On the relation of Potamomyces armatisporus to the fossil form-type Mediaverrunites and its taxonomical and ecological implications

This study links the spores of the recent ascomycete genus Potamomyces with the fossil form-taxa Mediaverrunites. Spores of the only known representative of Potamomyces, P. armatisporus, were found in recent material from Nepal together with a previously unknown spore type described here for the first time as Potamomyces nepalensis-type. Potamomyces is thus not a monotypic genus. The rarely isolated type species P. armatisporus is known as a lignicolous freshwater ascomycete from tropical rivers. Our findings indicate that the genus also lives in damp conditions in terrestrial habitats, and is recently distributed also in subtropical regions. Based on the fossil findings of Mediaverrunites, the genus Potamomyces evolved at least 25 million yr ago at the onset of younger Tertiary. Potamomyces is an excellent example of the potential of interdisciplinary fungal research, combining insights from fungal evolution, taxonomy, ancient and recent distribution and ecology.     

Investigation of specific European Brown Hare Syndrome antibodies in wild hares using blood samples dried on blotting paper

European Brown Hare Syndrome (EBHS) is a viral pathology described in Sweden in the early 1980s and which has spread to other European countries. Using an enzyme-linked immunosorbent assay method, we have tested blood samples dried on blotters versus sera to evaluate the utility of this sampling procedure for field research about EBHS. The samples were obtained from 20 captive hares and 43 wild hares. We conclude that the advantage of easiness of blotter sampling and transporting counterbalances the slight underestimation of titres and that the method can thus be recommended in field studies.     

Ultrasensitive green spectrofluorimetric approach for quantification of Hg(II) in environmental samples (water and fish samples) using cysteine@MnO2 dots

Mercury (Hg²⁺) is a natural element present in foods such as fish, water and soil. Exposure to mercury leads to severe toxic effects on the nervous, digestive, and immune systems. Here, a novel, green, and environmentally friendly fluorescent probe decorated with cysteine/MnO₂ quantum dots (Cys@MnO₂ QDs) was synthesized. This synthesis was carried out using a simple ultrasound technique with the aid of cysteine for fabricating Cys@MnO₂ QDs to estimate Hg levels in fish and water samples. In this morphological study, Cys@MnO₂ QDs were fully characterized using high-resolution transmission electron microscopy, zeta potential analysis, fluorescence, ultraviolet–visible and infrared spectroscopy. The fluorescence of the synthesized Cys@MnO₂ QDs was significantly quenched by gradually increasing the Hg(II) concentration. The quenching mechanism based on the Hg–S bonds strengthened the utility of the Cys@MnO₂ QDs as a novel luminescent nanoprobe. The estimation of Hg was linear in the concentration range 0.7–100.0 ng mL⁻¹ with a limit of quantitation equal to 0.30 ng mL⁻¹. The Cys@MnO₂ QDs are fluorescent probes with various benefits such as speed, ease of use, cost- effective, and being environmentally friendly; they are easily applied in food manufacturing and for public health improvement.     

Ecology and seasonal distribution of Vibrio parahaemolyticus in aquatic environments of a temperate region

Abstract An environmental survey was done to study the ecology and distribution of Vibrio parahaemolyticus in 5 selected stations in Okayama Prefecture, which included fresh, brackish, and marine aquatic environments. Water and plankton samples were collected monthly for quantitative and qualitative analyses during the period October, 1987 to October, 1989 for V. parahaemolyticus . The pathogen was not detected from fresh water environments. A seasonality of the organism was observed in brackish and marine environments where average salinity ranged between 0.39 and 1.28%.Plankton samples yielded higher densities of V. parahaemolyticus compared with water samples. By applying several enrichment techniques, the pathogen was detected quite frequently during the winter months in the environments with temperatures ranging between 10 and 14°C. The identification following conventional tests, by the API 20E system and by serological methods reveal that the API 20E system is satisfactory to identify V. parahaemolyticus and further confirms that the serological method could be a simpler and more rapid procedure for V. parahaemolyticus identification.     

Pitfalls of hypothesis tests and model selection on bootstrap samples: Causes and consequences in biometrical applications

The bootstrap method has become a widely used tool applied in diverse areas where results based on asymptotic theory are scarce. It can be applied, for example, for assessing the variance of a statistic, a quantile of interest or for significance testing by resampling from the null hypothesis. Recently, some approaches have been proposed in the biometrical field where hypothesis testing or model selection is performed on a bootstrap sample as if it were the original sample. P‐values computed from bootstrap samples have been used, for example, in the statistics and bioinformatics literature for ranking genes with respect to their differential expression, for estimating the variability of p‐values and for model stability investigations. Procedures which make use of bootstrapped information criteria are often applied in model stability investigations and model averaging approaches as well as when estimating the error of model selection procedures which involve tuning parameters. From the literature, however, there is evidence that p‐values and model selection criteria evaluated on bootstrap data sets do not represent what would be obtained on the original data or new data drawn from the overall population. We explain the reasons for this and, through the use of a real data set and simulations, we assess the practical impact on procedures relevant to biometrical applications in cases where it has not yet been studied. Moreover, we investigate the behavior of subsampling (i.e., drawing from a data set without replacement) as a potential alternative solution to the bootstrap for these procedures.     

MALDI imaging mass spectrometry as a novel tool for detecting histone modifications in clinical tissue samples

Histone post-translational modifications (PTMs), histone variants and enzymes responsible for the incorporation or the removal of the PTMs are being increasingly associated with human disease. Combinations of histone PTMs and the specific incorporation of variants contribute to the establishment of cellular identity and hence are potential markers that could be exploited in disease diagnostics and prognostics and therapy response prediction. Due to the scarcity of suitable antibodies and the pre-requirement of tissue homogenization for more advanced analytical techniques, comprehensive information regarding the spatial distribution of these factors at the tissue level has been lacking. MALDI imaging mass spectrometry provides an ideal platform to measure histone PTMs and variants from tissues while maintaining the information about their spatial distribution. Discussed in this review are the relevance of histones in the context of human disease and the contribution of MALDI imaging mass spectrometry in measuring histones in situ.     

Sex identification assay useful in great apes is not diagnostic in a range of other primate species.

The ability to identify the sex of individuals from noninvasive samples can be a powerful tool for field studies. Amelogenin, a nuclear gene proximate to the pseudoautosomal region of mammalian sex chromosomes, has a 6 base-pair (bp) size difference between human X and Y chromosomes that can be PCR-amplified and sized to distinguish male from female DNA. We examined whether this test can be used to identify sex from different DNA sources across a number of nonhuman primate taxa. Using human amelogenin primers, we were able to amplify diagnostic products from the four great ape species tested, but products from five other primate species were not sexually dimorphic.     

Serological identification and quantification of potato cyst nematodes from clean cysts and processed soil samples

Two monoclonal antibodies which specifically recognise each of the two species of potato cyst nematodes (PCN) and do not cross react with other species of soil nematodes, were used successfully in an immunoassay to identify and quantify PCN species using clean cysts and mixed populations. These antibodies show reactivity only towards antigens prepared from live eggs and they recognise antigens which are easily released from the nematodes. The results presented in this paper show that serological identification and quantification of PCN, not only from clean cysts but also from processed soil samples is achievable. A simple procedure to recover nematodes from soil samples and then to release nematode antigens was devised. The use of these procedures and the immunoassay for quantification of PCN was validated in tests with soil samples from Northern Portugal. The flotation method proved to be as efficient as the Fen wick Can for cyst recovery from soil samples. A significant correlation was obtained between results from immunoassay estimates and the traditional method of cyst picking and egg counting. The amount of organic matter (OM) present in the soil samples affected the sensitivity of the immunoassay but quantification of nematodes extracted from soil samples was possible with soils containing up to 14% of OM. The challenge remains to optimise the extraction procedures and the immunoassay, in practical conditions with highly organic soils containing cysts of different sizes and ages.     

A DNA microarray facilitates the diagnosis of Bacillus anthracis in environmental samples

Aims:  In order to improve the diagnosis of Bacillus anthracis in environmental samples, we established a DNA microarray based on the ArrayTube technology of Clondiag.
Methods and Results:  Total DNA of a bacterial colony is randomly biotinylated and hybridized to the array. The probes on the array target the virulence genes, the genomic marker gene rpoB , as well as the selective 16S rDNA sequence regions of B. anthracis , of the Bacillus cereus group and of Bacillus subtilis . Eight B. anthracis reference strains were tested and correctly identified. Among the analysed environmental Bacillus isolates, no virulent B. anthracis strain was detected.
Conclusions:  This array clearly differentiates B. anthracis from members of the B. cereus group and other Bacillus species in environmental samples by chromosomal ( rpoB ) and plasmid markers. Additionally, recognition of B. cereus strains harbouring the toxin genes or atypical B. anthracis strains that have lost the virulence plasmids is feasible.
Significance and Impact of the Study:  The array is applicable to the complex diagnostics for B. anthracis detection in environmental samples. Because of low costs, high security and easy handling, the microarray is applicable to routine diagnostics.