Pitfalls in molecular diagnosis in a family with severe factor VII (FVII) deficiency—misdiagnosis by direct sequence analysis using a PCR product

Molecular diagnostic tests are becoming a routine analysis in many laboratories. These modern analyses are widely used in clinical medicine, forensic, genetic and prenatal diagnosis and also in preimplantation genetic diagnosis. The accuracy of analysis is highly dependent on the success achieved in minimising genotyping errors. The pitfalls in molecular diagnostic tests can be due to a simple technique such as the polymerase chain reaction (PCR) used universally. This technique is routinely used for its apparent accuracy, but it is also a well-known source of errors. We report an error introduced during PCR reaction that leads to a wrong sequence result and consequently to a ‘false’ molecular result in a next prenatal diagnosis in a family with severe factor VII (FVII) deficiency. This error was verified using an unsuitable primer design in a rich repetitive sequence of the FVII gene that leads to a false annealing and then to a wrong molecular diagnosis. It is essential to link closely molecular data with clinical and phenotype analysis in order to avoid false-negative or false-positive results, which is of great importance to diagnosis and molecular prevention. Copyright © 2003 John Wiley & Sons, Ltd.     

A spatial-statistical approach for modeling the effect of non-point source pollution on different water quality parameters in the Velhas river watershed--Brazil

In this article, a methodology for evaluating the effect of land use/land cover on the quality of nearby stream water in a semiarid environment is described and tested on a large watershed in Southeastern Brazil. The approach aims at identifying the width of the riparian area having the strongest effect on different water quality parameters. The land use/land cover data were generated from remotely sensed data while water quality point data were supplied by a government agency. Testing was conducted for both the rainy and dry seasons in an effort to understand the direct effect of surface runoff. The approach combines cartographic modelling using a geographical information system (GIS) and statistics to establish the strength of the relationship between water quality, land use and the distance from the stream. Results suggest a strong relationship between land use/land cover and turbidity, nitrogen and fecal coliforms. They also suggest that each of these parameters has a unique behavior when distance from the stream is considered. Finally, although it was expected that the models would apply better during the wet season, some parameters had the opposite behavior and displayed a better fit during the dry season.     

Local Perception of Environmental Change in a Semi-Arid Area of Northeast Brazil: A New Approach for the Use of Participatory Methods at the Level of Family Units

The diversity of plant resources in the Brazilian semi-arid region is being compromised by practices related to agriculture, pastures, and forest harvesting, especially in areas containing Caatinga vegetation (xeric shrublands and thorn forests). The impact of these practices constitutes a series of complex factors involving local issues, creating a need for further scientific studies on the social-environmental dynamics of natural resource use. Through participatory methods, the present study analyzed people’s representations about local environmental change processes in the Brazilian semi-arid region, taking into consideration local production systems, natural resources, and their importance. Environmental historical graphs were developed with nine local families to analyze landscape changes with regard to cultivated areas and pastures, and their relationship with the availability of native vegetation. Punctuation exercises were performed to observe the importance of each unit that supplied native and cultivated resources. The availability of native resources in the environment is subject to stability, as observed by a majority of the local families. The role of the production units (crops and pastures) was emphasized by most families in the study, especially because of the need for products for subsistence needs and income generation. The current decline of such practices is a consequence of an exodus of field workers and also relates to the conservation of native species that otherwise would have been deforested in favor of agricultural practices.     

pp´DDT and pp´DDE Accumulation in a Food Chain of Lake Maggiore (Northern Italy): Testing Steady-State Condition

- DOI: http://dx.doi.org/10.1065/espr2006.01.010 Background, Aims and Scope Although pp'DDT usage was strongly limited or banned in most parts of the world during the last three or four decades, the parent compound, its homologues and their metabolites still occur at levels which might pose a risk for many ecosystem components. A case of DDT pollution of industrial origin was discovered in 1996 in Lake Maggiore, the second largest (212 km2) and deepest (370 m) lake in Italy, causing concern for wildlife and human health. The extensive monitoring of many biotic and abiotic compartments which followed from 1998 in order to assess the pollution level and its trend in time, provided a great availability of data referring to DDT contamination of the different fish species of the lake. In this study, the recent contamination levels in selected fish species were compared to those measured in 1998 to evaluate the temporal pollution trend of the lake and its natural recovery, given that no remediation measures were carried out on the contaminated soils and sediments in this time span. Moreover, a modelling approach to test the equilibrium condition between water and pelagic fish species was used. Analytical results of pp'DDT and pp'DDE concentrations in lake water were used as input data in the bioenergetic model by Connolly & Pedersen (1988) to calculate concentrations in two fish species and to compare the predicted and the measured contamination. Methods Sampling and analytical determination of DDT homologues in lake water: Five water sampling campaigns were carried out from May 2002 to February 2004 in three sampling sites of Lake Maggiore. Suspended and dissolved pollutants were determined separately. Quantitative DDT homologue analyses were performed by HRGC coupled with ECD detection by the external standard method. Single water extracts were put together in correspondence with the stratification zones of the water column inferred on the basis of the temperature profile to improve analytical sensitivity. Selection of fish data: Concentrations of DDT and DDE in fishes were selected from recent literature (CIPAIS 2003, 2004). Bioaccumulation model: The bioenergetic model proposed by Connolly & Pedersen (1988) was used to assess the bioaccumulation of pp'DDT and pp'DDE of Alosa fallax (landlocked shad) and Coregonus spp. (whitefish), selected among the different species as representative of a secondary consumer level. Results and Discussion The average concentrations of pp'DDT and pp'DDE in water to be used as input data in the bioenergetic model were obtained considering all the concentrations measured at the three sampling stations in the epylimnion where the fish species considered in this study spend most of their life. The resulting values were 0.05 and 0.16 ng/L for pp'DDT and pp'DDE, respectively. Average measured pp'DDT and pp'DDE concentrations in landlocked shad were 0.81 +/- 0.39 and 1.69 +/- 0.71 mg/kg lipids, respectively, and were 0.29 +/- 0.12 and 1.06 +/- 0.41 mg/kg lipids for the whitefish. Calculated and measured values turned out to be in quite good agreement for pp'DDT, while measured pp'DDE concentrations were higher than expected on the basis of the bioenergetic model in both species. Probably metabolic transformations of pp'DDT accumulated in fish tissues in the past are responsible for the observed differences between calculated and expected pp'DDE concentrations in fish. Conclusions Pelagic fishes of Lake Maggiore seem to maintain the DDT accumulated during their life time and the most efficient mechanism responsible for the fish population recoveries is probably their generation changes; for this reason, equilibrium models cannot be used until negligible pp'DDT concentrations are reached in fish tissues. Recommendations and Outlook The limit proposed for pp'DDT in water by the EU Directive 2000/60, which will come in force in 2008, is 0.2 ng/L, four times higher than the average concentration measured in Lake Maggiore waters. Nevertheless, concentrations measured in Lake Maggiore fish were very close and sometimes exceeded the Maximum residue limits (MRLs) settled by the Italian legislation for foods (0.1 mg/kg w.w. for fish containing 5–20% lipid). It seems, therefore, that the 'environmental quality standard' of 0.2 ng/L cannot guarantee the suitability of fish for human consumption.     

Effect of sewage amendment on the dissipation of terbuthylazine,its degradation compound desethyl-terbuthylazine,and S-metolachlor in a field study

This study evaluates the effect of sewage amendment (SA) on the dissipation of terbuthylazine, its degradation compound desethyl-terbuthylazine, and S-metolachlor in the soil. The experiment was conducted at Padua Experimental Farm (Italy). Herbicides dissipation was evaluated in soils differently fertilized for three years: with inorganic fertilizer, with sewage sludge, and with a combination of them. Terbuthylazine and S-metolachlor were applied on sorghum as a formulated product at a dose of 2.8?L ha^?1, and their dissipation was followed for 2.5 months. The concentrations of herbicides and one metabolite in soil were analyzed by liquid chromatography-mass spectrometry. The dissipation of terbuthylazine and S-metolachlor followed a pseudo first order kinetics; they dissipated faster in soil amended only with inorganic fertilizer than in soils amended with sewage or sewage?+?inorganic fertilizer. The reduction in mineralization of the herbicides after sewage addition can be attributed to the reduced herbicide availability to microorganisms. The degradation of terbuthylazine led to the formation of desethyl-terbuthylazine. SA slowed down the formation and the degradation of desethyl-terbuthylazine, leading to a higher amount measured at the end of the incubation. These findings have practical implications for the assessment of the environmental fate of terbuthylazine and S-metolachlor in agricultural areas.     

Spatio-temporal log-Gaussian Cox processes for modelling wildfire occurrence: the case of Catalonia, 1994–2008

Wildfires have become one of the principal environmental problems in the Mediterranean basin. While fire plays an important role in most terrestrial plant ecosystems, the potential hazard that it represents for human lives and property has led to the application of fire exclusion policies that, in the long term, have caused severe damage, mainly due to the increase of fuel loadings in forested areas, in some forest systems. The lack of an easy solution to forest fire management highlights the importance of preventive tasks. The observed spatio-temporal pattern of wildfire occurrences may be idealized as a realization of some stochastic process. In particular, we may use a space–time point pattern approach for the analysis and inference process. We studied wildfires in Catalonia, a region in the north-east of the Iberian Peninsula, and we analyzed the spatio-temporal patterns produced by those wildfire incidences by considering the influence of covariates on trends in the intensity of wildfire locations. A total of 3,166 wildfires from 1994–2008 have been recorded. We specified spatio-temporal log-Gaussian Cox process models. Models were estimated using Bayesian inference for Gaussian Markov Random Field through the integrated nested Laplace approximation algorithm. The results of our analysis have provided statistical evidence that areas closer to humans have more human induced wildfires, areas farther have more naturally occurring wildfires. We believe the methods presented in this paper may contribute to the prevention and management of those wildfires which are not random in space or time.