Sample coherence – a field study approach to assess similarity of macroinvertebrate samples

The EU-funded STAR-project provided an opportunity to analyse 1418 macroinvertebrate samples from 310 sampling sites throughout Europe. At most of the sites, samples were taken in two seasons using both national protocols and the project’s STAR-AQEM protocol. At a subset of sites (86), two replicate samples were taken by each method in each of the two seasons. The resulting taxalists were analysed in terms of community similarity using the Bray–Curtis Index, Jaccard, and Renkonen Indices. A new concept of sample ‘coherence’ is used to measure the relative strength of within-site, within-season and within-method similarity and to determine their importance on variability in community composition. Site-coherence (i.e., highest similarity to another sample from the same site) was much higher where replicate samples were available. Season-coherence of samples was nearly 100% even if different methods were compared. Season appeared to be one of the major determinants of in-stream fauna. The STAR-AQEM method is most comparable to the Nordic, Portuguese and Czech (PERLA) national methods and less comparable to the Italian (IBE) and Latvian methods. Samples collected by these latter methods had higher similarities to other sites sampled with the same methods than to samples of the same site using the STAR-AQEM method, thus there was low site-coherence. In three stream types from Italy, Latvia and Greece 28–38% of the samples were most similar to a sample from a different site than to a replicate sample from the same site. This fact could have serious consequences for follow up bioassessments or impact assessments by cluster analysis based on similarity measures. Replicate samples are less coherent within site, season or method if the taxonomic resolution is family rather than species. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

DNA methylation in pre-diagnostic serum samples of breast cancer cases: Results of a nested case–control study

Background: Promoter methylation of tumor suppressor genes is a frequent and early event in breast carcinogenesis. Paired tumor tissue and serum samples from women with breast cancer show that promoter methylation is detectable in both sample types, with good concordance. This suggests the potential for these serum markers to be used for breast cancer detection. Methods: The current study was a case–control study nested within the prospective New York University Women's Health Study cohort aimed to assess the ability of promoter methylation in serum to detect pre-clinical disease. Cases were women with blood samples collected within the 6 months preceding breast cancer diagnosis (n = 50). Each case was matched to 2 healthy cancer-free controls and 1 cancer-free control with a history of benign breast disease (BBD). Results: Promoter methylation analysis of four cancer-related genes: — RASSF1A, GSTP1, APC and RARβ2, — was conducted using quantitative methylation-specific PCR. Results showed that the frequency of methylation was lower than expected among cases and higher than expected among controls. Methylation was detected in the promoter region of: RASSF1A in 22.0%, 22.9% and 17.2% of cases, BBD controls and healthy controls respectively; GSTP1 in 4%, 10.4% and 7.1% respectively; APC in 2.0%, 4.4% and 4.2% respectively and RARβ2 in 6.7%, 2.3% and 1.1% respectively. Conclusion: Methylation status of the four genes included in this study was unable to distinguish between cases and either control group. This study highlights some methodological issues to be addressed in planning prospective studies to evaluate methylation markers as diagnostic biomarkers.     

Areas of endemism in the Antarctic – a case study of the benthic hydrozoan genus Oswaldella (Cnidaria,Kirchenpaueriidae)

Aim The aim of this study is to investigate areas of endemism within the distribution of Oswaldella species in the Southern Ocean, thereby testing previous hypotheses and proposing alternative scenarios for Antarctic evolution. Location Southern Ocean, Antarctic and sub-Antarctic waters of southern South America. Methods We prepared a database for the 31 currently known species of the Antarctic genus Oswaldella, which includes geographical locations gathered from published taxonomic studies as well as materials from museums and expeditions. A parsimony analysis of endemicity (PAE) was used to test hypotheses of distribution patterns. Results Four areas of endemism are hypothesized: southern South America, two high Antarctic areas (eastern and western) and a larger area, mainly in western Antarctica at lower latitudes and including insular areas (but not the Balleny Islands). Main conclusions The results support, in part, previous hypotheses for the Southern Ocean region, while providing more detailed resolution. The areas of endemism may reflect both historical and ecological processes that influenced the Antarctic biota. The Magellanic area reflects the well-known affinities of the Antarctic biota with that of South America and may be a consequence of dispersal through deeper (and colder) waters, followed by speciation. The second area, the largest one, encompasses most of the insular faunas and may also be associated with deeper waters formed since 43 Ma. The third area may be explained by the development of seaways in the circum-Antarctic region beginning 50 Ma. Finally, the fourth zone, with a very poor fauna, coincides with the opening of the Tasman Strait and the formation of the Australo-Antarctic Gulf, associated with a minor wind-driven current.     

Multi-frequency rhythms in activity of mixed human population in social networking sites – a preliminary study

There has been a global surge in the use of social networking sites (SNSs), like Facebook (FB) and WhatsApp (WA). Many studies have been conducted thus far highlighting the effects of use of SNSs on psychosocial behavior, but none on biological rhythms. The main aim of this study was to ascertain rhythms in intensity of FB use and WA chats as a group/population phenomenon. Of the two authors, RA has a FB account consisting of 291 friends, whereas AKP has 1031 friends at the time of this study. RA used Raipur Rockers (RR) group and AKP used BHU-MSc’77 (BHU) group from their respective WA accounts. The findings indicate the presence of multi-frequency rhythms in the intensity of online activity among the FB friends and in the frequency of chat postings among the members of the RR and BHU groups. A difference in the peak timings of activity between RR and BHU groups could be attributed to the factor, ‘age.’ While more intensive research is warranted in this area, for the time being, the difference in the pattern of activity between young and old SNSs users might have a bearing on the success of e-business possibly through appropriate scheduling of e-advertisements.     

Analysis of the microbial communities on corroded concrete sewer pipes – a case study

Conventional as well as molecular techniques have been used to determine the microbial communities present on the concrete walls of sewer pipes. The genetic fingerprint of the microbiota on corroded concrete sewer pipes was obtained by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. The DGGE profiles of the bacterial communities present on the concrete surface changed as observed by shifts occurring at the level of the dominance of bands from non-corroded places to the most severely corroded places. By means of statistical tools, it was possible to distinguish two different groups, corresponding to the microbial communities on corroded and non-corroded surfaces, respectively. Characterization of the microbial communities indicated that the sequences of typical bands showed the highest level of identity to sequences from the bacterial strains Thiobacillus thiooxidans, Acidithiobacillus sp., Mycobacterium sp. and different heterotrophs belonging to the alpha-, beta- and gamma-Proteobacteria, Acidobacteria and Actinobacteria. In addition, the presence of N-acyl-homoserine lactone signal molecules was shown by two bio-assays of the biofilm on the concrete under the water level and at the most severely corroded places on the concrete surface of the sewer pipe.     

Estimation of ecological exergy using weighing parameters determined from DNA contents of organisms – a case study

We studied the changes of exergy and specific exergy with data of benthic macrofauna communities, periodically sampled along an estuarine gradient of eutrophication in the Mondego estuary (Western Portugal). Exergy estimates were calculated from organism biomass, based on weighing factors for the relative content of exergy per unit of biomass determined from DNA contents of organisms. Results were discussed in terms of both the macrofauna biomass production and the structural organisation of the system. Estimates for the exergy indices provided useful indications for the evaluation of environmental impact due to the eutrophication process. Different average values for the indices of exergy and specific exergy were estimated relatively to areas with different levels of eutrophication, in the spatial gradient of eutrophication. Higher exergy levels and lower exergy content per unit of biomass (specific exergy) were associated to populations more stabilized or areas less perturbed. Additionally, the index of specific exergy seemed capable of providing indications for the qualitative alterations in the communities (in temporal and spatial terms) that go in the direction of the observations made in this ecosystem.     

The effect of hay blowing instead of hay raking on plant biodiversity – a case study of a dry meadow in a Swiss mountain region

Low-input dry meadows are habitats of high nature value. More and more, less time-consuming harvesting techniques replace different steps of the traditional hay making process. The use of leaf blowers instead of rakes for hay making became popular in the last ten years in Switzerland. Thus, we set up a case study to test effects on the conservation value. The studied dry meadow of high nature value is located in the municipality of Stans (Switzerland). After five years no significant differences between blown and raked plots in species richness, richness of target an indicator species, medium plant-indicator values, i.e. nutrients, humidity, light or in the species assemblages were observed. From 2010 until 2014 the moss cover increased in all plots. The differences between raked and blown plots were not significant. In 2015, however, the difference between the two treatments increased to 13%. While the moss cover of the blown plots remained at 20%, the moss cover of the raked plots dropped to 7%. These results from only one case study and only a short observation period of five years do not allow a generalization, but they give a first impression of the short-term effects. We recommend managers of dry meadows with high nature values to keep an eye on the change of moss cover and potential changes of conservation values when leaf blowers instead of rakes are used for hay harvesting.     

Effects of short term pollution on the level of fluctuating asymmetry – a case study using damselflies

Fluctuating asymmetry (FA), a measure of developmental stability, has been suggested as a monitoring tool for environmental pollution. However, there have been few investigations into the effects of short term pollution on the level of FA. This paper explores effects of exposing late instar larvae to short term pollution on the level of FA in the wings of adult damselflies. In these insects FA in wing length and in cell patterns have different windows of opportunity in relation to environmental stress. If increased environmental stress is applied after the window of opportunity of one trait had closed, while the window of the other trait was still open then the level of FA of the first trait should not be altered whereas that of the latter should increase. If short term pollution killed part of a population, symmetrical individuals (low FA) should survive better than highly asymmetrical ones, because FA reflects the overall ability of an individual to cope with stress. If the pollution event occurred at a time when the level of FA was already fixed, the level of FA of the remaining population should be lower than that in controls. An experiment was carried out, using 10 artificial ponds, each holding a population of larvae of the damselfly Xanthocnemis zealandica (McLachlan). Damselfly larvae were exposed to carbaryl at a nominal concentration of 100 g l^–1, which reduced emergence success after 10–20 days by ca. 50%. Based on laboratory experiments, it was assumed that despite the high mortality, the short exposure to carbaryl late in the last instar would ensure that the wing cell patterns of the damselflies were not altered by the increased stress. The level of FA in wing length increased in the damselflies surviving the exposure to carbaryl but the level of FA in cell patterns did not differ significantly between the treatment and the control. The effects of differential mortality, as well as the effects of pollution, on the level of FA in traits with different windows of opportunity need further investigation.     

A holomorph approach to xiphosuran evolution—a case study on the ontogeny of Euproops

Specimens of Euproops sp. (Xiphosura, Chelicerata) from the Carboniferous Piesberg quarry near Osnabrück, Germany, represent a relatively complete growth series of 10 stages. Based on this growth sequence, morphological changes throughout the ontogeny can be identified. The major change affects the shape of the epimera of the opisthosoma. In earlier stages, they appear very spine-like, whereas in later stages the bases of these spine-like structures become broader; the broadened bases are then successively drawn out distally. In the most mature stage known, the epimera are of trapezoidal shape and approach each other closely to form a complete flange around the thoracetron (=fused tergites of the opisthosoma). These ontogenetic changes question the taxonomic status of different species of Euproops, as the latter appear to correspond to different stages of the ontogenetic series reconstructed from the Piesberg specimens. This means that supposed separate species could, in fact, represent different growth stages of a single species. It could alternatively indicate that heterochrony (=evolutionary change of developmental timing) plays an important role in the evolution of Xiphosura. We propose a holomorph approach, i.e., reconstructing ontogenetic sequences for fossil and extant species as a sound basis for a taxonomic, phylogenetic, and evolutionary discussion of Xiphosura.     

Assessment of β-tubulin gene as a complementary molecular marker for desert truffle identification: a study case on Tunisian samples

Tunisian desert truffles have been identified on the basis of the internal transcribed spacer (ITS) locus as Tirmania nivea, Terfezia bouderii and T. arenaria. ITS and, for the first time, β-tubulin gene were employed in the phylogenetic analyses of these species to assess whether β-tubulin gene could be a complementary molecular tool for resolution of phylogenetic species. From their comparison, both markers showed to be suitable to distinguish Tirmania nivea from Terfezia bouderii and T. arenaria and, focusing on the T. boudieri complex, to assign the phylogenetic types previously described. In addition to give a first glimpse into the distribution of desert truffles from north to south of Tunisia, we then suggest to use the β-tubulin gene as a complementary marker to ITS. This indication can be useful above all for the phylogenetic reconstruction of the T. boudieri complex.     

Correction to: Preliminary insights of a mixed‑species shark aggregation: a case study of two carcharhinids from the Mediterranean Sea

Environmental Biology of Fishes -     

Policy measures to address bird interactions with power lines – a comparative case study of four countries

Bird mortality caused by electric power lines has been an issue in several countries for more than three decades now. Despite serious efforts by conservationists, government agencies and utility companies assisted by increasing biological and technological knowledge, only a minority of countries has made significant progress in mitigation. In the present article I argue that the policy aspects, which have not been so widely researched so far, have considerable effects on the efficiency of mitigation measures. The problem management methods of four countries—Hungary, Slovakia, South Africa and the USA—are discussed in detail to reveal success criteria. The role of contextual factors, stances and relations of different actors, plus actions and tools applied in the solution process, are demonstrated together with the resulting outcomes. To help strategic planning, I review favourable solution methods (volunteer agreements, legislative steps, mixed solutions, etc.) used in different country-specific contexts, and point out probable consequences of the strategy chosen.     

Public involvement in pharmacogenomics research: a national survey on patients’ attitudes towards pharmacogenomics research and the willingness to donate DNA samples to a DNA bank in Japan

To assess the attitude of Japanese patients towards pharmacogenomics research and a DNA bank for identifying genomic markers associated with adverse drug reactions (ADRs) and their willingness to donate DNA samples, we conducted a survey of 550 male and female patients. The majority of the respondents showed a positive attitude towards pharmacogenomics research (87.6%) and a DNA bank (75.1%). The willingness to donate DNA samples when experiencing severe ADRs (55.8%) was higher than when taking medications (40.4%). Positive attitudes towards a DNA bank and organ donation were significantly associated with an increased willingness to donate. Though the level of positive attitude in the patient population was higher than that in the general public in our former study (81.0 and 70.4%, respectively), the level of the willingness of patients to donate was 40.4% when taking medications and 55.8% when experiencing severe ADRs which was lower than that of the general public in our former study (45.3 and 61.7%). The results suggested that the level of true willingness in the patient population was lower than that of the general public considering the fictitious situation presented to the public (to suppose that they were patients receiving medication). It is important to assess the willingness of patients who are true potential donors, not the general public.     

Novel insights on effect of atrioventricular programming of biventricular pacemaker in heart failure – a case series

Background

Echocardiography plays an integral role in the diagnosis of congestive heart failure including measurement of left heart pressure as well as mechanical dyssynchrony.

Methods

In this report we describe novel therapeutic uses of echo pulsed wave Doppler in atrioventricular pacemaker optimization in patients who had either not derived significant symptomatic benefit post biventricular pacemaker implantation or deteriorated after deriving initial benefit. In these patients atrioventricular optimization showed novel findings and improved cardiac output and symptoms.

Results

In 3 patients with Cheyne Stokes pattern of respiration echo Doppler showed worsening of mitral regurgitation during hyperpneac phase in one patient, marked E and A fusion in another patient and exaggerated ventricular interdependence in a third patient thus highlighting mechanisms of adverse effects of Cheyne Stokes respiration in patients with heart failure. All 3 patients required a very short atrioventricular delay programming for best cardiac output. In one patient with recurrent congestive heart failure post cardiac resynchronization, mitral inflow pulse wave Doppler showed no A wave until a sensed atrioventricular delay of 190 ms was reached and showed progressive improvement in mitral inflow pattern until an atrioventricular delay of 290 ms. In 2 patients atrioventricular delay as short as 50 ms was required to allow E and A separation and prevent diastolic mitral regurgitation. All patients developed marked improvement in congestive heart failure symptoms post echo-guided biv pacemaker optimization.

Conclusion

These findings highlight the value of echo-guided pacemaker optimization in symptomatic patients post cardiac resynchronization treatment.     

The influence of substratum age on patterns of protozoan assemblages in freshwater Aufwuchs — a case study

The sulfate reduction rate was measured for almost four years in the profundal sediments of Lake Kizaki, a mesotrophic lake in central Japan. The rate was generally highest in the surface layer and decreased with depth. Seasonally, sulfate reduction tended to be high in spring and summer, and then to decrease until the end of stratification (December) in spite of a constant in situ temperature of around 6 °C, although fluctuations were found in every year. The rate also fluctuated greatly according to year. The maximum rate of sulfate reduction was 0.33 mmol m⁻² d⁻¹ in May, 1990, and the minimum was 0.004 mmol m⁻² d⁻¹ in March, 1993. These relatively low rates, compared with those reported for freshwater sediments, seem to be due to low concentrations of sulfate in the sediments (5–23 μmol l⁻¹ in the surface layer). The rate was highly correlated with the concentration of sulfate in the sediments. The addition of sulfate stimulated sulfate reduction in all sediment samples tested, but adding lactate did not. Therefore, sulfate reduction should be limited mainly by the supply of sulfate. Measurements of sulfate reduction rates at different concentrations of added sulfate revealed a low concentration of half-saturation constant as low as 12 μmol l⁻¹.