CORAL: Building up QSAR models for the chromosome aberration test

A high level of chromosomal aberrations in peripheral blood lymphocytes may be an early marker of cancer risk, but data on risk of specific cancers and types of chromosomal aberrations are limited. Consequently, the development of predictive models for chromosomal aberrations test is important task. Majority of models for chromosomal aberrations test are so-called knowledge-based rules system. The CORAL software (http://www.insilico.eu/coral, abbreviation of “CORrelation And Logic”) is an alternative for knowledge-based rules system. In contrast to knowledge-based rules system, the CORAL software gives possibility to estimate the influence upon the predictive potential of a model of different molecular alerts as well as different splits into the training set and validation set. This possibility is not available for the approaches based on the knowledge-based rules system. Quantitative Structure–Activity Relationships (QSAR) for chromosome aberration test are established for five random splits into the training, calibration, and validation sets. The QSAR approach is based on representation of the molecular structure by simplified molecular input-line entry system (SMILES) without data on physicochemical and/or biochemical parameters. In spite of this limitation, the statistical quality of these models is quite good.     

Mineral element content in Ulva lactuca L. with reference to eutrophication in Hong Kong coastal waters

The amounts of tissue nitrogen, phosphorus, potassium, sodium, calcium and iron were estimated in the green alga Ulva lactuca L. collected from 9 rural and 14 urban littoral sites in the waters around Hong Kong Island during 1978 and 1979. The mean levels of tissue nitrogen and phosphorus were respectively 65% and 87% more in urban sites than in rural ones. Very significant correlation (r = 0.920) was found between the logarithmic concentration of seawater inorganic nitrogen and that of tissue nitrogen. The same applied to soluble reactive phosphorus in seawater and tissue phosphorus (r = 0.886). The levels of potassium, sodium and calcium in the alga were relatively uniform. However considerable variation in the level of iron was detected. The potential use of Ulva as an indicator species for eutrophication is discussed.     

Detection of Naegleria fowleri cysts in environmental samples by using a DNA probe

Abstract In this study we tried to detect DNA Naegleria fowleri in artificially contaminated environmental samples, with or without sediments, containing 10⁴ cysts of this pathogenic amoeba. We used two assays to extract DNA from samples: first, direct DNA extraction, which gave positive results only for water samples without sediment; second, DNA extraction after sample incubation on agar plates, which allowed us to remove amoeba growing out of the sediments, and which gave positive results for all samples, even those initially with sediments (5, 500 or 500 mg). Thus, this molecular identification appears as a powerful tool to investigate N. fowleri growth in environmental samples.     

Genetic characterization of antibiotic-resistant Staphylococcus aureus from milk in the North-West Province,South Africa

Food borne diseases are a major public health concern worldwide. Staphylococcus aureus is one of the potential food borne pathogens which causes nosocomial and community acquired infections. In the present study, 74 representative strains of S. aureus isolated and characterized in previous study from different milk samples were subjected to random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR to generate fingerprints to determine the genetic relationships of the isolated strains. A total of 20 RAPD patterns were generated and the number of amplified fragments obtained ranged from 0 to 8 with molecular weight ranging from 250 to 2000 bp. A dendrogram based on fingerprinting pattern grouped isolates into twelve major clusters (I–XII). In the case of ERIC-PCR 9 banding patterns were obtained with amplicons ranging from 1 to 8 and band sizes ranging from 250 to 2000 bp. A total of four major clusters (I–IV) were observed in the dendrogram based on ERIC fingerprints. The discrete banding patterns obtained both from ERIC-PCR and RAPD-PCR showed remarkably the genetic diversity of S. aureus. The findings of this study indicate that raw, bulk and pasteurized milk in the North-West Province was contaminated with toxigenic and multi-drug resistant S. aureus strains. This emphasizes the need to implement appropriate control measures to reduce contamination as well as the spread of virulent S. aureus strains to reduce the burden of disease in humans.     

Prescribed moorland burning meets good practice guidelines: A monitoring case study using aerial photography in the Peak District,UK

Upland moors in the UK have been managed for centuries using rotational prescribed-burning, but in recent years there has been contentious debate over its continuing use due to varying effects on moorland ecosystem services. Prescribed-burning should only be carried out using good-practice codes, which include restrictions on the size, location and frequency of burns. Good burning practice is an indicator of management standards and habitat condition in moorland landscapes. However, there has been little attempt to assess management performance with respect to these restrictions. We investigated prescribed-burning on a case-study estate (Howden Moor) in the Peak District National Park from 1988 to 2009 using management maps and aerial photography. The annual area burned (0.9%) was far below recommendations (10%) and patches were in keeping with the target sizes specified (mean ± se: 2370 ± 70 m²). The risk of a large or escaped fire was very low, with less than 1% of fires greater than 15,000 m². However, only 28.9% of the total burnable area was burned, leaving the rest unmanaged and accumulating fuel. Future guidelines might recommend the application of prescribed-burning across the range of Calluna vulgaris growth phases, to reduce fuel load and promote biodiversity at the landscape scale. We show that vegetation mapping and aerial photography are an effective method for monitoring prescribed-burning practice on moorlands. The information derived from such monitoring studies should lead to greater confidence in the standard of prescribed-burning and adherence to good-practice guidelines and requirements imposed by statutory authorities.     

Relative effectiveness of neutrons and X-rays in induction of crossing over in drosophila males

Relative biological effectiveness of neutrons vs. X-rays in inducing crossing-over in males of D. melanogaster was investigated using 812 and 834 rad of neutrons and the same dose of X-rays. Crossing-over was induced in spermatocytes and spermatogonia of adults and pupae. Neutrons were 4 times more effective in spermatocytes of adults and their effectiveness in pupal spermatocytes was even more. Neutrons also induced more exchanges in spermatogonial cells including predefinitive spermatogonia. Higher effectiveness of neutrons can be attributed to their high linear energy transfer.     

Use of maize pollen by adult Chrysoperla carnea (Neuroptera: Chrysopidae) and fate of Cry proteins in Bt-transgenic varieties

We investigated the use of maize pollen as food by adult Chrysoperla carnea under laboratory and field conditions. Exposure of the insects to insecticidal Cry proteins from Bacillus thuringiensis (Bt) contained in pollen of transgenic maize was also assessed. Female C. carnea were most abundant in a maize field when the majority of plants were flowering and fresh pollen was abundant. Field-collected females contained an average of approximately 5000 maize pollen grains in their gut at the peak of pollen shedding. Comparable numbers were found in females fed ad libitum maize pollen in the laboratory. Maize pollen is readily used by C. carnea adults. When provided with a carbohydrate source, it allowed the insects to reach their full reproductive potential. Maize pollen was digested mainly in the insect's mid- and hindgut. When Bt maize pollen passed though the gut of C. carnea, 61% of Cry1Ab (event Bt176) and 79% of Cry3Bb1 (event MON 88017) was digested. The results demonstrate that maize pollen is a suitable food source for C. carnea. Even though the pollen grains are not fully digested, the insects are exposed to transgenic insecticidal proteins that are contained in the pollen.     

Environmental stress inhibits the synthesis de novo of proteins involved in the photodamage-repair cycle of Photosystem II in Synechocystis sp. PCC 6803

The Photosystem II complex (PSII) is susceptible to inactivation by strong light, and the inactivation caused by strong light is referred to as photoinactivation or photoinhibition. In photosynthetic organisms, photoinactivated PSII is rapidly repaired and the extent of photoinactivation reflects the balance between the light-induced damage (photodamage) to PSII and the repair of PSII. In this study, we examined these two processes separately and quantitatively under stress conditions in the cyanobacterium Synechocystis sp. PCC 6803. The rate of photodamage was proportional to light intensity over a range of light intensities from 0 to 2000 μE m⁻² s⁻¹, and this relationship was not affected by environmental factors, such as salt stress, oxidative stress due to H₂O₂, and low temperature. The rate of repair also depended on light intensity. It was high under weak light and reached a maximum of 0.1 min⁻¹ at 300 μE m⁻² s⁻¹. By contrast to the rate of photodamage, the rate of repair was significantly reduced by the above-mentioned environmental factors. Pulse-labeling experiments with radiolabeled methionine revealed that these environmental factors inhibited the synthesis de novo of proteins. Such proteins included the D1 protein which plays an important role in the photodamage-repair cycle. These observations suggest that the repair of PSII under environmental stress might be the critical step that determines the outcome of the photodamage-repair cycle.     

Metapopulation dynamics with quasi-local competition

Stepping-stone models for the ecological dynamics of metapopulations are often used to address general questions about the effects of spatial structure on the nature and complexity of population fluctuations. Such models describe an ensemble of local and spatially isolated habitat patches that are connected through dispersal. Reproduction and hence the dynamics in a given local population depend on the density of that local population, and a fraction of every local population disperses to neighboring patches. In such models, interesting dynamic phenomena, e.g. the persistence of locally unstable predator-prey interactions, are only observed if the local dynamics in an isolated patch exhibit non-equilibrium behavior. Therefore, the scope of these models is limited. Here we extend these models by making the biologically plausible assumption that reproductive success in a given local habitat not only depends on the density of the local population living in that habitat, but also on the densities of neighboring local populations. This would occur if competition for resources occurs between neighboring populations, e.g. due to foraging in neighboring habitats. With this assumption of quasi-local competition the dynamics of the model change completely. The main difference is that even if the dynamics of the local populations have a stable equilibrium in isolation, the spatially uniform equilibrium in which all local populations are at their carrying capacity becomes unstable if the strength of quasi-local competition reaches a critical level, which can be calculated analytically. In this case the metapopulation reaches a new stable state, which is, however, not spatially uniform anymore and instead results in an irregular spatial pattern of local population abundance. For large metapopulations, a huge number of different, spatially non-uniform equilibrium states coexist as attractors of the metapopulation dynamics, so that the final state of the system depends critically on the initial conditions. The existence of a large number of attractors has important consequences when environmental noise is introduced into the model. Then the metapopulation performs a random walk in the space of all attractors. This leads to large and complicated population fluctuations whose power spectrum obeys a red-shifted power law. Our theory reiterates the potential importance of spatial structure for ecological processes and proposes new mechanisms for the emergence of non-uniform spatial patterns of abundance and for the persistence of complicated temporal population fluctuations.     

Long-Term Changes of a Coastal Bird Breeding Community on a Small Island – Does Natural Succession Compromise Conservation Values?

Limited spatial resources available for conservation lead to controversy about whether to apply single-species management or ecosystemary approaches in order to maintain biodiversity. In this study I analyse changes in a community of breeding coastal birds over a 90-year period, in order to examine whether natural processes on an unmanaged island are in accordance with requirements to save endangered species. Both diversity and species richness of the community increased significantly over time, and evenness increased after having been severely reduced by human impact. Diversity, evenness and species richness seemed to approach an equilibrium in the past decade, but number of breeding pairs declined as a consequence of altered natural disturbance regime. Species identity changed over time, with two initially very common species recently becoming locally extinct. These species are of high conservation concern, and their disappearance causes a problem for the concept of naturalness on islands. I conclude that natural processes need to be applied to the entire landscape in order to maintain dynamic processes that are essential for the survival of these species. The natural changes on the island should not be interrupted, but rather demonstrated to the public in order to increase conservation mindedness and gain support for changes in anthropogenic influences on a larger spatial scale.