Evolution of secondary structure in the family of 7SL-like RNAs

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the signal recognition particle) is conserved from prokaryotes to distant eukaryotic species. Yet only in primates and rodents did this molecule give rise to retroposing Alu and B1 RNAs and to apparently functional BC200 and 4.5S RNAs. To understand this transition and the underlying molecular events, we examined, by comparative analysis, the evolution of RNA structure in this family of molecules derived from 7SL RNA.RNA sequences of different simian (mostly human) and prosimian Alu subfamilies as well as rodent B1 repeats were derived from their genomic consensus sequences taken from the literature and our unpublished results (prosimian and New World Monkey). RNA secondary structures were determined by enzymatic studies (new data on 4.5S RNA are presented) and/or energy minimization analyses followed by phylogenetic comparison. Although, with the exception of 4.5S RNA, all 7SL-derived RNA species maintain the cruciform structure of their progenitor, the details of 7SL RNA folding domains are modified to a different extent in various RNA groups. Novel motifs found in retropositionally active RNAs are conserved among Alu and B1 subfamilies in different genomes. In RNAs that do not proliferate by retroposition these motifs are modified further. This indicates structural adaptation of 7SL-like RNA molecules to novel functions, presumably mediated by specific interactions with proteins; these functions were either useful for the host or served the selfish propagation of RNA templates within the host genome.Abbreviations FAM fossil Alu element - FLAM free left Alu monomer - FRAM free right Alu monomer - L-Alu left Alu subunit - R-Alu right Alu subunit Correspondence to: D. LabudaDedicated to Dr. Robert Cedergren on the occasion of his 25th anniversary at the University of Montreal     

Algae as indicators of environmental change

Despite an increased awareness by governments and the general public of the need for protecting all types of aquatic habitats, human impacts continue to impair the services that these ecosystems provide. Increased monitoring activities that locus on all major biological compartments are needed to quantify the present condition of Earth's aquatic resources and to evaluate the effectiveness of regulations designed to rehabilitate damaged ecosystems. Algae are an ecologically important group in most aquatic ecosystems but are often ignored as indicators of aquatic ecosystem change. We attribute this situation both to an underappreciation of the utility of algal indicators among non-phycologists and to a lack of standardized methods for monitoring with algae.Because of their nutritional needs and their position at the base of aquatic foodwebs, algal indicators provide relatively unique information concerning ecosystem condition compared with commonly used animal indicators. Algae respond rapidly and predictably to a wide range of pollutants and, thus, provide potentially useful early warning signals of deteriorating conditions and the possible causes. Algal assemblages provide one of the few benchmarks for establishing historical water quality conditions and for characterizing the minimally impacted biological condition of many disturbed ecosystems. Preliminary comparisons suggest that algal indicators are a cost-effective monitoring tool as well.Based on available evidence from field studies, we recommend development of taxonomic indicators based on diatoms (Bacillariophyceae) as a standardized protocol for monitoring ecosystem change. Both population- and community-level indices have inherent strengths, and limitations and information from both levels of biological organization should be utilized in tandem. However, further information concerning species tolerances to a variety of anthropogenic stressors is needed if autecological indices are to be used routinely for monitoring purposes. While functional measures (e.g. productivity) may also prove useful as monitoring tools, further investigation is required to characterize the reliability of alternative methodologies and to assess the consistency of these indicators under varying field conditions.Author for correspondence     

Different UmuC requirements for generation of different kinds of UV-induced mutations in Escherichia coli

An Escherichia coli strain bearing the dnaQ49 mutation, which results in a defective s subunit of DNA polymerase III, and carrying the lexA71 mutation, which causes derepression of the SOS regulon, is totally unable to maintain high-copy-number plasmids containing the umuDC operon. The strain is also unable to maintain the pAN4 plasmid containing a partial deletion of the umuD gene but retaining the wild-type umuC gene. These results suggest that a high cellular level of UmuC is exceptionally harmful to the defective DNA polymerase III of the dnaQ49 mutant. We have used this finding as a basis for selection of new plasmid umuC mutants. The properties of two such mutants, bearing the umuC61 or umuC95 mutation, are described in detail. In the umuC122:: Tn 5 strain harbouring the mutant plasmids, UV-induced mutagenesis is severely decreased compared to that observed with the parental umuDC ⁺ plasmid. Interestingly, while the frequency of UV-induced GC → AT transitions is greatly reduced, the frequency of AT → TA transversions is not affected. Both mutant plasmids bear frameshift mutations within the same run of seven A residues present in umuC ⁺; in umuC61 the run is shortened to six A whereas in umuC95 is lengthened to eight A. We have found in both umuC61 and umuC95 that translation is partially restored to the proper reading frame. We propose that under conditions of limiting amounts of UmuC, the protein preferentially facilitates processing of only some kinds of UV-induced lesions.     

Intracellular calcium oscillations induced in a T-cell line by a weak 50 Hz magnetic field

Applied weak magnetic fields have been shown to affect cellular activity on several levels, but the mechanisms involved remain elusive. We have decided to study an early signal transduction event in the human T cell line Jurkat; oscillations of free [Ca²⁺]i, of the type seen by crosslinking the CD3 complex. Cells were exposed to a 50 Hz, 0.1 mT, sinusoidal magnetic field while intracellular free calcium was measured in individual cells, using fura-2 as a probe. An acute response was observed with oscillatory increases in [Ca²⁺]i, which subsided when the field was turned off. The effect of the magnetic field on [Ca²⁺]i was comparable to that achieved by an anti-CD3 monoclonal antibody. © 1993 Wiley-Liss, Inc.     

Determining desirable levels of ecosystem services per capita

Ecosystem services are the numerous, essential processes that natural ecosystems provide free to human societies. Examples include the maintenance of breathable air; the movement, storage, and purification of water; the breakdown of wastes; and the provision of food, building materials, and medicines. However, the exponential increases in human population and concomitant environmental destruction make it likely that the level of ecosystem services available per capita will decline. There are three possible scenarios. First, if present practices continue, ecosystem services per capita will surely decline. Second, if a no-net-loss policy is implemented for habitats and species, ecosystem services per capita will still decline due to increases in human population, but the declines will be less precipitous. Third, if habitat is restored (including concomitant ecosystem services) at a rate exceeding that of destruction, then, perhaps the current level of ecosystem services per capita can be maintained, or even expanded to provide increased levels of ecosystem services per capita to more of the world's people.     

Empirical testing of cryoconite granulation: Role of cyanobacteria in the formation of key biogenic structure darkening glaciers in polar regions

Cryoconite, the dark sediment on the surface of glaciers, often aggregates into oval or irregular granules serving as biogeochemical factories. They reduce a glacier's albedo, act as biodiversity hotspots by supporting aerobic and anaerobic microbial communities, constitute one of the organic matter (OM) sources on glaciers, and are a feeder for micrometazoans. Although cryoconite granules have multiple roles on glaciers, their formation is poorly understood. Cyanobacteria are ubiquitous and abundant engineers of cryoconite hole ecosystems. This study tested whether cyanobacteria may be responsible for cryoconite granulation as a sole biotic element. Incubation of Greenlandic, Svalbard, and Scandinavian cyanobacteria in different nutrient availabilities and substrata for growth (distilled water alone and water with quartz powder, furnaced cryoconite without OM, or powdered rocks from glacial catchment) revealed that cyanobacteria bind mineral particles into granules. The structures formed in the experiment resembled those commonly observed in natural cryoconite holes: they contained numerous cyanobacterial filaments protruding from aggregated mineral particles. Moreover, all examined strains were confirmed to produce extracellular polymeric substances (EPS), which suggests that cryoconite granulation is most likely due to EPS secretion by gliding cyanobacteria. In the presence of water as the only substrate for growth, cyanobacteria formed mostly carpet-like mats. Our data empirically prove that EPS-producing oscillatorialean cyanobacteria isolated from the diverse community of cryoconite microorganisms can form granules from mineral substrate and that the presence of the mineral substrate increases the probability of the formation of these important and complex biogeochemical microstructures on glaciers.     

Toxicity versus avoidance response of golden shiner, Notemigonus crysoleucas, to five metals

Avoidance thresholds and 96-h LC50 values were determined for golden shiners, Noiemigonus crysoleucas , for five individual elements: chromium, Cr; copper, Cu; cadmium, Cd; arsenic, As; selenium, Se. The avoidance concentrations were 73, 26 and 28 μgl^-1 for Cr-VI, Cu and As-III, respectively. Cadmium and Se were not avoided at experimental concentrations up to 68 and 3489 μg1^-1, respectively. Acute flow-through 96-h LC50 values were Cr-VI 55·0, Cu 84·6, and As-III 12·5 mg 1^-1, which were more than two orders of magnitude above avoidance concentrations. The acute flow-through 96-h LC50 values for Cd and Se were 2·8 and 11·2 mg 1^-1, respectively. These concentrations are 31 and 2·2 times the highest concentration employed in the avoidance tests, neither of which were avoided by the test organisms. Thus, simple toxicity tests do not identify the environmental hazard of some elements, and the most toxic elements may not elicit a behavioural response. When used in concert with tests of organism function, more realistic indicators of environmental hazard or safety may be determined.     

Discontinuities in technological and natural systems caused by exotic species

This discussion focuses on discontinuities in both natural and technological systems caused by the introduction of exotic species into areas which they would not have been able to reach without human assistance or other alterations to native communities. The case histories of both the Asian clam and the zebra mussel are particularly instructive because of their recent introductions and the dramatic impact they have had on both natural and technological systems. Control of these mollusc species in technological systems (e.g. water intake systems) is effective to a degree but requires constant attention and utilization of resources. If control is neglected there could be extremely serious consequences. At present, no inexpensive means exist for controlling their effects, and further geographical distribution in North America is highly probable. The mollusc case histories do not appear to be linear and, in some instances, may not be continuous. Some importations of exotic species were deliberate (such as the gypsy moth, Porthetria dispar), but their escape into natural systems has often been accidental or, a less charitable person might say, careless. A viable strategy for coping with discontinuities is elusive. Discontinuities will, undoubtedly, have a major effect on the possibility of sustainable use of the planet or, to use the currently popular term, sustainable development.