficiency is possible only on a surface that constrains the mobility of macromolecule replicators. Based on the results of the models reviewed, we suggest that open chaotic flows ('soup') and surface dynamics ('pizza') both played key roles in the sequence of evolutionary events ultimately concluding in the appearance of the first living cell on Earth.

Animals↗
PubMed1986

Dissipative structures in a two-cell system: Numerical and experimental approaches.

It has been shown that the coupling between the photoreduction of the oxidized form of dichloroindophenol (an artificial electron acceptor) by thylakoids and the incident light intensity can lead to the appearance of multiple steady states when the system is operated under open conditions. In the present work, a numerical study and experimental evidence are presented on the occurrence of dissipative structures in an arrangement of two continuously stirred tank reactors with mutual mass exchange of dichloroindophenol through an inert membrane. The stable spatial structures are generated by the creation of transient internal and external asymmetries. A nontrivial hysteresis effect between symmetric and asymmetric stable steady states has been observed.

Journal Article↗
PubMed2000

Tryptophan 140 is important, but serine 141 Is essential for the formation of the integrated conformation of staphylococcal nuclease.

A series of N-terminal fragments of staphylococcal nuclease with different chain lengths has been taken as an in vitro nascent peptide folding model. Previous studies have shown that nascent peptide folding of the nuclease may begin early in the synthetic process with the content of ordered secondary structure increases with increasing peptide chain length, and that conformational adjustments are observed at certain stages during nascent peptide folding. Here, we focus attention on the conformational changes in the later stage of nascent peptide folding of the nuclease when the N-terminal fragment elongates nearly to the C-terminus of the nuclease in order to determine the role of the C-terminal region of the nuclease in the formation of the integrated conformation of the nuclease. We compared the conformational features of SNase R and its larger N-terminal fragments SNR135, SNR139, SNR140, and SNR141 using circular dichroism spectra, ANS-binding fluorescence and intrinsic fluorescence spectra. The results show that Trp140 is important for the enrichment of ordered secondary structure and for producing a greater ability to fold into a native-like conformation, but Ser141 is essential for the formation of the integrated conformation of the nuclease with a tightly packed tertiary structure. Note that the addition of only one residue to the C-terminus of elongating peptide chain can cause a dramatic change in conformation. The data also show the occurrence of continuous adjustments in conformation during peptide elongation, even after a rigid tertiary structure has formed, suggesting that the last eight residues (residues 142-149), which are disordered at the C-terminus of the nuclease, also possess a structural role, forming the native tertiary structure to provide a framework for the active site, even though they are remote from the active site in both sequence and spatial structure.

Anilino Naphthalenesulfonates↗
PubMed2000

Spiral intensity patterns in the internally pumped optical parametric oscillator

We describe a nonlinear optical system that supports spiral pattern solutions in the field intensity. This new spatial structure is found to bifurcate above a secondary instability in the internally pumped optical parametric oscillator. The analytical predictions of threshold and spatial scale for the instability are supplemented by detailed numerical investigations of the formation of spiral patterns.

Journal Article↗
PubMed2004

Hierarchical Bayesian modeling in dichotomous processes in the presence of nonresponse.

Sampling units that do not answer a survey may dramatically affect the estimation results of interest. The response may even be conditional on the outcome of interest in the survey. If estimates are found using only those who responded, the estimate may be biased, known as nonresponse bias. We are interested in finding estimates of success rates from a survey. We begin by looking at two current Bayesian approaches to treating nonresponse in a hierarchical model. However, these approaches do not consider possible spatial correlations between domains for either success rate or response rate. We build a Bayesian hierarchical spatial model to explicitly estimate the success rate, response rate given success, and response rate given failure. The success rates in the domains of the survey are allowed to be spatially correlated. We also allow spatial dependence between domains in both response rate given success and response rate given failure. Spatial dependence is induced by a common latent spatial structure between the two conditional response rates. We use the 1998 Missouri Turkey Hunting Survey to illustrate this methodology. We find significant spatial correlation in the success rates and incorporating nonrespondents has an impact on the success rate estimates.

Animals↗
PubMed2005

Wave-like spread of Ebola Zaire.

In the past decade the Zaire strain of Ebola virus (ZEBOV) has emerged repeatedly into human populations in central Africa and caused massive die-offs of gorillas and chimpanzees. We tested the view that emergence events are independent and caused by ZEBOV variants that have been long resident at each locality. Phylogenetic analyses place the earliest known outbreak at Yambuku, Democratic Republic of Congo, very near to the root of the ZEBOV tree, suggesting that viruses causing all other known outbreaks evolved from a Yambuku-like virus after 1976. The tendency for earlier outbreaks to be directly ancestral to later outbreaks suggests that outbreaks are epidemiologically linked and may have occurred at the front of an advancing wave. While the ladder-like phylogenetic structure could also bear the signature of positive selection, our statistical power is too weak to reach a conclusion in this regard. Distances among outbreaks indicate a spread rate of about 50 km per year that remains consistent across spatial scales. Viral evolution is clocklike, and sequences show a high level of small-scale spatial structure. Genetic similarity decays with distance at roughly the same rate at all spatial scales. Our analyses suggest that ZEBOV has recently spread across the region rather than being long persistent at each outbreak locality. Controlling the impact of Ebola on wild apes and human populations may be more feasible than previously recognized.

Animals↗
PubMed2000

Structure and folding of bacteriophage T4 gene product 9 triggering infection. II. Study Of conformational changes of gene product 9 mutants using monoclonal antibodies.

Gene product 9 (gp9) of bacteriophage T4, whose spatial structure we have recently solved to 2.3 A resolution, is a convenient model for studying the folding and oligomerization mechanisms of complex proteins. The gp9 polypeptide chain consists of 288 amino acids forming three domains. Three monomers, packed in parallel, assemble to a functionally active protein. The main aim of this work was to study conformational changes and trimerization of gp9 deletion mutants using monoclonal antibodies (mAbs). We selected a set of mAbs interacting with the amino, middle, and carboxyl regions of the protein, respectively. Eighteen mAbs bind to native as well as to denatured protein, and two mAbs bind to denatured protein only. Using mAbs, we found that deletions of the gp9 N-terminal region result in conformational changes in the middle and C-terminal domains. The study of mAb binding to the CDelta. truncated mutant by competitive ELISA and immunoblotting shows that the C-terminus of the gp9 sequence is essential for protein trimerization and stability. A single point substitution of the Gln282 residue causes formation of a labile trimer that has significant conformational changes in the protein domains. The results of our study show that folding and trimerization of gp9 is a cooperative process that involves all domains of the protein.

Animals↗
PubMedDate not supplied

[Structural organization of alpha-melanotropin molecules].

Using a semi-empirical method, and a priori conformational analysis of the tridecapeptide alpha-melanocyte-stimulating (alpha-MSH) was carried out. The spatial structure of alpha-MSH can be described by ten low-energy conformations. Calculations produced the values of all dihedral angles of the backbones and side chains of these forms as well as intra- and inter-residue interaction energies.

Melanocyte-Stimulating Hormones↗
PubMed2005

Nanoconstructions based on double-stranded nucleic acids.

We describe the formation and properties of nanoconstruction that consists of the double-stranded DNA molecules located at distance of 35-50 A in the spatial structure of particles of their cholesteric liquid-crystalline dispersions and cross-linked by artificial nanobridges. The resulting nanostructures possess the peculiar spatial and optical properties.

Chitosan↗
PubMed2003

[Microphytobenthos assemblage mapping by spatial visible-infrared remote sensing in a shellfish ecosystem].

The aim of this work is to assess the use of (SPOT) multispectral visible infrared remote sensing to study microphytobentos assemblages in a shellfish ecosystem (Bay of Bourgneuf, France). SPOT satellite images (acquired at low tide in spring or autumn between 1986 and 1998) were calibrated using in situ radiometric data, and the normalised vegetation index (NDVI) obtained from these images showed microphytobenthos on bay mudflats. Proliferation was mainly along a north-south strip, essentially localised around the +2 m isobath and covering a surface area of 19 to 25% of the total mudflat area studied (420 to 550 ha). Three factors seem to be responsible for the spatial structure of the assemblages: bathymetry, nutrient input from the Falleron River and its channel, and the location of oyster-farming areas. Although spatial and spectral resolutions of multispectral remote sensing data have certain limitations, this approach opens up a new field of application for hyperspectral remote sensing, particularly for synoptic mapping of biomass distribution.

Animals↗
PubMed1995

Effect of substitution for arginine residues near position 146 of the A subunit of Escherichia coli heat-labile enterotoxin on the holotoxin assembly.

Escherichia coli heat-labile enterotoxin (LT) is a holotoxin which consists of one A and five B subunits. Although B subunit monomers released into periplasm can associate into pentameric structures in the absence of the A subunit, the A subunit accelerates the assembly. To express the function, A subunit constructs the proper spatial structure. However, the regions involved in the construction are unknown. To identify the regions, we substituted arginine residues near position 146 of the A subunit with glycine by oligonucleotide-directed site-specific mutagenesis and obtained the mutants expressing LT(R141G), LT(R143G), LT(R146G), LT(R143G, R146G), LT(R141G, R143G, R146G) and LT(R143G, R146G, R148G). We purified these mutant LTs by using an immobilized D-galactose column and analyzed the purified mutant LTs by SDS-PAGE to examine the amount of A subunit associated with B-subunit oligomer. The substitution of an arginine residue at any position did not induce a significant alteration in the amount of A subunit associated with B-subunit oligomer. However, the substitution of more than two arginine residues induced a significant decrease in the amount of A subunits associated with the B-subunit oligomer. Subsequently, we measured the level of the intracellular B-subunit oligomer of these mutant strains. The measurement revealed that the amount of B-subunit oligomer in cells decreased as the number of substituted arginine residues increased. These results show that all arginine residues near position 146 are important for the construction of the functional A subunit, and thus for holotoxin formation, although each individual arginine residue is not an absolute requirement.

Amino Acid Sequence↗
PubMed1995

Spatial analysis of nuclear and mitochondrial RFLP genotypes in populations of the chestnut blight fungus, Cryphonectria parasitica.

Spatial structure of both nuclear and mitochondrial RFLPs were studied in several populations of the chestnut blight fungus, Cryphonectria parasitica, using a variety of spatial autocorrelation tests designed to detect nonrandom patterns. Fungal individuals were sampled from cankers on infected chestnut trees, and the location of each tree was mapped. Single-locus nuclear RFLPs, nuclear fingerprints, and mitochondrial DNA haplotypes were determined for each individual. Individuals with the same DNA fingerprint genotypes occurred closer together than would be expected at random in four of the five plots, while mitochondrial DNA haplotypes were aggregated in all five plots. Genetic distances between individuals, expressed as one minus the proportion of shared restriction fragment size classes for fingerprints and mitochondrial haplotypes, were significantly correlated with Euclidean distances between individuals in four of the five populations, but these correlations were very weak (r < 0.18). The same DNA fingerprint and single-copy nuclear RFLP alleles occurred on the same trees or immediately neighbouring trees more often than would be expected at random. Most of the aggregation for all three genetic markers occurred among individuals within the same cluster of chestnut stems or on neighbouring trees. Lack of spatial autocorrelation in one population was probably due to sampling on a larger scale that was too coarse to detect any patterns. Significant aggregation of genotypes in C. parasitica is most likely caused by some degree of restricted dispersal within populations. The implications of restricted dispersal are discussed in relation to the breeding system and isolation by distance in populations of C. parasitica.

Cell Nucleus↗
PubMedDate not supplied

[Approach to a priori calculation of stable forms of proteins].

Basing on semi-empirical conformational analysis an approach is suggested to the calculation of stable forms of protein molecules. The physical model proposed implies: 1) that the most stable conformation of a protein corresponds to its native state, 2) that interactions of three types which determine conformational states of every residue should be treated separately, 3) that the protein molecule is highly compact structure with interactions of different kinds compensating each other, 4) that interactions of the three types contribute differently to the formation of the spatial structure of a globule. These interactions are: 1) those of peptide chain atoms within a particular residue, 2) interactions of the residue with the nearest neighbours in the chain, 3) interactions with residues which are remote in the chain but close in the globule. The approach proposed allows to separate the conformational analysis of a protein into a number of subsequently solved problems. The scheme of the calculation of stable forms is presented.

Drug Stability↗
PubMed1996

The structure of bovine mitochondrial adenylate kinase: comparison with isoenzymes in other compartments.

In vertebrates, there are different adenylate kinases in the compartments cytosol, mitochondrial intermembrane space, and mitochondrial matrix. Here, we report the spatial structure of the intermembrane species established in two crystal forms by X-ray diffraction analyses at 1.92 and 2.1 A resolution. In both structures, the enzyme is unligated, and thus in an "open" conformation. The enzyme was prepared from bovine liver, containing at least five variants arisen from posttranscriptional and posttranslational modifications. It could only be crystallized after removing some of these variants. A comparison with the known structures of the adenylate kinases from cytosol and mitochondrial matrix reveals structural differences that should play a role in protein targeting because none of these enzymes contains a cleavable signal peptide. A further comparison with adenylate kinases from Gram-positive bacteria showed that the structural Zn2+ ion of these species is replaced by a strictly conserved assembly of hydrogen bonded residues.

Adenylate Kinase↗
PubMed2005

Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution.

Contrary to the well known diffraction limit, the fluorescence microscope is in principle capable of unlimited resolution. The necessary elements are spatially structured illumination light and a nonlinear dependence of the fluorescence emission rate on the illumination intensity. As an example of this concept, this article experimentally demonstrates saturated structured-illumination microscopy, a recently proposed method in which the nonlinearity arises from saturation of the excited state. This method can be used in a simple, wide-field (nonscanning) microscope, uses only a single, inexpensive laser, and requires no unusual photophysical properties of the fluorophore. The practical resolving power is determined by the signal-to-noise ratio, which in turn is limited by photobleaching. Experimental results show that a 2D point resolution of <50 nm is possible on sufficiently bright and photostable samples.

Fluorescence↗