RAG: RNA-As-Graphs database--concepts, analysis, and features

MOTIVATION: Understanding RNA's structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA's structural repertoire. RESULTS: Our RNA-As-Graphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as two-dimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as 'tree graphs' and other RNAs, including pseudoknots, as general 'dual graphs'. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs. AVAILABILITY: The database is accessible on the web at http://monod.biomath.nyu.edu/rna     

Modulation of hyaluronan in the migratory pathway of mouse primordial germ cells

In the present report we followed the distribution of hyaluronan during the phases of separation, migration, and colonization of the primordial germ cell migratory process. Hyaluronan was detected by the use of two cytochemical methods: (1) ruthenium hexammine trichloride (RHT) associated with enzymatic treatment with hyaluronate lyase and (2) a binding specific probe for hyaluronan. After RHT treatment the proteoglycans and/or glycosaminoglycans were observed as a meshwork formed by electron-dense granules connected by thin filaments. After enzymatic digestion, no filaments could be detected in the migratory pathway. Quantitative analysis showed a close correlation between cell migration and the concentration of RHT-positive filaments. It was also shown that high amounts of hyaluronan were expressed in the separation phase and migration phases whereas during the colonization phase the amount of hyaluronan was clearly diminished. This study showed that the presence of primordial germ cells in each compartment of the migratory pathway was always accompanied by a high expression of hyaluronan. These results indicate that hyaluronan is an important molecule in the migratory process, providing the primordial germ cells with a hydrated environment that facilitates their movement toward the genital ridges.     

Differential expression of glycosaminoglycans and proteoglycans in the migratory pathway of the primordial germ cells of the mouse

Primordial germ cells are an embryonic cell line that give rise to gametes in vertebrates. They originate outside the embryo proper and migrate by a well-defined route to the genital ridges. Proteoglycans and glycosaminoglycans have distinctive properties that affect many of the characteristics of the extracellular microenvironment of migratory pathways in a variety of developmental systems. The purpose of this work was to identify the proteoglycans and glycosaminoglycans that are spatially and temporally expressed in the migratory pathway of primordial germ cells. We showed that the expression of proteoglycans and glycosaminoglycans in the primordial germ cells migratory pathway changes according to the different phases of the migratory process. Some molecules such as chondroitin-0-sulfate, decorin, and biglycan are present only in certain phases of the migratory process of primordial germ cells. Heparan sulfate, chondroitin-6-sulfate, versican, perlecan, and syndecan-4, although exhibiting some variation in expression were detected during all phases of the migratory process. Our results indicate that the successive steps of primordial germ cell migration require a coordinated expression of proteoglycans and glycosaminoglycans, that should be present in appropriate levels and in specific areas of the embryo, and that the sequential expression of these extracellular matrix molecules is under a genetic program that appears to be common to a variety of cell types during embryonic development.     

Influence of hatching order on growth rate and resting metabolism of kestrel nestlings

Hatching asynchrony in altricial birds may result in a competitive disadvantage for the youngest nestlings compared to older siblings. We studied the effects of a size hierarchy on the growth rate of Eurasian kestrels Falco tinnunculus chicks in nests with and without access to supplemented food in western Finland. Body mass stopped increasing on the 19th day after hatching while body size, estimated by a combination of bone and feather lengths continued to increase at least until fledging at 26 days. Body condition, reflecting muscle and fat, did not change markedly during the growth period from the 12th day to fledging. Body temperature and resting metabolism were usually lower in nestlings 12 days old than in nestlings at fledging. Growth of body mass, size and condition, and resting metabolism were delayed in last-hatched nestlings aged 19 days. Just before fledging, last-hatched nestlings attained a similar body mass and size, and had a similar resting metabolism to those of older siblings. At fledging, only in nests without access to supplemented food was the body condition of last-hatched chicks lower than that of its siblings, but in nests with access to supplemented food no such difference was detected. Our results highlight that the level of lipids in the last-hatched nestling can be affected by the food restriction imposed by hatching order.     

GABA uptake inhibitors produce a greater antinociceptive response in the mouse tail-immersion assay than other types of GABAergic drugs

Antinociception produced by the GABA uptake inhibitors d,l- SKF-89976A and SKF-100330A was characterized and compared to that produced by other types of GABAergic drugs. Using the mouse tail-immersion assay it was found that the antinociception produced by the uptake inhibitors was antagonized by scopolamine, a cholinergic muscarinic receptor antagonist. However, neither SKF compound demonstrated any significant affinity for muscarinic receptor binding sites suggesting that they are not direct-acting cholinomimetics. In vitro uptake experiments revealed that the SKF compounds selectively inhibit GABA transport, having no effect on the accumulation of aspartic acid, glutamic acid, beta-alanine or glycine. Moreover, antinociception and GABA uptake inhibition were stereoselective for SKF-89976A, with the d-isomer being more active in both tests. When comparing antinociceptive responses at maximally effective doses it was also found that the SKF compounds were substantially more efficacious than direct-acting GABA receptor agonists or a GABA transaminase inhibitor. These data suggest that uptake inhibitors may be facilitating GABA transmission in a system that is less affected by other types of GABAergic compounds.     

Rabl's model of the interphase chromosome arrangement tested in Chinise hamster cells by premature chromosome condensation and laser-UV-microbeam experiments

Summary In 1885 Carl Rabl published his theory on the internal structure of the interphase nucleus. We have tested two predictions of this theory in fibroblasts grown in vitro from a female Chinese hamster, namely (1) the Rabl-orientation of interphase chromosomes and (2) the stability of the chromosome arrangement established in telophase throughout the subsequent interphase. Tests were carried out by premature chromosome condensation (PCC) and laser-UV-microirradiation of the interphase nucleus. Rabl-orientation of chromosomes was observed in G1 PCCs and G2 PCCs. The cell nucleus was microirradiated in G1 at one or two sites and pulse-labelled with ³H-thymidine for 2h. Cells were processed for autoradiography either immediately thereafter or after an additional growth period of 10 to 60h. Autoradiographs show unscheduled DNA synthesis (UDS) in the microirradiated nuclear part(s). The distribution of labelled chromatin was evaluated in autoradiographs from 1035 cells after microirradiation of a single nuclear site and from 253 cells after microirradiation of two sites. After 30 to 60h postincubation the labelled regions still appeared coherent although the average size of the labelled nuclear area fr increased from 14.2% (0h) to 26.5% (60h). The relative distance dr, i.e. the distance between two microirradiated sites divided by the diameter of the whole nucleus, showed a slight decrease with increasing incubation time. Nine metaphase figures were evaluated for UDS-label after microirradiation of the nuclear edge in G1. An average of 4.3 chromosomes per cell were labelled. Several chromosomes showed joint labelling of both distal chromosome arms including the telomeres, while the centromeric region was free from label. This label pattern is interpreted as the result of a V-shaped orientation of these particular chromosomes in the interphase nucleus with their telomeric regions close to each other at the nuclear edge. Our data support the tested predictions of the Rabl-model. Small time-dependent changes of the nuclear space occupied by single chromosomes and of their relative positions in the interphase nucleus seem possible, while the territorial organization of interphase chromosomes and their arrangement in general is maintained during interphase. The present limitations of the methods used for this study are discussed.Part of this work is included in the doctoral thesis of H. Baumann to be submitted to the Faculty of Biology of the University of HeidelbergPart of this work is included in the doctoral thesis of V. Teuber to be submitted to the Faculty of Medicine of the University of Freiburg i. Br.     

Prolactin induces proliferation of vascular smooth muscle cells through a protein kinase C-dependent mechanism

The effects of prolactin (PRL) on A10 (aortic smooth muscle) cell proliferation were examined by measuring both [3H]thymidine incorporation and increases in cell number. PRL induced a significant proliferative response from 10(-11) to 10(-7) M, with optimal activity at 10(-10) M. PRL also enhanced platelet-derived growth factor (PDGF)-induced proliferation. The possibility that PRL induces proliferation through a protein kinase C (PKC)-mediated mechanism was also examined. PRL caused activation of PKC from 10(-12) to 10(-8) M. Antiserum to PRL, a monoclonal antibody directed against the PRL receptor and the immunosuppressive agent cyclosporine A, were able to inhibit PRL-induced proliferation and activation of PKC. The PKC inhibitors, staurosporine, sphingosine, and 1-(-5-iso-quinoline-sulfonyl)-2-methylpiperazine (H-7) also antagonized both proliferation and PKC activation. These data strongly suggest that PRL-induced A10 cell proliferation is mediated through the PKC pathway and that this may play a role in vascular smooth muscle cell hyperplasia, characteristic of the pathogenesis of cardiovascular diseases such as hypertension and atherosclerosis.     

Organization of intermediate filaments and their association with collagen-containing phagosomes in mouse decidual cells

We have analyzed the distribution of intermediate filaments (IF) in the cytoplasm of mature decidual cells of mice. IF were scattered throughout the cytoplasm of these cells although there was a preferential accumulation around the nuclei. In many cells a large area of the cytoplasm was occupied by a rich network of IF that extended from the perinuclear region toward the cell surface. Thin bundles of IF crossed the cytoplasm without a preferential orientation. IF were also seen in close association with nuclear pore complexes, gap junctions, mitochondria, and lysosomes. A very developed network of IF surrounded phagosomes that contained collagen fibrils. Longitudinal and cross sections of these phagosomes showed a very close association of IF with the phagosome membrane.     

Remodeling of the mouse endometrial stroma during the preimplantation period.

An ultrastructural cytochemical study of acid phosphatase activity performed in mouse endometrium on the second day of pregnancy showed that stromal cells which were heavily labeled by the cytochemical reaction had disarranged organelles. On the other hand, the cytoplasm of several stromal cells had collagen-containing phagosomes that were also labeled, indicating that the collagen fibrils were being digested by lysosomal enzymes. It is suggested that cell death and phagocytosis of collagen are events of the remodeling of the mouse endometrium that occur prior to decidualization.     

Localized ultraviolet laser microbeam irradiation of early Drosophila embryos: fate maps based on location and frequency of adult defects.

Drosophila embryos were locally irradiated with a 257-nm laser microbeam during blastoderm and germ band stages. Depending on stage and beam diameter (10–30 μm), from 0 to 45 nuclei were exposed to the uv radiation. The doses used, 5 or 10 erg, did not eliminate nuclei or cells at once, but up to 50% of the adult survivors from irradiated eggs carried defects in the thorax. These were scored with reference to the imaginal discs from which the affected structures derive. For each thoracic disc a “target center” was calculated as the weighted mean value of all beam locations affecting the respective adult derivatives. The target centers for the germ band stage map within the respective germ band segments. The pattern of target centers for the blastoderm stage is comparable to the thoracic region of published fate maps, and the distances between adjacent leg centers (approximately three cell diameters) agree with recent evidence based on mosaic flies. We discuss the question whether the target centers mark the position of the respective disc progenitor cells at the stages of irradiation and conclude that these positions are rendered rather correctly at least with reference to the longitudinal egg axis.