Substructure Pattern Research Articles

Investigations into the Genetic Variation, Population Structure, and Breeding Systems of the Fern Asplenium trichomanes subsp. quadrivalens.

The genetic structure of five populations of the tetraploid fern Asplenium trichomanes subsp. quadrivalens in northern Switzerland was analyzed. Asplenium trichomanes subsp. quadrivalens is one of the most common and most widespread ferns in Europe. In this study we have combined genetic investigations, spatial autocorrelation, and breeding experiments to investigate in detail five populations from natural rock faces. Enzyme electrophoresis revealed very low genetic variability within and among the populations. The small amount of variation was partitioned mainly among the localities, indicated by high Fst values up to 0.764. Overall means of the proportion of polymorphic loci (P=0.076), the mean number of alleles per locus (A=1.086), and the mean expected heterozygosity (H=0.018) were low compared with other ferns (e.g., Kirkpatrick et al. 1990). Very few heterozygous individuals were found. Values of the fixation index (F) were high, ranging between 0.732 and 1.000 and indicating substantial inbreeding. Spatial autocorrelation showed different patterns of substructure in populations of A. trichomanes subsp. quadrivalens with a tendency for patches in short distances (up to 1.5 m). The breeding experiments with isolated prothalli and prothalli pairs showed that a mean of 56.4% of the isolated prothalli were successful in sporophyte formation. The highest rate in one population was 83.3%. We conclude that genetic load must be low in A. trichomanes subsp. quadrivalens. Sporophyte formation was statistically more successful in the experiments with gametophyte pairs than in isolates, indicating that additional cross-fertilization occurred. The latter agreed with the occurrence of few heterozygote samples and the small number of multilocus phenotypes found in natural habitats. Asplenium trichomanes subsp. quadrivalens is shown to be a highly inbreeding taxon with the capability of single spore colonization and subsequent founding of new populations. Such features can be hypothesized to have contributed to the postglacial colonization and the widespread distribution of this taxon in Europe.

Diamine oxidase-gold enzyme-affinity ultrastructural demonstration that human gut mucosal mast cells secrete histamine by piecemeal degranulation in vivo

Biopsy specimens of human ilea were prepared for the ultrastructural detection of histamine in vivo with a new enzyme-affinity method (Dvorak et al., J Histochem Cytochem 1993; 41:787-800). Human gut mucosal mast cells contained histamine in cytoplasmic secretory granules that were electron dense, regardless of underlying substructural patterns. Partially and completely empty cytoplasmic granules, characteristic for piecemeal degranulation (Dvorak et al., Int Arch Allergy Immunol 1992;99:74-83) had diminished and absent histamine stores, whereas electron-dense granules in the same cells retained their histamine. Interstitial collagen (but not basal lamina of other cells) near secretory mast cells avidly bound histamine, thereby providing a potential source for re-release of extracellular histamine stores. These studies provide the first documentation of histamine secretion in vivo during piecemeal degranulation of human mast cells.

Ultrastructural detection of histamine in human mast cells developing from cord blood cells cultured with human or murine recombinant c-kit ligands.

Immature human mast cells, arising from cord blood mononuclear cells cultured in the presence of the c-kit ligand of human or murine origin, contain mixtures of morphologically immature and mature secretory granules. Use of a new cytochemical technique to localize histamine in ultrastructural samples (based on the affinity of the enzyme, histaminase, for its substrate, histamine) localized this amine to mature mast cell granules of all substructural patterns present, as well as to condensation foci appearing in immature cytoplasmic granules. This cytochemical evidence of histamine bound to condensation foci during granule building in developing mast cells is analogous to evidence obtained during granule recovery of degranulated human basophils and mast cells.

Ultrastructure of lingual salivary glands in the American chameleon: Anolis carolinensis

That portion of the dorsal surface of the tongue of Anolis carolinensis that is covered by plumose papillae is underlaid by a series of tubular salivary glands that open between the papillae; glands persist into the posterior zone of the tongue, where they open between cylindriform papillae. Anterior glands are serous in nature--they consist of simple columnar epithelial cells that contain abundant secretory granules exhibiting a variety of substructural patterns. The Golgi apparatus is large and of unusual appearance, with numerous closely packed terminal dilatations and condensing vacuoles. Near the posterior border of the lingual zone covered by plumose papillae, mucous cells begin to appear in the glandular epithelium. More posteriorly, the apical portions of the glands consist entirely of mucous cells, whereas the blind ends of the glands are composed of serous cells. The most posterior glands are of the pure mucous variety. The glands finally disappear a short distance posterior to the cylindriform papillae. The functions of the abundant and highly differentiated salivary glands of the Anolis tongue remain obscure.

The use of mathematical logics in drug design

Topological pharmacophores are two-dimensional substructural patterns characteristic of compounds possessing a desired biological property (e.g. high activity) while absent from compounds devoid of this property. Two methods, LOGANA and LOCON, for the evaluation of such pharmacophores are presented. They extract essential information from large and diverse sets of compounds. The reported algorithm for the development of topological pharmacophores is based on the stepwise combination of substructural descriptors by means of logical operations.

Human Mast Cells Synthesize New Granules During Recovery From Degranulation. In Vitro Studies With Mast Cells Purified From Human Lungs

Secretory cells undergoing release and recovery events related to constitutive and/or stimulus-initiated secretion might be expected to undergo distinctive changes in morphology as well. We studied the release and recovery events of human mast cell secretion stimulated by antibody to immunoglobulin E. We used enzymatically digested mast cells from human lung specimens further purified by countercurrent centrifugation elutriation. Release kinetics were like those reported for isolated human lung mast cells. In two complete kinetic experiments we restudied these early release patterns (0 to 30 minutes). Mast cells, either stimulated or controls, were then cultured and sampled for electronmicroscopic studies at periodic intervals (3 to 48 hours). We describe events of the late recovery period here, although some overlap with processes seen in early recovery samples occurred. Mast cells that released nearly all their cytoplasmic granules and exteriorized the containers, eg, granule-channel membranes, underwent progressive enlargement of Golgi structures and development of numerous small cytoplasmic vesicles and small, membrane-bound granules filled with particulate and dense content. Ultimately, new mature cytoplasmic granules of all substructural patterns occurred. Nuclear blast changes and expansion of cytoplasmic mass accompanied this period of new granule synthesis. Mixed recovery patterns were present in individual cells. These represented the morphological expression of a variety of recovery events. Thus, some cells showed a combination of channel recovery and remodeling to form new granule containers within which condensation of content produced crystalline patterns, as well as synthesis of new granules, as described here. This morphological versatility resulted in multiple mast cell morphological phenotypes during these release and recovery processes.

Human mast cells synthesize new granules during recovery from degranulation. In vitro studies with mast cells purified from human lungs

Secretory cells undergoing release and recovery events related to constitutive and/or stimulus-initiated secretion might be expected to undergo distinctive changes in morphology as well. We studied the release and recovery events of human mast cell secretion stimulated by antibody to immunoglobulin E. We used enzymatically digested mast cells from human lung specimens further purified by countercurrent centrifugation elutriation. Release kinetics were like those reported for isolated human lung mast cells. In two complete kinetic experiments we restudied these early release patterns (0 to 30 minutes). Mast cells, either stimulated or controls, were then cultured and sampled for electronmicroscopic studies at periodic intervals (3 to 48 hours). We describe events of the late recovery period here, although some overlap with processes seen in early recovery samples occurred. Mast cells that released nearly all their cytoplasmic granules and exteriorized the containers, eg, granule-channel membranes, underwent progressive enlargement of Golgi structures and development of numerous small cytoplasmic vesicles and small, membrane-bound granules filled with particulate and dense content. Ultimately, new mature cytoplasmic granules of all substructural patterns occurred. Nuclear blast changes and expansion of cytoplasmic mass accompanied this period of new granule synthesis. Mixed recovery patterns were present in individual cells. These represented the morphological expression of a variety of recovery events. Thus, some cells showed a combination of channel recovery and remodeling to form new granule containers within which condensation of content produced crystalline patterns, as well as synthesis of new granules, as described here. This morphological versatility resulted in multiple mast cell morphological phenotypes during these release and recovery processes.

Substructural QSAR approaches and topological pharmacophores.

For large and diverse data sets, simple QSAR methods based on linear and additive models can no longer be applied. In such cases topological methods using descriptors directly derivable from two-dimensional chemical structures provide a useful alternative. The results of such analyses can be used for lead optimization, to guide biological testing and even aid in the design of novel compounds. Various types of topological descriptors and algorithms are briefly discussed. Which of those is to be selected depends on the objective of the investigation and the properties of the data set. Two new methods, LOGANA and LOCON, are discussed in some more detail. With the help of these methods, substructural patterns ("topological pharmacophores") characteristic of compounds possessing a certain biological property can be evaluated. Both methods are designed in such a way that full use can be made of the data handling capacity of computers while maintaining an optimal impact of the experience of the researcher. They are model-free and do not require any mathematical knowledge. While LOGANA deals with semiquantitative or even qualitative biological data, LOCON can be applied to activity data on a continuous scale. The basic procedure in both cases consists in the stepwise combination of substructural descriptors by the logical operations "and," "or" and "not." With a simple example the utility of the methods is demonstrated.

Substructural QSAR Approaches and Topological Pharmacophores

For large and diverse data sets, simple QSAR methods based on linear and additive models can no longer be applied. In such cases topological methods using descriptors directly derivable from two-dimensional chemical structures provide a useful alternative. The results of such analyses can be used for lead optimization, to guide biological testing and even aid in the design of novel compounds. Various types of topological descriptors and algorithms are briefly discussed. Which of those is to be selected depends on the objective of the investigation and the properties of the data set. Two new methods, LOGANA and LOCON, are discussed in some more detail. With the help of these methods, substructural patterns ("topological pharmacophores") characteristic of compounds possessing a certain biological property can be evaluated. Both methods are designed in such a way that full use can be made of the data handling capacity of computers while maintaining an optimal impact of the experience of the researcher. They are model-free and do not require any mathematical knowledge. While LOGANA deals with semiquantitative or even qualitative biological data, LOCON can be applied to activity data on a continuous scale. The basic procedure in both cases consists in the stepwise combination of substructural descriptors by the logical operations "and," "or" and "not." With a simple example the utility of the methods is demonstrated.

Bonafide Substructure in the Core of Ferritin

Each molecule of ferritin (d = 130Å) contains a core of iron surrounded by a 24-subunit protein shell. The amount of iron stored is variable and is present within the central cavity (d = 80Å) as a hydrated ferric oxide equivalent to the mineral, ferrihydrite. Many early ultrastructural studies of ferritin detected regular patterns of a multiparticulate substructure in the iron-rich core [e.g., 3,4], Each small particle was termed a “micelle“; a theory became widely accepted that a core consisted of up to six micelles positioned at the vertices of an octahedron. Other workers recognized that the apparent micelles were smaller or even disappeared if images were recorded closer to exact focus [e.g., 5]. In 1969, Haydon clearly established that the observed substructure was really an imaging artifact; each apparent micelle was only a dot in the underfocused phase contrast image of the supporting film superimposed on the amplitude image of the strongly scattering metal.

Topological Pharmacophores New Methods and Their Application to a Set of Antimalarials Part 1: The Methods LOGANA and LOCON

AbstractTopological pharmacophores are two‐dimensional substructural patterns characteristic of compounds possessing a desired biological property (e.g., high activity) while absent from compounds devoid of this property. Two new methods for the evaluation of such pharmacophores, LOGANA and LOCON, are presented which are both designed in such a way that full use can be made of the data handling capacity of computers while maintaining an optimal impact of the professional skill and experience of medicinal chemists with no special mathematical knowledge required. Both methods are based on the stepwise combination of substructural descriptors by means of the logical operations “and”, “or” and “not”. No assumptions about additivity of effects, linear models or the validity of certain statistical formalisms are necessary. While LOGANA deals with biological data in the form of classifications LOCON can be applied to activity data on a continuous scale. The advantages and limitations of the two methods are discussed.

Topological Pharmacophores New Methods and Their Application to a Set of Antimalarials Part 3: Results from LOCON

AbstractThe LOCON procedure described in the first part of this series is applied to a set of antimalarials as a test case. Its principle consists in the stepwise evaluation of conjunctions such that sets of compounds characterized by these conjunctions have high mean values of biological activity. The conjunctions are obtained from binary descriptors which characterize the presence or absence of predefined substructural features using the logical operator “and”. Clear substructural patterns typical of the highly active compounds are obtained which supplement the LOGANA results presented in Part 2 of this series. There is very good agreement with corresponding Hansch equations taken from the literature so that similar predictions result from both approaches.

Topological Pharmacophores New Methods and Their Application to a Set of Antimalarials Part 2: Results from LOGANA

AbstractThe LOGANA procedure described in part 1 of this series is applied to a set of antimalarials as a test case. Its principle consists in the stepwise combination of binary descriptors characterizing the presence or absence of substructural features into conjunctions using the logical operator “and”, such that the structural patterns described by these conjunctions are typical of the class of high activity compounds. Clear substructural patterns for antimalarial activity are obtained which are consistent with corresponding Hansch equations taken from the literature.

Studies on the isolation and substructure of mammalian neurofilaments

Intact neurofilaments were isolated from minced segments of desheathed rat peripheral nerve by subjecting tissues to osmotic shock in media containing chelating agents and sedimenting heavier tissue components by centrifugation. Isolated neurofilaments were layered on carbon—Formvar-coated grids, fixed by flotation on 5% formalin, and visualized by negative staining with unbuffered uranyl acetate. Neurofilaments comprised the predominant constituent organelle of these preparations. Individual neurofilaments coursed as discrete unbranching linear structures for distances of at least 10 μm. Fresh or fixed neurofilaments appeared as compact cylindrical structures 80–110 A in diameter; lateral sidearm projections were not evident. Exposure to 0.5 M urea prior to fixation altered neurofilaments and exposed substructural configurations. Urea-treated preparations revealed the presence of 20- to 25-A protofilaments. Pairs of protofilaments appeared to be arranged in helical configurations as evidenced by profiles with herringbone substructural patterns. Accordingly, mammalian neurofilaments appear to closely resemble similar organelles of invertebrate species.

The postacrosomal region of the spermatozoa of man and Macaca arctoides

The postacrosomal sheath of human spermatozoa consists of two morphologically distinct areas. The anterior one shows a substructural pattern consisting of evenly spaced, circumferentially oriented densities extending to the inner aspect of the cell membrane from a dense, homogeneous layer parellel to the cell membrane. The posterior one consists of obliquely oriented cordlike structures extending from the posterior margin of the anterior area to the striated band, which is a circumferential close union between the cell membrane and the nuclear envelope at the posterior margin of the postacrosomal sheath. The same substructural pattern seen in the anterior area of the human sperm is seen throughout the postacrosomal sheath of spermatozoa of Macaca arctoides, but here the linear densities are oriented longitudinally instead of circumferentially. In both species the redundant nuclear envelope in the neck region is the only part of the nuclear envelope which contains nuclear pores, and they are arranged in a regular hexagonal pattern.

Echinococcus granulosus: Ultrastructure of microtriches

The tegumental microtriches of Echinococcus granulosus are covered by a plasma membrane with two electron-dense layers each 40–55 Å thick and 40–60 Å apart. It is different from most plasma membranes in showing a “sieve-like” structure, forming a surface “mosaic” with a roughly hexagonal pattern presumably related to the assimilatory function of the body surface. Each microthrix has two distinct regions, the shaft and the base. The shaft is bounded by a second membrane, also with two electron-dense layers each 40–55 Å thick and 20–40 Å apart, inside the modified outer plasma membrane. Each of these electron-dense layers covering the microtriches shows a “globular” substructural pattern at higher magnifications, which may indicate their enzymatic activity. The electron dense core of the shaft contains microtubules running parallel to the longitudinal axis of the shaft. The occurrence of these microtubules supports the view that microtriches are analogous in structure and function to the brush border of gut epithelia.

Occurrence of a Crystalline Inclusion in the Chloroplasts of Macadamia Leaves

PLANT cells are known to contain several types of crystals1 and crystal-containing bodies2–5, but there are only a few reports in the literature of crystalline structures in chloroplasts. Price, Martinez and Warmke6 found a crystalline inclusion in chloroplasts of healthy and virus-infected coconut palms. The inclusion was rhomboidal, consisting of particles with a maximum diameter of 12 mµ which were tightly packed in a hexagonal pattern. The crystal was contained in a single unit membrane within the chloroplast. Engelbrecht and Esau7 described, in chloroplasts of virus-infected sugar beet, an angularinclusion with parallel-linear and cross-hatched substructural patterns. Sun8 reported that in the last stages of virus-induced degeneration of Abutilon chloroplasts, a dense crystal may form inside the chloroplast. His micrographs do not, however, offer clear evidence that the crystals are within the chloroplasts. The crystals in Abutilon appeared as rhombic bodies composed of parallel electron-dense lines of 80 A spacing.