Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness

Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.     

Comparison of S-phase fractions measured by flow cytometry and autoradiography in human transplant tumors

The 3H-thymidine labeling index (TLI) and the percentage of cells in the S-phase have been determined by autoradiography and by flow cytometry, (FCM), respectively, in six malignant tumors of human origin transplanted on athymic nude mice. The Dean and Jett model and the graphical model were used to determine the percent of S-phase cells by FCM. Cell cycle analysis was performed using 1) no correction for background; 2) an algebraic function for background correction; and 3) an exponential function for background subtraction. Each of these three data sets was evaluated using both the Dean and Jett model and a graphical model for the evaluation of DNA histograms. The S-phase fractions (SPF) were compared to the corresponding labeling index results. SPF without background correction were 1.54 times higher than the TLI. SPF, after correction using the algebraic model, were 1.29-fold higher than the TLI, whereas SPF obtained after background subtraction according to the exponential model were only 1.05-fold higher than the TLI. Student's t-test revealed significant differences between the mean TLI values (16.25 +/- 9.06) and the mean SPF obtained by FCM without background correction (mean 25.0 +/- 9.36, P less than 0.01), but not between the mean TLI values and the mean SPF percentages after algebraic (mean 21.0 +/- 10.29) and exponential background correction (mean 17.11 +/- 11.59), P greater than 0.05 each. There was no difference between the results obtained using the Dean and Jett model and those obtained using the graphic evaluation.(ABSTRACT TRUNCATED AT 250 WORDS)     

Demographic characteristics of young-of-year freshwater mussel populations in ponds

We describe demographics of young-of-year (YOY) Pondmussels (Ligumia subrostrata) and Giant Floaters (Pyganodon grandis) in ponds during 2009 and 2011. YOY attained large size by approximately 6 months (Pondmussel, mean = 48.5 mm; Floater = 57.5), most individuals were sexually mature, and most females were gravid. Size and sex ratios varied among ponds. Pondmussel size was negatively related to mussel density, suggesting food competition; Floater size was not related to density. Size was not related to glochidial infestation pressure on fishes, suggesting that acquired immunity did not affect YOY performance. The percentage of gravid female Pondmussels varied between years from 27 to 100%, and 91% of female Floaters were gravid in 2011. Mean fecundity was high (Pondmussel = 34,311; Floater = 38,873). The proportion of gravid females and mean fecundity were not related to male density, showing that fertilization was efficient. Variation in size, sex ratios, and gravidity among ponds suggests that small differences in environmental conditions or demographic stochasticity can have large effects on populations. Rapid growth, early maturity, efficient fertilization, and high fecundity of YOY are contrary to traditional views of mussel life history, but these traits may allow Pondmussels and Floaters to rapidly colonize disturbed, unstable habitats.