Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.     

Potential toxicity of chrysophytes affiliated with Poterioochromonas and related 'Spumella-like' flagellates

The chrysophyte genera Poterioochromonas and Ochromonas andtheir heterotrophic analogons, i.e. the ‘Spumella-like’flagellates, account for a significant and often dominatingfraction of the pelagic nanoplankton. Even though several osmotrophicallyand autotrophically grown strains of Ochromonas and Poterioochromonasare assumed to produce toxins, the potential toxicity has beeninvestigated neither for its association with bacterivorousnutrition nor within the related exclusively heterotrophic ‘Spumella-like’flagellates. We investigated the toxic potential of severalflagellate strains using cultures of flagellates, cell extractsand filtrate of flagellate cultures. The effect on potentialpredators was exemplarily tested for the cladoceran Daphniamagna and the rotifer Platyias sp. All tested heterotrophicand mixotrophic flagellate strains were toxic to zooplanktonat abundances exceeding 10⁴ flagellates mL^–1. For therotifers, survival on any of the flagellate strains was significantlylower than that in the control treatment (P < 0.001) alreadyafter 24 h. We conclude that (i) ‘Spumella-like’flagellates can be toxic to zooplankton, (ii) all tested flagellates,i.e. heterotrophic and mixotrophic flagellates, feeding phagotrophicallycan be toxic to zooplankton and (iii) sublethal effects maybe observed at typical field abundances, even though acute toxicityseems to be restricted to flagellate abundances observed onlyat peak events.     

SARS--beginning to understand a new virus

The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralyzed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again.     

Cell cycle associated changes in histamine release from rat basophilic leukemia cells separated by counterflow centrifugal elutriation

This study evaluated histamine release from cells at different stages of the cell cycle. Cells from the cloned rat basophilic leukemia subline (RBL-2H3) were fractionated by counterflow elutriation according to size and density. The smallest cells were predominantly in the G1 phase of the cell cycle. These cells contained the least histamine and after IgE-mediated triggering released the lowest fraction of their total histamine. In contrast cells in the S, G2, and M stages were larger, contained more histamine and released more of their histamine after activation. When G1 stage cells were recultured, there was an increase in cell size, in histamine content and histamine release. Therefore, there is heterogeneity in the capacity of cells for IgE-mediated triggering at different stages in the cell cycle, with optimal release from the more mature cells.     

Alignment of RNA base pairing probability matrices

MOTIVATION: Many classes of functional RNA molecules are characterized by highly conserved secondary structures but little detectable sequence similarity. Reliable multiple alignments can therefore be constructed only when the shared structural features are taken into account. Since multiple alignments are used as input for many subsequent methods of data analysis, structure-based alignments are an indispensable necessity in RNA bioinformatics. RESULTS: We present here a method to compute pairwise and progressive multiple alignments from the direct comparison of base pairing probability matrices. Instead of attempting to solve the folding and the alignment problem simultaneously as in the classical Sankoff's algorithm, we use McCaskill's approach to compute base pairing probability matrices which effectively incorporate the information on the energetics of each sequences. A novel, simplified variant of Sankoff's algorithms can then be employed to extract the maximum-weight common secondary structure and an associated alignment. AVAILABILITY: The programs pmcomp and pmmulti described in this contribution are implemented in Perl and can be downloaded together with the example datasets from http://www.tbi.univie.ac.at/RNA/PMcomp/. A web server is available at http://rna.tbi.univie.ac.at/cgi-bin/pmcgi.pl     

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

HIV virulence, i.e. the time of progression to AIDS, varies greatly among patients. As for other rapidly evolving pathogens of humans, it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown. We apply the phylogenetic comparative approach (PCA) to estimate the heritability of a trait from one infection to the next, which indicates the control of the virus genotype over this trait. The idea is to use viral RNA sequences obtained from patients infected by HIV-1 subtype B to build a phylogeny, which approximately reflects the transmission chain. Heritability is measured statistically as the propensity for patients close in the phylogeny to exhibit similar infection trait values. The approach reveals that up to half of the variance in set-point viral load, a trait associated with virulence, can be heritable. Our estimate is significant and robust to noise in the phylogeny. We also check for the consistency of our approach by showing that a trait related to drug resistance is almost entirely heritable. Finally, we show the importance of taking into account the transmission chain when estimating correlations between infection traits. The fact that HIV virulence is, at least partially, heritable from one infection to the next has clinical and epidemiological implications. The difference between earlier studies and ours comes from the quality of our dataset and from the power of the PCA, which can be applied to large datasets and accounts for within-host evolution. The PCA opens new perspectives for approaches linking clinical data and evolutionary biology because it can be extended to study other traits or other infectious diseases.     

Ant attendance in aphids: why different degrees of myrmecophily?

1. Aphids show a range of associations with ants from nonattendance to obligate myrmecophily. Aphis fabae cirsiiacanthoides is facultatively associated with ants, while Symydobius oblongus is an obligate myrmecophile. The selection pressures that have shaped these associations are unknown. 2. The consequences for these aphids of their different degrees of associations with ants were determined, in terms of costs and benefits to individuals and colonies in laboratory and field experiments. In the laboratory, individuals of A. f. cirsiiacanthoides performed worse and those of Symydobius oblongus performed better when attended by the ant Lasius niger than when unattended. For example, when ant-attended, A. f. cirsiiacanthoides developed more slowly, were smaller, and invested less in gonads, whereas S. oblongus developed more quickly, were larger, and invested more in gonads. In addition, the ant regulated the population size of S. oblongus to an average of 50–70 individuals per birch sapling by removing aphids, but did not regulate the population size of A. f. cirsiiacanthoides. 3. Under field conditions, ant-attended colonies of both A. f. cirsiiacanthoides and S. oblongus achieved higher peak numbers and lasted longer, and ant-attended colonies of A. f. cirsiiacanthoides produced more alate dispersers than unattended colonies. 4. The implications of divergent selection pressures for the development of myrmecophily in aphids are discussed.