Direct and transgenerational effects of an experimental heatwave on early life stages in a freshwater snail

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A graphical method for detecting recombination in phylogenetic data sets

Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.      

A global comparison of plant invasions on oceanic islands

Oceanic islands have long been considered to be particularly vulnerable to biotic invasions, and much research has focused on invasive plants on oceanic islands. However, findings from individual islands have rarely been compared between islands within or between biogeographic regions. We present in this study the most comprehensive, standardized dataset to date on the global distribution of invasive plant species in natural areas of oceanic islands. We compiled lists of moderate (5–25% cover) and dominant (>25% cover) invasive plant species for 30 island groups from four oceanic regions (Atlantic, Caribbean, Pacific, and Western Indian Ocean). To assess consistency of plant behaviour across island groups, we also recorded present but not invasive species in each island group.We tested the importance of different factors discussed in the literature in predicting the number of invasive plant species per island group, including island area and isolation, habitat diversity, native species diversity, and human development. Further we investigated whether particular invasive species are consistently and predictably invasive across island archipelagos or whether island-specific factors are more important than species traits in explaining the invasion success of particular species.We found in total 383 non-native spermatophyte plants that were invasive in natural areas on at least one of the 30 studied island groups, with between 3 and 74 invaders per island group. Of these invaders about 50% (181 species) were dominants or co-dominants of a habitat in at least one island group. An extrapolation from species accumulation curves across the 30 island groups indicates that the total current flora of invasive plants on oceanic islands at latitudes between c. 35°N and 35°S may eventually consist of 500–800 spermatophyte species, with 250–350 of these being dominant invaders in at least one island group. The number of invaders per island group was well predicted by a combination of human development (measured by the gross domestic product (GDP) per capita), habitat diversity (number of habitat types), island age, and oceanic region (87% of variation explained). Island area, latitude, isolation from continents, number of present, non-native species with a known invasion history, and native species richness were not retained as significant factors in the multivariate models.Among 259 invaders present in at least five island groups, only 9 species were dominant invaders in at least 50% of island groups where they were present. Most species were invasive only in one to a few island groups although they were typically present in many more island groups. Consequently, similarity between island groups was low for invader floras but considerably higher for introduced (but not necessarily invasive) species – especially in pairs of island groups that are spatially close or similar in latitude. Hence, for invasive plants of natural areas, biotic homogenization among oceanic islands may be driven by the recurrent deliberate human introduction of the same species to different islands, while post-introduction processes during establishment and spread in natural areas tend to reduce similarity in invader composition between oceanic islands. We discuss a number of possible mechanisms, including time lags, propagule pressure, local biotic and abiotic factors, invader community assembly history, and genotypic differences that may explain the inconsistent performance of particular invasive species in different island groups.     

The evolution of sex and recombination in response to abiotic or coevolutionary fluctuations in epistasis

Evolutionary biologists have identified several factors that could explain the widespread phenomena of sex and recombination. One hypothesis is that host-parasite interactions favor sex and recombination because they favor the production of rare genotypes. A problem with many of the early models of this so-called Red Queen hypothesis is that several factors are acting together: directional selection, fluctuating epistasis, and drift. It is thus difficult to identify what exactly is selecting for sex in these models. Is one factor more important than the others or is it the synergistic action of these different factors that really matters? Here we focus on the analysis of a simple model with a single mechanism that might select for sex: fluctuating epistasis. We first analyze the evolution of sex and recombination when the temporal fluctuations are driven by the abiotic environment. We then analyze the evolution of sex and recombination in a two-species coevolutionary model, where directional selection is absent (allele frequencies remain fixed) and temporal variation in epistasis is induced by coevolution with the antagonist species. In both cases we contrast situations with weak and strong selection and derive the evolutionarily stable (ES) recombination rate. The ES recombination rate is most sensitive to the period of the cycles, which in turn depends on the strength of epistasis. In particular, more virulent parasites cause more rapid cycles and consequently increase the ES recombination rate of the host. Although the ES strategy is maximized at an intermediate period, some recombination is favored even when fluctuations are very slow. By contrast, the amplitude of the cycles has no effect on the ES level of sex and recombination, unless sex and recombination are costly, in which case higher-amplitude cycles allow the evolution of higher rates of sex and recombination. In the coevolutionary model, the amount of recombination in the interacting species also has a large effect on the ES, with evolution favoring higher rates of sex and recombination than in the interacting species. In general, the ES recombination rate is less than or equal to the recombination rate that would maximize mean fitness. We also discuss the effect of migration when sex and recombination evolve in a metapopulation. We find that intermediate parasite migration rates maximize the degree of local adaptation of the parasite and lead to a higher ES recombination rate in the host.     

Maturation of newly replicated chromatin of simian virus 40 and its host cell

The DNA in replicating simian virus 40 chromatin and cellular chromatin was labeled with short pulses of [³H]thymidine. The structure of pulse-labeled nucleoprotein complexes was studied by micrococcal nuclease digestion. It was found that in both newly replicated viral and cellular chromatin, a structural state appears which is characterized by an increased sensitivity to nuclease and a faster than usual rate of cleavage to DNA fragments of monomeric nucleosome size and smaller. Pulse-chase experiments show that each of these effects requires a characteristic time to disappear in both systems, suggesting the existence of different sub-processes of chromatin maturation. One of these processes, detectable by the reversion of the unusually fast production of subnucleosomal fragments, is delayed in SV40 chromatin replication.     

HIV-1 adapts to a retrocyclin with cationic amino acid substitutions that reduce fusion efficiency of gp41

Retrocyclin (RC)-101 is a cationic theta-defensin that inhibits HIV-1 entry. Passaging HIV-1(BAL) under selective pressure by this cyclic minidefensin resulted in only a 5- to 10-fold decrease in viral susceptibility to RC-101. Emergent viral isolates had three amino acid substitutions in their envelope glycoprotein. One was in a CD4-binding region of gp120, and the others were in the heptad repeat (HR) domains of gp41 (HR1 and HR2). Each mutation replaced an electroneutral or electronegative residue with one that was positively charged. These mutations were evaluated either alone or in combination in a single-round viral entry assay. Although the mutation in gp120 did not affect viral entry, the mutation in HR1 of gp41 conferred relative resistance to RC-101. Interestingly, the envelope with the HR2 mutation was less efficient and became codependent on the presence of RC-101 for entry. The adaptive response of HIV-1 to this cationic host defense peptide resembles the responses of bacteria that modulate their surface or membrane charge to evade analogous host defense peptides. These findings also suggest that interactions between theta-defensins and gp41 may contribute to the ability of these cyclic minidefensins to prevent HIV-1 entry into target cells.     

The neolignans of Licaria canella

The trunk wood of Licaria canella contains, besides dillapiol and elemicin, the neolignans canellin-A, -B and -C, for which the respective structures of 1-allyl-4,8-dihydroxy-3,5-dimethoxy-7-methyl-6-piperonylbicyclo-[3,2,1]octane; 3a-allyl-4,5-dimethoxy-3-methyl-2-piperonyl-2,3,3a,6,7,7a-hexahydro-6-oxobenzofuran and 1-allyl-4,8-dihydroxy-5-methoxy-7-methyl-6-piperonyl-3-oxobicyclo-[3,2,1] octane are proposed.     

RATT: Rapid Annotation Transfer Tool

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.     

Upregulation of gap junction protein connexin43 in alveolar epithelial cells of rats with radiation-induced pulmonary fibrosis

 The degree of immunoreactive connexin43 (Cx43) in rat lung was evaluated during the development of radiation-induced pulmonary fibrosis in rat by a double immunofluorescence technique using polyclonal antisera to Cx43 and monoclonal antibodies to cytokeratins on cryostat sections. In normal rat lungs, Cx43 was detected in pneumocytes type II and I, in large blood vessel endothelia, in peribronchial smooth muscle cells, and in some peribronchial and perivascular interstitial cells. As early as 1 week after irradiation, enhanced immunoreactivity for Cx43 in the epithelial cells was detected. In severely injured lungs (about 3 months after irradiation), Cx43 was found also in the cytoplasm of type II pneumocytes. These findings were confirmed by western blot data. Western blot analysis also revealed increased phosphorylation of Cx43. It remains to be investigated whether the increased content of Cx43 in irradiated rat lung may be due to an enhanced number of gap junctions between type I and II alveolar epithelial cells. Accepted: 20 May 1996