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PubMed2002

Size-class differences in genetic structure and individual distribution of Camellia japonica L. in a Japanese old-growth evergreen forest.

Size-class differences in genetic structure and individual spatial distribution were investigated for Camellia japonica within a 1-ha plot in a Japanese old-growth evergreen forest using microsatellite markers. Three size-classes were considered containing plants that were: 30-32.5 cm tall, 103.8 cm-200 cm tall and those that had a diameter at breast height > or =5 cm, designated JV1, JV2, and ADL, respectively. Each size-class contained 174 individuals. Morisita's index of dispersion indicated clumping of individuals was present within all size-classes, with JV2 displaying the highest level. The clumped distribution of JV1 individuals may be a result of limited seed dispersal, while that of JV2 may be attributed to heterogenieties of favourable microsites, such as canopy gaps. There were no significant differences in allele frequencies among size-classes. There were, however, some differences in spatial genetic structure among them. Moran's I spatial autocorrelation analysis revealed clear spatial genetic structure in class JV1 probably due to limited seed dispersal. In class JV2, genetic structure was not observed. Overlapping seed shadows, probably in canopy gaps, may lead to blurred genetic structure in JV2.

Camellia↗
PubMed2003

3,3-Diethyl-and 3,3-dibenzyl-1,2-diferrocenylcyclopropenes.

Reactions of 2,3-diferrocenylcyclopropenone 1 with ethyl- and benzylmagnesium chlorides afford 3,3-diethyl-and 3,3-dibenzyl- 1,2-diferrocenylcyclopropenes 2 and 3, respectively, and products of nucleophilic opening of the three-membered ring resulting from the addition of RMgCl to the carbonyl group, viz., saturated ketones(4,5-diferrocenylheptan-3-ones 4a,b and 3,4-diferrocenyl-1,5-diphenylpentan-2-ones 5a,b as ca. 3: 1 mixtures of two diastereomers) and other products. The spatial structures of compounds 2 and 4a were established by X-ray diffraction analysis of single crystals. Protonation of the cyclopropenes 2 and 3 with tetrafluoroboric acid at -40 degrees C yields the corresponding 3,3-dialkyl-1 ,2-diferrocenylcyclopropylium tetrafluoroborates. Transformation of the latter into diferrocenylallylic cations upon increasing the temperature to 20 degrees C and their eprotonation under the action of N,N-dimethylaniline were studied. Electrochemical investigation of 1 and 2 shows that in both complexes the cyclopropene spacer allows electronic communication between the two outer ferrocenyl groups, this being notably greater for 2 than for 1.

Crystallography, X-Ray↗
PubMed2003

Dendrimers in drug research.

Dendrimers are versatile, derivatisable, well-defined, compartmentalised chemical polymers with sizes and physicochemical properties resembling those of biomolecules e.g. proteins. The present critical review (citing 158 references) briefly describes dendrimer design, nomenclature and divergent/convergent dendrimer synthesis. The characteristic physicochemical features of dendrimers are highlighted, showing the effect of solvent pH and polarity on their spatial structure. The use of dendrimers in biological systems are reviewed, with emphasis on the biocompatibility of dendrimers, such as in vitro and in vivo cytotoxicity, as well as biopermeability, biostability and immunogenicity. The review deals with numerous applications of dendrimers as tools for efficient multivalent presentation of biological ligands in biospecific recognition, inhibition and targeting. Dendrimers may be used as drugs for antibacterial and antiviral treatment and have found use as antitumor agents. The review highlights the use of dendrimers as drug or gene delivery devices in e.g. anticancer therapy, and the design of different host-guest binding motifs directed towards medical applications is described. Other specific examples are the use of dendrimers as 'glycocarriers' for the controlled multimeric presentation of biologically relevant carbohydrate moieties which are useful for targeting modified tissue in malignant diseases for diagnostic and therapeutic purposes. Finally, the use of specific types of dendrimers as scaffolds for presenting vaccine antigens, especially peptides, for use in vaccines is presented.

Amines↗
PubMed1990

Reversible and irreversible cross-linking of immunoglobulin heavy chains through their carbohydrate residues.

After periodate oxidation and incubation with a dihydrazide, cross-linking of the two heavy chains of immunoglobulins G from several species proceeds specifically through their oligosaccharides. We have used malonic acid dihydrazide, adipic acid dihydrazide and dithiodipropionic acid dihydrazide. The last compound is introduced in this work as a cleavable-carbohydrate-specific cross-linker. It was found that in rabbit and human immunoglobulins the degree of cross-linking was strongly dependent on the oxidation conditions but only very weakly dependent on the concentration and size of the dihydrazides. Papain cleavage of the cross-linked rabbit IgG indicated that the cross-linking occurred predominantly, if not exclusively, in the Fc region, probably through the two glycans linked to Asn-297 in the CH2 domain of each of the two heavy chains. The immunoglobulins from sheep, pig, goat and guinea pig show a comparable cross-linking pattern, indicating that the sugar chains from these immunoglobulins have a spatial structure closely related to that of rabbit and human IgG. When dithiodipropionic acid dihydrazide was used as the cross-linker, the cross-link could be cleaved by mercaptoethanol.

Animals↗
PubMed2002

Study of the three-dimensional geometry of the central conducting airways in man using computed tomographic (CT) images.

Clinical research on the deposition of inhaled substances (e.g. inhaled medications, airborne contaminants, fumes) in the lungs necessitates anatomical models of the airways. Current conducting airway models lack three-dimensional (3D) reality as little information is available in the literature on the distribution of the airways in space. This is a limitation to the assessment or predictions of the particle deposition in relation to the subject's anatomy. Detailed information on the full topology and morphology of the airways is thus required to model the airway tree realistically. This paper presents the length, diameter, gravity, coronal and sagittal angles that together describe completely the airways in 3D space. The angle at which the airways branch out from their parent (branching angle) and the rotation angle between successive bifurcation planes are also included. These data are from the study of two sets of airways computed tomography (CT) images. One CT scan was performed on a human tracheobronchial tree cast and the other on a healthy male volunteer. The airways in the first nine generations of the cast and in the first six conducting generations of the volunteer were measured using a computer-based algorithm. The data contribute to the knowledge of the lung anatomy. In particular, the spatial structure of the airways is shown to be strongly defined by the central airways with clear angular lobar patterns. Such patterns tend to disappear with a mean gravity, coronal and sagittal angles of 90 degrees in each generation higher than 13-15. The mean branching angle per generation appears independent of the lobe to which the airways belong. Non-planar geometry at bifurcation is observed with the mean (+/- SD) bifurcation plane rotation angle of 79 +/- 410 (n = 229). This angle appears constant over the generations studied. The data are useful for improving the 3D realism of the conducting airway structure modelling as well as for studying aerosol deposition, flow and biological significance of non-planar airway trees using analytical and computational flow dynamics modelling.

Adult↗
PubMed2000

Methodological principles for fractal analysis of trabecular bone.

A standardized methodology for the fractal analysis of histological sections of trabecular bone has been established. A modified box counting method has been developed for use on a PC-based image analyser. The effect of image analyser settings, magnification, image orientation and threshold levels was determined. Also, the range of scale over which trabecular bone is effectively fractal was determined and a method formulated to calculate objectively more than one fractal dimension from the modified Richardson plot. The results show that magnification, image orientation and threshold settings have little effect on the estimate of fractal dimension. Trabecular bone has a lower limit below which it is not fractal (lambda < 25 microm) and the upper limit is 4250 microm. There are three distinct fractal dimensions for trabecular bone (sectional fractals), with magnitudes greater than 1.0 and less than 2.0. It has been shown that trabecular bone is effectively fractal over a defined range of scale. Also, within this range, there is more than one fractal dimension, describing spatial structural entities. Fractal analysis is a model-independent method for describing a complex multifaceted structure, which can be adapted for the study of other biological systems. This may be at the cell, tissue or organ level and complements conventional histomorphometric and stereological techniques.

Femur↗
PubMed2000

Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus).

Habitat fragmentation and destruction associated with the rapid urban and rural development of southeast Queensland presents an immediate threat to the survival of koala populations within this region. A sensitive method combining heteroduplex analysis (HDA) with temperature gradient gel electrophoresis (TGGE) was optimized to detect within-species variation in a mitochondrial DNA (mtDNA) control-region fragment, approximately 670 bp in length, from the koala. Eight different haplotypes were characterized in koalas, of which four were novel. Analysis of mtDNA diversity in 96 koalas from five populations in southeast Queensland revealed that the number of haplotypes in a single population ranged from one to five, with an average within-population haplotype diversity of 0.379 +/- 0.016, and nucleotide diversity of 0.22 +/- 0.001%. Nucleotide divergence between populations averaged 0.09 +/- 0.001% and ranged from 0.00 to 0.14%. Significant genetic heterogeneity was observed among most populations, suggesting that koala populations may be spatially structured along matrilines, although this may not be universal. The limited distribution of the central phylogenetic haplotype suggested the possibility of historical population bottlenecks north of the Gold Coast, while the presence of two highly divergent haplotypes at the Moreton site may indicate the occurrence of one or more undocumented translocation events into this area.

Animals↗
PubMed2001

Correspondence between genet diversity and spatial distribution of above- and below-ground populations of the ectomycorrhizal fungus Hebeloma cylindrosporum.

Population studies of ectomycorrhizal fungal species have largely relied upon fruit body (the reproductive organ) sampling. Analysis of the fruit bodies alone supposes that they reflect the present and spatial organization of all below-ground genets (mycorrhizas and extramatrical mycelia). The relation between fruit bodies and ectomycorrhizas was investigated for the basidiomycete agaric Hebeloma cylindrosporum in four Pinus pinaster stands in south-west France. Genet identification was based on the comparison of polymorphisms within a hypervariable segment of the ribosomal intergenic spacer amplified by polymerase chain reaction (PCR) using a H. cylindrosporum species-specific primer. Mycorrhizas were sorted from soil samples collected underneath patches of fruit bodies or patches where fruit bodies had or had not been observed during the years prior to mycorrhiza collection. On average 65% of the 1026 mycorrhizas collected underneath fruit bodies were formed by H. cylindrosporum, whereas only 2% of the 954 collected in places from where fruit bodies were absent were formed by this species. All genotypes identified above ground were also identified below ground. In patches where one genotype formed all or more than 90% of the fruit bodies, the same genotype formed all or a large majority of the mycorrhizas. In patches occupied by several different fruiting genotypes, additional nonfruiting ones could be present on the root systems. In all cases, the mycorrhizas of one genotype were found no more than 10-20 cm away from its corresponding fruit bodies, and fruit body disappearance at a given place was associated with the disappearance of the corresponding mycorrhizas within 1 year. Although there was not a strict coincidence between the total numbers of genets present below ground and of those forming fruit bodies, fruit body analysis for H. cylindrosporum appears to reflect both the genetic diversity and the spatial structure of its below-ground populations. The results obtained also illustrate the rapid turnover of ectomycorrhizal fungal species on the root systems in the absence of any obvious major disturbance of the ecosystem.

Basidiomycota↗
PubMed2003

Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose.

The wrinkly spreader (WS) genotype of Pseudomonas fluorescens SBW25 colonizes the air-liquid interface of spatially structured microcosms resulting in formation of a thick biofilm. Its ability to colonize this niche is largely due to overproduction of a cellulosic polymer, the product of the wss operon. Chemical analysis of the biofilm matrix shows that the cellulosic polymer is partially acetylated cellulose, which is consistent with predictions of gene function based on in silico analysis of wss. Both polar and non-polar mutations in the sixth gene of the wss operon (wssF ) or adjacent downstream genes (wssGHIJ ) generated mutants that overproduce non-acetylated cellulose, thus implicating WssFGHIJ in acetylation of cellulose. WssGHI are homologues of AlgFIJ from P. aeruginosa, which together are necessary and sufficient to acetylate alginate polymer. WssF belongs to a newly established Pfam family and is predicted to provide acyl groups to WssGHI. The role of WssJ is unclear, but its similarity to MinD-like proteins suggests a role in polar localization of the acetylation complex. Fluorescent microscopy of Calcofluor-stained biofilms revealed a matrix structure composed of networks of cellulose fibres, sheets and clumped material. Quantitative analyses of biofilm structure showed that acetylation of cellulose is important for effective colonization of the air-liquid interface: mutants identical to WS, but defective in enzymes required for acetylation produced biofilms with altered physical properties. In addition, mutants producing non-acetylated cellulose were unable to spread rapidly across solid surfaces. Inclusion in these assays of a WS mutant with a defect in the GGDEF regulator (WspR) confirmed the requirement for this protein in expression of both acetylated cellulose polymer and bacterial attachment. These results suggest a model in which WspR regulation of cellulose expression and attachment plays a role in the co-ordination of surface colonization.

Acetylation↗
PubMed2003

Monoclonal antibodies inducing conformational changes on the antigen molecule.

Monoclonal antibodies (MoAbs) are extensively used as biological tools because of their invariable specificity. However, the interpretation of results can be misled by the behaviour of MoAb displaying allosteric effects, i.e. long-range conformational changes on the antigen (Ag). It has been shown that some MoAbs are able to modify the spatial structure of the corresponding protein Ag, affecting in this way its biological activity as well as its binding to a second MoAb. Thus, a researcher using a MoAb as a tool to investigate some features of an antigenic molecule must be aware of the possible positive or negative allosteric properties of the antibody.

Antibodies, Monoclonal↗
PubMed1997

Identification of a methyl jasmonate-responsive region in the promoter of a lipoxygenase 1 gene expressed in barley grain.

A genomic DNA fragment was isolated containing 5' upstream sequences and part of the open reading frame corresponding to the lipoxygenase 1 cDNA (LoxA) expressed in barley grains during development and germination. Lox1 transcription was shown to be methyl jasmonate (MeJA)- and wound-inducible in leaves, but Lox1 transcripts were not detected in mildew-infected leaves, although this is a commonly observed response to pathogenic attack in various plants. Transient gene expression assays were used to identify a promoter region involved in MeJA-responsive expression. Analysis of 5' and 3' promoter deletions indicated that sequences between -363 and -294 conferred MeJA-responsive expression. Deletions/replacements covering this part of the promoter further defined a MeJA-responsive region between -331 and -291. Insertion of the region -328 to -293 into the constitutive CaMV 35S promoter conferred MeJA-responsive expression. The 36 bp fragment contains the motif TGACG as inverted repeats, which has been previously identified as a binding site for bZIP transactivating factors. Site-directed mutagenesis on these TGACG motifs abolished MeJA-responsive expression, clearly identifying them as MeJA-responsive elements. Sequence comparisons found no similar motif in other characterized promoters of MeJA-inducible genes, but suggested a common spatial structure which may serve as a binding site for transacting factors involved in the MeJA signal transduction pathway.

Abscisic Acid↗
PubMed1999

Human chemokine receptors CCR5, CCR3 and CCR2B share common polarity motif in the first extracellular loop with other human G-protein coupled receptors implications for HIV-1 coreceptor function.

Chemokine receptors (CRs) are 7-helix membrane proteins from the family of G-protein coupled receptors (GPCRs). A few human CRs act as cofactors for macrophage-tropic (M-tropic) human immunodeficiency virus type-1 (HIV-1) entry into cells, while others do not. In this study, we describe an application of molecular modeling techniques to delineate common molecular determinants that might be related to coreceptor activity, and the use of the data to identify other GPCRs as putative cofactors for M-tropic HIV-1 entry. Subsequently, the results were confirmed by an experimental approach. The sequences of extracellular domains (ECDs) of CRs were employed in a compatibility search against a database of environmental profiles derived for proteins with known spatial structure. The best-scoring sequence-profile alignments obtained for each ECD were compared in pairs to check for common patterns in residue environments, and consensus sequence-profile fits for ECDs were also derived. Similar hydrophobicity motifs were found in the first extracellular loops of the CRs CCR5, CCR3, and CCR2B, and are all used by M-tropic HIV-1 for cell entry. In contrast, other CRs did not reveal common motifs. However, the same environmental pattern was also delineated in the first extracellular loop of some human GPCRs showing either high (group 1) or low (group 2) degree of similarity of their polarity patterns with those in HIV-1 coreceptors. To address the question of whether the delineated molecular determinant plays a critical role in the receptor-virus binding, three of the identified GPCRs, bradykinin receptor (BRB2) and G-protein receptor (GPR)-CY6 from group 1, and GPR8 from group 2, were cloned and transfected into HeLa-CD4 cells, which are nonpermissive to M-tropic HIV-1 infection. We demonstrate that, similar to CCR5, the two selected GPCRs from group 1 were capable of mediating M-tropic HIV-1 entry, whereas GPR8 from group 2 did not serve as HIV-1 coreceptor. The potential biological significance of the identified structural motif shared by the human CCR5, CCR3, CCR2B and other GPCRs is discussed.

Amino Acid Sequence↗
PubMed1999

Polypeptide neurotoxins from spider venoms.

Spider venoms contain a variety of toxic components. The polypeptide toxins are divided into low and high molecular mass types. Small polypeptide toxins interacting with cation channels display spatial structure homology. They can affect the functioning of calcium, sodium, or potassium channels. A family of high molecular mass toxic proteins was found in the venom of the spider genus Latrodectus. These neurotoxins, latrotoxins, cause a massive transmitter release from a diversity of nerve endings. The latrotoxins are proteins of about 1000 amino acid residues and share a high level of structure identity. The structural and functional properties of spider polypeptide toxins are reviewed in this paper.

Amino Acid Sequence↗
PubMed1999

Snake venom alpha-neurotoxins and other 'three-finger' proteins.

The review is mainly devoted to snake venom alpha-neurotoxins which target different muscle-type and neuronal nicotinic acetylcholine receptors. The primary and spatial structures of other snake venom proteins as well as mammalian proteins of the Ly-6 family, which structurally resemble the 'three-finger' snake proteins, are also briefly discussed. The main emphasis is placed on recent data characterizing the alpha-neurotoxin interactions with nicotinic acetylcholine receptors.

Amino Acid Sequence↗
PubMedDate not supplied

In vitro reconstituted skin as a tool for biology, pharmacology and therapy: a review.

Various culture procedures, suitable to maintain the differentiated phenotype of various types of cells in vitro, have been devised during the past decade. These culture systems use macromolecular components extracted from extracellular matrixes or synthetic polymers which provide cells with a three-dimensional, spatially structured support. Substantial information has come from the use of collagen lattices. Many types of cells, of mesenchymal or other origin, are able to organize collagen fibrils in these models and to form a connective tissue-like structure. Prerequisites for this process are active function of the cytoskeleton and the expression of alpha(2)beta(1) integrin collagen receptors. Interaction of cells with such a matrix has profound effects on morphologic status, proliferation, cellular metabolism, and state of differentiation. The in vitro procedures reviewed and described in this article offer the possibility to combine different types of cells to approximate the in vivo environment and to investigate such physiologic processes as cell-cell and cell-matrix interactions which are otherwise not easily accessible. In pathologic conditions of the skin, these models have proven to be useful tools in investigating diseases relating to impaired recognition of extracellular matrix structures or alterations of cytoskeletal assembly. In pharmacologic and toxicologic studies, activity of drugs and potentially useful therapeutic substances has been evaluated. The use of cells and matrix components derived from skin has lead to refined systems which could be adapted and extended to other organs in an attempt to better understand pathophysiologic mechanisms.

Journal Article↗
PubMedDate not supplied

Molecular characterization of Mycobacterium tuberculosis complex isolates from wild ungulates in south-central Spain.

The role of European wild ungulates in the epidemiology of tuberculosis (TB) is still under discussion. This study describes the geographical distribution and molecular typing of 77 Mycobacterium tuberculosis complex isolates belonging either to M. bovis or to M. caprae, cultivated from hunter harvested red deer (Cervus elaphus) and European wild boar (Sus scrofa) in 24 Spanish localities, and compares them with spoligotypes detected previously in humans, livestock or wild animals, as described in the literature. The distribution of the molecular type patterns suggests that the population of M. tuberculosis complex strains isolated from Spanish wild ungulates is spatially structured despite the lack of important geographical barriers and despite the increasingly frequent wildlife translocations. Red deer and the European wild boar can share the same molecular types in localities in which the M. tuberculosis complex was isolated from both species. Strains of bovine and caprine origin do circulate in the same local wildlife populations. Six out of 11 spoligotypes were similar to types described in human cases. The isolation of TB strains in fenced estates from wild animals that have not had contact with domestic livestock for at least the past two decades, strongly suggests that the M. tuberculosis complex is able to survive in these populations. Therefore, wildlife including cervids and the wild boar need to be considered in the epidemiology and control of tuberculosis.

Animals↗
PubMed2005

Pulmonary amyloidosis in hematological disorders.

Amyloidosis is defined by tissue deposits of amyloid, a proteic substance with a characteristic spatial structure of beta-sheet fibrils assembled into bundles. This structure results in specific staining with Congo red dye, with green birefringence under polarized light microscope. AL amyloid forms from amyloidogenic immunoglobulins produced by clonal plasma cells. Pulmonary amyloidosis may be either part of systemic amyloidosis (primary amyloidosis or associated with myeloma) or organ-limited. Pulmonary interstitial amyloidosis in systemic amyloidosis is rarely symptomatic unless amyloid deposits severely affect gas exchange alveolar structures, thus resulting in serious respiratory impairment. Localized parenchymal involvement may present as nodular amyloidosis or as amyloid deposits in the vicinity of pulmonary lymphomas. Tracheobronchial amyloidosis, which is not associated with evident clonal proliferation, results in airway stenoses necessitating iterative laser treatment. Treatment of systemic amyloidosis aims at reducing the clonal cell populations producing amyloidogenic immunoglobulins, using high-dose chemotherapy followed by autologous stem cell transplantation in carefully selected patients. Its efficiency in treating diffuse pulmonary amyloidosis has not been established.

Amyloidosis↗
PubMed2003

Discrete breathers in classical ferromagnetic lattices with easy-plane anisotropy.

Discrete breathers (nonlinear localized modes) have been shown to exist in various nonlinear Hamiltonian lattice systems. This paper is devoted to the investigation of a classical d-dimensional ferromagnetic lattice with easy plane anisotropy. Its dynamics is described via the Heisenberg model. Discrete breathers exist in such a model and represent excitations with locally tilted magnetization. They possess energy thresholds and have no analogs in the continuum limit. We are going to review the previous results on such solutions and also to report new results. Among the new results we show the existence of a big variety of these breather solutions, depending on the respective orientation of the tilted spins. Floquet stability analysis has been used to classify the stable solutions depending on their spatial structure, their frequency, and other system parameters, such as exchange interaction and local (single-ion) anisotropy.

Journal Article↗