Decoding a substantial set of samples in parallel by massive sequencing

There has been a dramatic increase of throughput of sequenced bases in the last years but sequencing a multitude of samples in parallel has not yet developed equally. Here we present a novel strategy where the combination of two tags is used to link sequencing reads back to their origins from a pool of samples. By incorporating the tags in two steps sample-handling complexity is lowered by nearly 100 times compared to conventional indexing protocols. In addition, the method described here enables accurate identification and typing of thousands of samples in parallel. In this study the system was designed to test 4992 samples using only 122 tags. To prove the concept of the two-tagging method, the highly polymorphic 2(nd) exon of DLA-DRB1 in dogs and wolves was sequenced using the 454 GS FLX Titanium Chemistry. By requiring a minimum sequence depth of 20 reads per sample, 94% of the successfully amplified samples were genotyped. In addition, the method allowed digital detection of chimeric fragments. These results demonstrate that it is possible to sequence thousands of samples in parallel without complex pooling patterns or primer combinations. Furthermore, the method is highly scalable as only a limited number of additional tags leads to substantial increase of the sample size.     

Analysis of microsatellite mutations in buccal cells from a case-control study for lung cancer

Exposure to tobacco carcinogens is the major cause of human lung cancer, but even heavy smokers have only about a 10% life-time risk of developing lung cancer. Currently used screening processes, based largely on age and exposure status, have proven to be of limited clinical utility in predicting cancer risk. More precise methods of assessing an individual's risk of developing lung cancer are needed. Because of their sensitivity to DNA damage, microsatellites are potentially useful for the assessment of somatic mutational load in normal cells. We assessed mutational load using hypermutable microsatellites in buccal cells obtained from lung carcinoma cases and controls to test if such a measure could be used to estimate lung cancer risk. There was no significant association between smoking status and mutation frequency with any of the markers tested. No significant association between case status and mutation frequency was observed. Age was significantly related to mutation frequency in the microsatellite marker D7S1482. These observations indicate that somatic mutational load, as measured using mutation frequency of microsatellites in buccal cells, increases with increasing age but that subjects who develop lung cancer have a similar mutational load as those who remain cancer free. This finding suggests that mutation frequency of microsatellite mutations in buccal cells may not be a promising biomarker for lung cancer risk.     

Genotoxicity of inhaled nanosized TiO(2) in mice

In vitro studies have suggested that nanosized titanium dioxide (TiO(2)) is genotoxic. The significance of these findings with respect to in vivo effects is unclear, as few in vivo studies on TiO(2) genotoxicity exist. Recently, nanosized TiO(2) administered in drinking water was reported to increase, e.g., micronuclei (MN) in peripheral blood polychromatic erythrocytes (PCEs) and DNA damage in leukocytes. Induction of micronuclei in mouse PCEs was earlier also described for pigment-grade TiO(2) administered intraperitoneally. The apparent systemic genotoxic effects have been suggested to reflect secondary genotoxicity of TiO(2) due to inflammation. However, a recent study suggested that induction of DNA damage in mouse bronchoalveolar lavage (BAL) cells after intratracheal instillation of nanosized or fine TiO(2) is independent of inflammation. We examined here, if inhalation of freshly generated nanosized TiO(2) (74% anatase, 26% brookite; 5 days, 4 h/day) at 0.8, 7.2, and (the highest concentration allowing stable aerosol production) 28.5 mg/m(3) could induce genotoxic effects in C57BL/6J mice locally in the lungs or systematically in peripheral PCEs. DNA damage was assessed by the comet assay in lung epithelial alveolar type II and Clara cells sampled immediately following the exposure. MN were analyzed by acridine orange staining in blood PCEs collected 48 h after the last exposure. A dose-dependent deposition of Ti in lung tissue was seen. Although the highest exposure level produced a clear increase in neutrophils in BAL fluid, indicating an inflammatory effect, no significant effect on the level of DNA damage in lung epithelial cells or micronuclei in PCEs was observed, suggesting no genotoxic effects by the 5-day inhalation exposure to nanosized TiO(2) anatase. Our inhalation exposure resulted in much lower systemic TiO(2) doses than the previous oral and intraperitoneal treatments, and lung epithelial cells probably received considerably less TiO(2) than BAL cells in the earlier intratracheal study.     

Nectar Sugar Composition in Relation to Pollination Syndromes in Sinningieae (Gesneriaceae)

A putative correlation between nectar sugar composition andpollination syndrome was evaluated in the tribe Sinningieae(Neotropical Gesneriaceae). Sucrose, fructose and glucose werequantified in the nectar of 45 species using high performanceanion-exchange chromatography. Representative species of thehummingbird, bee, bat and moth pollination syndromes were sampledin relation to their numeric importance in the tribe. In hummingbirdand bee flowers, which represent 95% of the species in Sinningieae,nectar was sucrose-dominant (ratio [sucrose]/[hexose] > 1).Sugar ratios below one were only found in the nectar of threespecies with moth and bat syndromes. Sugar concentration averaged23.9 ± 10.6% (wt/total wt) in hummingbird flowers and28.7 ± 10.6% in bee flowers, whereas diluted nectar (7.1± 3.4%) was restricted to bat flowers. Similarities inthe nectar of hummingbird and bee flowers contrast with thepresence of specific morphological traits associated with thesetwo syndromes, indicating that plant-pollinator relationshipsrely on flower display rather than on nectar characteristics.By contrast, distinct nectar chemistry is correlated with thebat syndrome in which a particularly low sucrose productionis responsible for hexose dominance. Copyright 2001 Annals ofBotany Company Nectar sugar composition, pollination syndrome, Sinningia, Gesneriaceae, Brazil     

Phylogenetic selection of Narcissus species for drug discovery

Plants are of immense importance in providing healthcare worldwide. With over 250 000 species of angiosperms alone, the potential for finding new medicinal plants and lead compounds for drug development is enormous. Some way of selecting plants for drug discovery programs is necessary. Phylogenies have great explanatory power and also enable a predictive perspective not offered by previous classifications of plants. Phylogenetic selection of target species is a new approach to drug discovery and the present study is the first attempt to correlate acetylcholine esterase (AChE) inhibitory activity and alkaloid distribution with a molecular phylogenetic hypothesis of Narcissus. The distribution of alkaloids with AChE inhibitory activity is significantly constrained by the phylogeny. Simultaneous evaluation of all available information of alkaloids and AChE inhibitory activity in a phylogenetic framework allowed us to discuss various strategies for selection of target species for further studies of AChE inhibitory activity.     

Replacement of the native crayfish Astacus astacus by the introduced species Pacifastacus leniusculus in a small, enclosed Finnish lake: a 30-year study

The native noble crayfish Astacus astacus L., and the introduced North American signal crayfish Pacifastacus leniusculus Dana, co‐occur in Slickolampi, a small lake in southern Finland. That both species have lived side‐by‐side for 30 yr without any signs of crayfish plague Aphanomyces astaci, indicates that the P. leniusculus population must be plague‐free. According to annual trap catches and population size estimates, A. astacus was clearly dominant in the 1970s and most of the 1980s. At the end of the 1980s, however, there was a shift in the relative abundances of the two species, and in the 1990s, P.leniusculus became dominant. As the 1990s drew to a close, it accounted for >98% of total catches. Originating from a minor stocking (only 900 2nd stage juveniles) P. leniusculus has not augmented the existing fauna in this lake but has almost completely replaced A. astacus. Both species seem to a great extent to prefer the same types of biotope but P. leniusculus is distinctly more demanding and was encountered less often than A. astacus on gently‐sloping soft shores. The proportion of A. astacus with chelae injuries (16 yr, mean 17.3%) was nearly twice that of P. leniusculus (9.3%), suggesting that agonistic interspecific encounters do occur and that P. leniusculus is much more competitive. However, the consistent weakening of A. astacus, even at sites with only a low density of P. leniusculus, indicates that the elimination of A. astacus is not adequately explained by competitive exclusion. We suggest that its disappearance is governed by a combination of several interacting mechanisms, of which harvest (≥100 mm specimens of both species) and interspecific competition with P.leniusculus were initially the main reasons for the decline in the population. The ultimate reason for the collapse of A. astacus seems to have been the almost complete cessation of successful reproduction, presumably due to reproductive interference between the two species. Interspecific mating results in females laying sterile eggs. Although both species suffer from the ensuing loss of recruitment, the consequences are less serious for P. leniusculus, which has a higher capacity for population increase than A. astacus: the smaller the proportion of A. astacus, the greater the role played by reproductive interference as a replacement mechanism.     

Genome-wide effects of postglacial colonization in Arabidopsis lyrata

The perennial outcrossing Arabidopsis lyrata is becoming a plant model species for molecular ecology and evolution. However, its evolutionary history, and especially the impact of the climatic oscillations of the Pleistocene on its genetic diversity and population structure, is not well known. We analyzed the broad-scale population structure of the species based on microsatellite variation at 22 loci. A wide sample in Europe revealed that glaciations and postglacial colonization have caused high divergence and high variation in variability between populations. Colonization from Central Europe to Iceland and Scandinavia was associated with a strong decrease of genetic diversity from South to North. On the other hand, the Russian population included in our data set may originate from a different refugium probably located more to the East. These genome-wide patterns must be taken into account in studies aiming at elucidating the genetic basis of local adaptation. As shown by sequence data, most of the loci used in this study do not evolve like typical microsatellite loci and show variable levels of homoplasy: this mode of evolution makes these markers less suitable to investigate the between-continent divergence and more generally the worldwide evolution of the species. Finally, a strong negative correlation was detected between levels of within-population diversity and indices of differentiation such as F(ST). We discuss the causes of this correlation as well as the potential bias it induces on the quantification and interpretation of population structure.     

Behavior and season affect crayfish detection and density inference using environmental DNA

Although the presence/absence of aquatic invertebrates using environmental DNA (eDNA) has been established for several species, inferring population densities has remained problematic. The invasive American signal crayfish, Pacifastacus leniusculus (Dana), is the leading cause of decline in the UK's only native crayfish species, Austropotamobius pallipes (Lereboullet). Methods to detect species at low abundances offer the opportunity for the early detection, and potential eradication, of P. leniusculus before population densities reach threatening levels in areas occupied by A. pallipes. Using a factorial experimental design with aquaria, we investigated the impacts of biomass, sex ratio, and fighting behavior on the amount of eDNA released by P. leniusculus, with the aim to infer density per aquarium depending on treatments. The amount of target eDNA in water samples from each aquarium was measured using the quantitative Polymerase Chain Reaction. We show that the presence of eggs significantly increases the concentration of crayfish eDNA per unit of mass, and that there is a significant relationship between eDNA concentration and biomass when females are egg‐bearing. However, the relationship between crayfish biomass and eDNA concentration is lost in aquaria without ovigerous females. Female‐specific tanks had significantly higher eDNA concentrations than male‐specific tanks, and the prevention of fighting did not impact the amount of eDNA in the water. These results indicate that detection and estimate of crayfish abundance using eDNA may be more effective while females are ovigerous. This information should guide further research for an accurate estimation of crayfish biomass in the field depending on the season. Our results indicate that detection and quantification of egg‐laying aquatic invertebrate species using eDNA could be most successful during periods when eggs are developing in the water. We recommend that practitioners consider the reproductive cycle of target species when attempting to study or detect aquatic species using eDNA in the field.     

High rate of adaptive evolution in two widespread European pines

Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ω_a), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ω_a. Moreover, population contraction–expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.     

MtDNA COI barcodes reveal cryptic diversity in the Baetis vernus group (Ephemeroptera, Baetidae)

Partial mitochondrial COI sequences (barcoding fragment) were explored for the understanding of the species boundaries of Baetis vernus group taxa (Ephemeroptera, Baetidae) in northern Europe. We sampled all species of this group occurring in Finland, but focused on taxa for which morphological and taxonomical confusion have been most apparent. The sequence matrix comprised 627 nucleotides for 96 specimens, and was analysed using parsimony. Results provided strong evidence that Baetis macani Kimmins and B. vernus Curtis comprise morphologically cryptic but molecularly distinct taxa, as intraspecific uncorrected divergences within haplogroups ranged between 0.3% and 1.4% and interspecific divergences were from 13.1% to 16.5%. These interesting findings prompt for further taxonomic studies of B. vernus taxa using more extensive specimen sampling from the known distributional areas in the Palaearctic/Holarctic region for better understanding of haplotype distributions. We stress the importance of integration of morphological and molecular data, and the necessity to employ additional nuclear DNA sequence data.