Species' identification and microarray-based comparative genome analysis of Streptomyces species isolated from potato scab lesions in Norway

Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequencing of the 16S rRNA gene identified 14 nonmelanin-producing strains to S. turgidiscabies. Fourteen melanin-producing strains were detected with primers specific to S. scabies, but whole-genome microarray analysis, based on 12 766 probes designed for 8848 predicted open reading frames (ORFs) of S. scabies, showed that the 14 strains were different from S. scabies. They were subsequently identified to be S. europaeiscabiei based on the internal transcribed spacer (ITS) sequences of the rRNA genes. This is the first report of the occurrence of S. turgidiscabies and S. europaeiscabiei in Norway. The putative 762 genes exhibiting the highest sequence differences between strains of S. europaeiscabiei and S. scabies according to microarray analysis were concentrated in relatively few gene ontology (GO) categories, including 'symbiosis and mutualism through parasitism', 'cell death' and 'responses to biotic stimulus', whereas genes related to primary metabolism appeared to be more conserved. Microarray data and 16S rRNA gene phylogeny showed, consistently, that there were two genetically distinguishable groups of S. europaeiscabiei on the basis of differences in 131 genes. The results provide novel information about the genetic variability of S. europaeiscabiei and the gene-specific variability between the genomes of S. europaeiscabiei and S. scabies. The usefulness of a custom-designed, whole-genome oligonucleotide microarray in a survey of bacterial plant pathogens was demonstrated.     

The importance of timing and number of surveys in fungal biodiversity research

Practical conservation of biological diversity is dependent on reliable knowledge about what kind, how much, and where the diversity is. To obtain such knowledge three questions, why, what, and how, must be answered before commencing any biodiversity survey. While the questions why and what are often value decisions and thus determined outside the realm of scientific research, the question about how the surveys are conducted lies in the heart of science. Here, we report an intensive repeated survey of wood-inhabiting fungi with the aim of determining the optimal timing and number of the surveys for reliable estimation of the diversity of this species group. The research focusing on the ecology of wood-inhabiting fungi has been increasing but little is known about the reliability of the methods. The variation in the estimates of diversity among surveys was high and the results varied between studied species groups. The site-scale detectability for species belonging to different groups varied from 10 to 95% depending on the survey month and the species group. We conclude that because detectability of many fungi turned out to be poor even when surveys were conducted at an optimal time, the common practice of using a single fruit body survey to estimate fungal diversity of any given area is not enough. We suggest that multiple surveys at an optimal time should be a norm in fungal diversity studies. Improper methodology results in unreliable outcomes that have potential to hamper our goal of conserving the biological diversity.     

Requirement for RNA helicase CsdA for growth of Yersinia pseudotuberculosis IP32953 at low temperatures

The expression of csdA, encoding an RNA helicase, was induced at 3°C in Yersinia pseudotuberculosis. The role of CsdA in Y. pseudotuberculosis under cold conditions was confirmed by impaired growth of insertional csdA mutants at 3°C. The results suggest that CsdA is crucial for Y. pseudotuberculosis survival in the chilled food chain.     

Quantitative determination of nitroglycerin in human plasma by capillary gas chromatography negative ion chemical ionization mass spectrometry

A quantitative method for determination of nitroglycerin in human plasma was developed. Nitroglycerin and the internal standard (butane-1,2,4-triyl trinitrate) were extracted from plasma with pentane. The extracts were analysed by gas chromatography mass spectrometry using fused silica capillary columns and electron capture negative ion chemical ionization. The quantitation limit of the method was about 50 pg ml-1. Linear calibration curves were obtained in the range of 50-1600 pg ml-1. Precision at the level of 100 pg ml-1 was 4%.     

Immunocompetence and resource holding potential in the damselfly, Calopteryx virgo L

It is generally believed that resource holding potential reliablyreflects male quality, but empirical evidence showing this isscarce. Here we show that the outcome of male-male competitionmay predict male immunocompetence in the territorial damselfly,Calopteryx virgo (Odonata: Calopterygidae). We staged contestsbetween 27 pairs of males and found that winners of the contestsshowed higher immunocompetence, measured as encapsulation response,compared with that of losers. Furthermore, the winners had largerfat reserves. We also collected 29 males that had not been usedin staged contests, and found that in these males encapsulationresponse correlated positively with an individual's fat reserves.Both immunocompetence and resource holding potential seem todepend on energy reserves, suggesting a trade-off between parasiteresistance and energetically costly territorial behavior. Theresults suggest that the outcome of male-male contest can beused to predict male quality in terms of immune defense.     

Migration of the clouded Apollo butterfly Parnassius mnemosyne in a network of suitable habitats – effects of patch characteristics

The clouded Apollo Parnassius mnemosyne is a food plant specialist with short but frequent movements between habitat patches. The short average dispersal distances suggest that the probability of colonisation of vacant patches decreases rapidly as the distance between the source and target patches increases, which means that a dense habitat network is needed for the conservation of the species. Both emigration rate and the number of immigrants varied among patches and were not affected only by isolation but also by several other patch characteristics. The model that explained most of the variation in emigration rates among patches included patch area and the number of conspecifics. The area and the population density of the target patch had significant effects on the number of arriving immigrants. Thus, the colonisation of vacant patches is dependent on these patch characteristics. Generally, emigration rates were lower and residence times longer in large patches with many conspecifics. Butterfly density was the most important single factor explaining the variation in the number of immigrants among patches, although the positive effect of the area of the target patch was also significant. As a consequence of the marked positive density dependence caused by conspecific attraction, small patches with higher than average butterfly density, receive more immigrants than could be expected based on the patch area only. Due to conspecific attraction, per capita immigration rates are higher in small than large patches. Thus, immigration may have a more significant effect on the local dynamics of small than large populations.     

Exposure to p,p′-DDE: A Risk Factor for Type 2 Diabetes

Background

Persistent organic pollutants (POPs), such as PCBs, DDT and dioxins have in several cross-sectional studies shown strong associations with type 2 diabetes mellitus. Reversed causality can however not be excluded. The aim of this case-control study was to evaluate whether POPs concentration is a risk factor for type 2 diabetes.

Methodology/Principal Findings

A case-control study was performed within a well-defined cohort of women, age 50–59 years, from the Southern part of Sweden. Biomarkers for POP exposure, 2,2′,4,4′,5,5′-hexachlorobiphenyl (CB-153) and 1,1-dichloro-2,2-bis (p-chlorophenyl)-ethylene (p,p′-DDE) were analyzed in stored serum samples, which were collected at the baseline examination when the cohort was established. For 107 out of the 371 cases, serum samples were stored at least three years before their type 2 diabetes was diagnosed. In this data set, CB-153 and p,p′-DDE were not associated with an increased risk to develop type 2 diabetes. However, when only the cases (n = 39) that were diagnosed more than six years after the baseline examination and their controls were studied, the women in the highest exposed quartile showed an increased risk to develop type 2 diabetes (OR of 1.6 [95% 0.61, 4.0] for CB-153 and 5.5 [95% CI 1.2, 25] for p,p′-DDE).

Conclusions/Significance

The results from the present case-control study, including a follow-up design, confirms that p,p′-DDE exposure can be a risk factor for type 2 diabetes.     

Carrion fly‐derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well‐known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal‐specific (16S) and vertebrate‐specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax , and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.     

Conservation status of freshwater mussels in Europe: state of the art and future challenges

Freshwater mussels of the Order Unionida provide important ecosystem functions and services, yet many of their populations are in decline. We comprehensively review the status of the 16 currently recognized species in Europe, collating for the first time their life‐history traits, distribution, conservation status, habitat preferences, and main threats in order to suggest future management actions. In northern, central, and eastern Europe, a relatively homogeneous species composition is found in most basins. In southern Europe, despite the lower species richness, spatially restricted species make these basins a high conservation priority. Information on freshwater mussels in Europe is unevenly distributed with considerable differences in data quality and quantity among countries and species. To make conservation more effective in the future, we suggest greater international cooperation using standardized protocols and methods to monitor and manage European freshwater mussel diversity. Such an approach will not only help conserve this vulnerable group but also, through the protection of these important organisms, will offer wider benefits to freshwater ecosystems.