Patterns of Genome Evolution among the Microsporidian Parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi

Microsporidia are intracellular parasites that are highly-derived relatives of fungi. They have compacted genomes and, despite a high rate of sequence evolution, distantly related species can share high levels of gene order conservation. To date, only two species have been analysed in detail, and data from one of these largely consists of short genomic fragments. It is therefore difficult to determine how conservation has been maintained through microsporidian evolution, and impossible to identify whether certain regions are more prone to genomic stasis.Here, we analyse three large fragments of the Enterocytozoon bieneusi genome (in total 429 kbp), a species of medical significance. A total of 296 ORFs were identified, annotated and their context compared with Encephalitozoon cuniculi and Antonospora locustae. Overall, a high degree of conservation was found between all three species, and interestingly the level of conservation was similar in all three pairwise comparisons, despite the fact that A. locustae is more distantly related to E. cuniculi and E. bieneusi than either are to each other.Any two genes that are found together in any pair of genomes are more likely to be conserved in the third genome as well, suggesting that a core of genes tends to be conserved across the entire group. The mechanisms of rearrangments identified among microsporidian genomes were consistent with a very slow evolution of their architecture, as opposed to the very rapid sequence evolution reported for these parasites

Combined effects of prevention and quarantine on a breakout in SIR model

Recent breakouts of several epidemics, such as flu pandemics, are serious threats to human health. The measures of protection against these epidemics are urgent issues in epidemiological studies. Prevention and quarantine are two major approaches against disease spreads. We here investigate the combined effects of these two measures of protection using the SIR model. We use site percolation for prevention and bond percolation for quarantine applying on a lattice model. We find a strong synergistic effect of prevention and quarantine under local interactions. A slight increase in protection measures is extremely effective in the initial disease spreads. Combination of the two measures is more effective than a single protection measure. Our results suggest that the protection policy against epidemics should account for both prevention and quarantine measures simultaneously

The effect of travel restrictions on the spread of a moderately contagious disease

BACKGROUND: Much research in epidemiology has been focused on evaluating conventional methods of control strategies in the event of an epidemic or pandemic. Travel restrictions are often suggested as an efficient way to reduce the spread of a contagious disease that threatens public health, but few papers have studied in depth the effects of travel restrictions. In this study, we investigated what effect different levels of travel restrictions might have on the speed and geographical spread of an outbreak of a disease similar to severe acute respiratory syndrome (SARS). METHODS: We used a stochastic simulation model incorporating survey data of travel patterns between municipalities in Sweden collected over 3 years. We tested scenarios of travel restrictions in which travel over distances >50 km and 20 km would be banned, taking into account different levels of compliance. RESULTS: We found that a ban on journeys >50 km would drastically reduce the speed and geographical spread of outbreaks, even when compliance is < 100%. The result was found to be robust for different rates of intermunicipality transmission intensities. CONCLUSION: This study supports travel restrictions as an effective way to mitigate the effect of a future disease outbreak

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Quantification of ocean heat uptake from changes in atmospheric O2 and CO2 composition

The ocean is the main source of thermal inertia in the climate system. Ocean heat uptake during recent decades has been quantified using ocean temperature measurements. However, these estimates all use the same imperfect ocean dataset and share additional uncertainty due to sparse coverage, especially before 2007. Here, we provide an independent estimate by using measurements of atmospheric oxygen (O2) and carbon dioxide (CO2) – levels of which increase as the ocean warms and releases gases – as a whole ocean thermometer. We show that the ocean gained 1.29 ± 0.79 × 1022 Joules of heat per year between 1991 and 2016, equivalent to a planetary energy imbalance of 0.80 ± 0.49 W watts per square metre of Earth’s surface. We also find that the ocean-warming effect that led to the outgassing of O2 and CO2 can be isolated from the direct effects of anthropogenic emissions and CO2 sinks. Our result – which relies on high-precision O2 atmospheric measurements dating back to 1991 – leverages an integrative Earth system approach and provides much needed independent confirmation of heat uptake estimated from ocean data

Amplification of a Zygosaccharomyces bailii DNA Segment in Wine Yeast Genomes by Extrachromosomal Circular DNA Formation

We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations

Taming of the shrewd: novel eukaryotic genes from RNA viruses

Genomes of several yeast species contain integrated DNA copies of complete genomes or individual genes of non-retroviral double-strand RNA viruses as reported in a recent BMC Biology article by Taylor and Bruenn. The integrated virus-specific sequences are at least partially expressed and seem to evolve under pressure of purifying selection, indicating that these are functional genes. Together with similar reports on integrated copies of some animal RNA viruses, these results suggest that integration of DNA copies of non-reverse-transcribing RNA viruses might be much more common than previously thought. The integrated copies could contribute to acquired immunity to the respective viruses

Inhibition of gastric H,K-ATPase activity and gastric epithelial cell IL-8 secretion by the pyrrolizine derivative ML 3000

BACKGROUND: ML 3000 ([2,2-dimethyl-6-(4-chlorophenyl)-7-phenyl-2,3-dihydro-1H-pyrrolizine-5-yl]-acetic acid) is an inhibitor of both cyclooxygenase and 5-lipoxygenase in vitro, and shows promise as a novel non-steroidal anti-inflammatory drug (NSAID). Unlike conventional NSAIDs which are associated with gastric ulcerogenic effects, ML 3000 causes little or no damage to the gastric mucosa, even though it significantly depresses gastric prostaglandin synthesis. METHODS: As part of an effort to clarify mechanisms underlying the gastric sparing properties of ML 3000, we studied the effects of ML 3000 on H,K-ATPase activity in vitro, on acid accumulation in isolated gastric parietal cells, and on IL-8 secretion by gastric epithelial cells in culture. RESULTS: SCH28080-sensitive H,K-ATPase activity in highly-purified pig gastric microsomes was dose-dependently inhibited by ML 3000 (IC(50) = 16.4 μM). Inhibition was reversible, and insensitive to ML 3000 acidification in the pH range 2.0–8.0. In rabbit gastric parietal cells, ML 3000 dose-dependently inhibited histamine-stimulated acid accumulation (IC(50) = 40 μM) and forskolin-stimulated acid accumulation (IC(50) = 45 μM). Lastly, in human gastric adenocarcinoma (AGS) cells, ML 3000 dose-dependently inhibited both baseline and IL-1β-stimulated (20 ng/ml) IL-8 secretion with IC(50)s of 0.46 μM and 1.1 μM respectively. CONCLUSION: The data indicate that ML 3000 affects acid-secretory mechanisms downstream of cAMP mobilization induced by histamine H(2) receptor activation, that it directly inhibits H,K-ATPase specific activity, and that baseline gastric epithelial cell IL-8 secretory inhibition may be mediated by ML 3000 inhibition of 5-lipoxygenase activity. We conclude that these gastric function inhibitory data may underlie the gastric sparing properties of ML 3000