Use of RNA Secondary Structure for Studying the Evolution of RNase P and RNase MRP

Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison of secondary structures support the identity of an RNase P–like sequence in the maize chloroplast genome. Overall, it is concluded that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned with confidence. Received: 19 July 1999 / Accepted: 3 May 2000     

Common Properties of Fusion Peptides from Diverse Systems

Although membrane fusion occurs ubiquitously and continuously in alleukaroytic cells, little is known about the mechanism that governs lipidbilayer fusion associated with any intracellular fusion reactions. Recentstudies of the fusion of enveloped viruses with host cell membranes havehelped to define the fusion process. The identification and characterizationof key proteins involved in fusion reactions have mainly driven recent advancesin our understanding of membrane fusion. The most important denominator amongthe fusion proteins is the fusion peptide. In this review, work done in thelast few years on the molecular mechanism of viral membrane fusion will behighlighted, focusing in particular on the role of the fusion peptide and themodification of the lipid bilayer structure. Much of what is known regardingthe molecular mechanism of viral membrane fusion has been gained using liposomesas model systems in which the molecular components of the membrane and the environmentare strictly controlled. Many amphilphilic peptides have a high affinity forlipid bilayers, but only a few sequences are able to induce membrane fusion. Thepresence of -helical structure in at least part of the fusion peptideis strongly correlated with activity whereas, -structure tends to beless prevalent, associated with non-native experimental conditions, and morerelated to vesicle aggregation than fusion. The specific angle of insertionof the peptides into the membrane plane is also found to be an importantcharacteristic for the fusion process. A shallow penetration, extending onlyto the central aliphatic core region, is likely responsible for the destabilization ofthe lipids required for coalescence of the apposing membranes and fusion.     

Leaf domatia and foliar mite abundance in broadleaf deciduous forest of north Asia

Plant morphology may be shaped, in part, by the third trophic level. Leaf domatia, minute enclosures usually in vein axils on the leaf underside, may provide the basis for protective mutualism between plants and mites. Domatia are particularly frequent among species of trees, shrubs, and vines in the temperate broadleaf deciduous forests in north Asia where they may be important in determining the distribution and abundance of mites in the forest canopy. In lowland and montane broadleaf deciduous forests at Kwangn;akung and Chumbongsan in Korea, we found that approximately half of all woody species in all forest strata, including many dominant trees, have leaf domatia. Pooling across 24 plant species at the two sites, mites occupied a mode of 60% (range 20-100%) of domatia and used them for shelter, egg-laying, and development. On average, 70% of all active mites and 85% of mite eggs on leaves were found in domatia; over three-quarters of these were potentially beneficial to their hosts. Further, mite abundance and reproduction (expressed as the proportion of mites at the egg stage) were significantly greater on leaves of species with domatia than those without domatia in both forests. Effects of domatia on mite abundance were significant only for predaceous and fungivorous mite taxa; herbivore numbers did not differ significantly between leaves of species with and without domatia. Comparable patterns in broadleaf deciduous forest in North America and other biogeographic regions suggest that the effect of leaf domatia on foliar mite abundance is general. These results are consistent with several predictions of mutualism between plants and mites, and indicate that protective mutualisms may be frequent in the temperate zone.     

Interaction between ants and seeds of a nonmyrmecochorous neotropical tree, Cabralea canjerana (Meliaceae), in the Atlantic forest of southeast Brazil

On the forest floor of two Atlantic forest sites in southeast Brazil, we recorded 26 ant species (12 genera) interacting with the seeds of Cabralea canjerana (Meliaceae), a typical ornithochorous tree whose seeds are covered by a lipid-rich aril. The ants treat the arillate seeds in three different ways: (1) the large ponerine ants Pachycondyla striata and Odontomachus chelifer individually remove the seeds to their nests, (2) many species (Pheidole spp.) recruit workers to remove the aril on the spot, or (3) Solenopsis spp. recruit nestmates and cover the seeds with soil before removing the aril on the spot. The ants remove the aril exceptionally rapidly, and removal greatly facilitates seed germination. Seed predation by insects below fruiting trees is severe, and field experiments using vertebrate exclosures showed that rodents also prey heavily upon seeds found near parent trees. Ponerine ants actively remove seeds from this predation-prone zone. By removing bird-manipulated and naturally fallen seeds, ants can play a key role in the fate of medium-sized seeds like those of C. canjerana.     

Palm heart harvesting in the Brazilian Atlantic forest: changes in industry structure and the illegal trade

1. Until the late 1960s, Euterpe edulis was the most important edible palm species in the Brazilian markets. Since then, overharvesting of natural stands and the limited scope of plantations have caused the industry to shift to the multistemmed E. oleracea from the Amazon river estuary.
2. As a result of the relocation of the industry, the structure of the palm harvesting industry has changed and illegal trade has continued to exploit the remaining natural stands of E. edulis .
3. It is suggested that, to avoid the total harvesting of E. edulis and to achieve sustainable management of the palm heart, it will be necessary to diversify the local economy, create incentives for small land owners to improve their management practices, while keeping their competitiveness against the illegal trade, create the incentive of new sources of palm hearts and create a 'green stamping' for management palms.
4. Transformation of the illegal structure of the palm heart industry is probably the only solution to avoid the total depletion of the wild stands of E. edulis .     

Epizoochorous dispersal by barbs, hooks, and spines in a lowland moist forest in central French Guiana

An analysis of the flowering plant flora of a lowland moist forest in central French Guiana reveals 25 species with adaptations for epizoochorous dispersal by barbs, hooks, or spines (stick-tights). This represents 1.5% of the flowering plant flora. Stick-tights are represented among the monocotyledons of the flora of central French Guiana by five species of Poaceae. The Fabaceae and Asteraceae, each with six species with stick-tight dispersal, are the richest families of flowering plants in terms of stick-tight dispersal in central French Guiana. This region possesses numerous potential mammal and bird dispersal agents, therefore it is a puzzle why stick-tight dispersal, especially among species of the canopy, is not more frequent.     

Effects of Canopy Gaps,Topography, and Soils on the Distribution of Woody Species in a Central Brazilian Deciduous Dry Forest1

The interrelationships between the distribution of woody species and environmental variables were investigated in an area of deciduous dry forest in Santa Vitöria, central Brazil. This is the first study of a vanishing type of dry forest which grows on base-rich soils originating from the basalt bedrocks of southern Goiás and western Minas Gerais. A survey of topography, soil properties, canopy gaps and woody plants (≥5 cm diameter at the base of the stem) was conducted in 50–15 × 15 m quadrats. The soils were classified into the following soil series: Hapludolls → Haplustolls → Haplustolls → Ustropepts → Rhodustalfs. This series corresponded to a gradient of increasing elevation and effective soil depth and decreasing slope gradient, soil organic matter and total exchangeable bases. A canonical correspondence analysis and a detrended correspondence analysis indicated that plant species’abundance distribution was significantly correlated with both the relative area of canopy gaps in the quadrats and the soil-topography gradient. Presumably, the critical factors involved in these two gradients are, respectively, light and ground water regimes. The influence of canopy gaps (i.e., light) was surprising and has not been documented previously for tropical deciduous dry forests.     

Seasonal Foliage Changes in the Eastern Amazon Basin Detected from Landsat Thematic Mapper Satellite Images1

Seasonal changes in tropical forests are difficult to measure from the ground, especially in areas of high species diversity and low phenological synchrony. Satellite images, which integrate individual tree canopies and cover a large spatial extent, facilitate tests for stand-level canopy phenology. Variability in near-infrated radiance (TM bands 4 and 5) of several distinct vegetation types was used to detect seasonal changes in a series of three Landsat Thematic Mapper (TM) images from the wet season to the dry season in Marabá, Brazil (eastern Amazon basin). Despite different atmospheric and instrumental conditions among the images, spectral changes were distinguishable. A phenological process (leaf aging, leaf drop, water stress) was determined from the spectral changes for each vegetation type. Changes in the spectral properties suggest that during the dry season, upland terra firme forest increased the rate of leaf exchange and some riparian vegetation was deciduous. Terra firme forest that had been altered by penetration of fires from nearby pastures increased in leaf biomass over a 14-month period. This study shows that a time series of images can provide information on temporal changes in primary vegetation and guide field studies to investigate seasonal changes that may not be detectable from the ground.     

Pattern and Performance of Understory Bamboos (Chusquea spp.) under Different Canopy Closures in Old-Growth Oak Forests in Costa Rica1

The effect of canopy closure on spatial and morphological patterns of three understory Chusquea species was studied in pristine upper montane oak forests. Plots with either Chusquea talamancenis Widmer & L.G. Clark or C. tomentosa Widmer & L.G. Clark were set out in gaps, under intermediate tree canopy and under closed canopy. The third species Chusquea foliosa L.G. Clark was only found in gap and intermediate canopy sites in the study area. Clumps of all bamboo species tend to be few and large under open conditions and numerous and small under more shady conditions. The larger size of clumps in gaps is reflected in the number of culms per clump, the diameter of the culms and, as a consequence, clump basal area, clump crown area, and biomass (index of plant volume) compared to intermediate and closed canopy. The smaller clump density in gaps compared to closed canopy implies that there is more intraspecific competition and density dependent mortality (self-thinning effect) when a bamboo species is dominant under favourable light conditions. Parameters of performance like culm length, number of nodes per culm, number and length of primary branches, and number of branch nodes seem not to be affected by the light regime, unlike total number of branches, total branch length, and the branching pattern. Species differ in their response to the light environment: C. tomentosa and C. foliosa have a higher degree of morphological plasticity than C. talamancensis, which in turn, appears to be more shade tolerant. No difference between species has been found regarding their contribution to vegetation, parameters reflecting abundance per unit area (site clump area, site crown area and site index of clump volume) were similar for all three species.