Non-invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an “in-house” target enrichment next generation sequencing—Solution for non-centralized NIPT laboratory?

Objective

Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities.

Method

From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods.

Results

The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant.

Conclusion

The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.     

Microbial and kinetic characterization of pure and mixed cultures aerobically degrading 4-nitrophenol

The molecular and kinetic characterization of a microorganism able to aerobically degrade 4-nitrophenol (4NP) is presented. The microorganism was isolated from a mixed culture operating in a laboratory-scale sequencing batch reactor with an aerobic anoxic cycle. It was identified as a member of Ralstonia genus within Betaproteobacteria. It is a gram negative coccobacillum (cell length of 2-3 microm) able to aerobically store lipid inclusions when grown aerobically on nitrophenol as the sole carbon source in the range of tested concentrations (80-320 mg l(-1)). Batch kinetic tests were performed with the pure culture, while the kinetics of the mixed biomass was directly investigated in the reactor. For pure cultures exponential growth was observed, with growth rate values in the range of 2-6 d(-1); in experiments with the mixed cultures 4NP concentrations were correlated with growth using the Haldane equation (k(max) = 0.30 mg 4NP mg(-1) VSSh(-1); K(s) = 55 mg 4NPl(-1) and K(I) = 15 mg 4NPl(-1)). Observed pure culture growth rates were higher than those of mixed cultures. This result can be explained by considering that in mixed culture the biomass is evaluated as volatile suspended solids, including both specialized biomass for 4NP removal and denitrifying bacteria.     

PCDD/Fs and PCBs in ambient air in a highly industrialized city in Northern Italy

Ambient air samples were collected in five locations around a polychlorobiphenyl (PCB) production plant in a highly industrialized city in the north of Italy, for the analysis of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) and PCBs.PCDD/F atmospheric concentrations were lower than those generally detected in urban areas, while PCB concentrations were higher than in urban and industrialized areas in other countries, especially in the locations closest to the plant. To identify source emissions responsible for air pollution we used principal component analysis (PCA) to compare the “fingerprint” of the air in Brescia with some source-related experimental and published data. This analysis showed that the PCDD/F fingerprints were more similar to steel plant emission data, while none of the PCB air patterns were comparable to emission profiles, indicating that different sources are responsible for the concentration of these two pollutants. The highest PCB concentrations detected in the areas closest to the chemical plant are indicative of its impact on the surrounding environment.     

Metal immobilization and phosphorus leaching after stabilization of pyrite ash contaminated soil by phosphate amendments

In this study we would like to show the importance of a holistic approach to evaluation of chemical stabilization using phosphate amendments. An extensive evaluation of metal stabilization in contaminated soil and an evaluation of the leaching of phosphorus induced after treatment were performed. The soil was highly contaminated with Cu (2894 mg kg(-1)), Zn (3884 mg kg(-1)), As (247 mg kg(-1)), Cd (12.6 mg kg(-1)) and Pb (3154 mg kg(-1)). To immobilize the metals, mixtures of soil with phosphate (from H(3)PO(4) and hydroxyapatite (HA) with varying ratios) were prepared with a constant Pb : P molar ratio of 1: 10. The acetic acid extractable concentration of Pb in the mixture with the highest amount of added phosphoric acid (n(H(3)PO(4)) : n(HA) = 3 : 1) was reduced to 1.9% (0.62 mg L(-1)) of the extractable Pb concentration in the untreated soil, but the content of water extractable phosphorus in the samples increased from 0.04 mg L(-1) in the untreated soil sample up to 14.3 mg L(-1) in the same n(H(3)PO(4)) : n(HA) = 3 : 1 mixture. The high increase in arsenic mobility was also observed after phosphate addition. The PBET test showed phosphate induced reduction in Pb bioavailability. In attempting to stabilize Pb in the soil with the minimum treatment-induced leaching of phosphorus, it was found that a mixture of soil with phosphate addition in the molar ratio of H(3)PO(4) : HA of 0.75 : 1 showed the most promising results, with an acetic acid extractable Pb concentration of 1.35 mg L(-1) and a water extractable phosphorus concentration of 1.76 mg L(-1). The time-dependent leaching characteristics of metals and phosphorus for this mixture were evaluated by a column experiment, where irrigation of the soil mixture with the average annual amount of precipitation in Slovenia (1000 mm) was simulated. The phosphorus concentration in the leachates decreased from 2.60 mg L(-1) at the beginning of irrigation to 1.00 mg L(-1) at the end.     

Spatial scales of variation in lichens: implications for sampling design in biomonitoring surveys

The variability of biological data is a main constraint affecting the quality and reliability of lichen biomonitoring surveys for estimation of the effects of atmospheric pollution. Although most epiphytic lichen bioindication surveys focus on between-site differences at the landscape level, associated with the large scale effects of atmospheric pollution, current protocols are based on multilevel sampling, thus adding further sources of variation and affecting the error budget. We test the hypothesis that assemblages of lichen communities vary at each spatial scale examined, in order to determine what scales should be included in future monitoring studies. We compared four sites in Italy, along gradients of atmospheric pollution and climate, to test the partitioning of the variance components of lichen diversity across spatial scales (from trunks to landscapes). Despite environmental heterogeneity, we observed comparable spatial variance. However, residuals often overcame between-plot variability, leading to biased estimation of atmospheric pollution effects.     

The effect of river damming on vegetation: is it always unfavourable? A case study from the River Tiber (Italy)

River damming leads to strong hydromorphological alterations of the watercourse, consequently affecting river vegetation pattern. A multitemporal and spatial analysis of the dam effect on composition, structure and dynamic of the upstream vegetation was performed on Tiber River at Nazzano-dam (Rome). The main research questions were as follows: How does plant landscape vary over time and along the river? Where does the dam effect on vegetation end? How does naturalistic importance of the vegetation affected by damming change over time? Data collection was performed mapping the vegetation in aerial photos related to the period before (1944), during (1954) and after dam construction (1984, 2000). The plant landscape has significantly changed over time and along the river, particularly as a result of the dam construction (1953). The major vegetation changes have involved riparian forests and macrophytes. Dam effect on vegetation is evident up to 3 km, and gradually decreases along an attenuation zone for about another 3 km. Despite the fact that the damming has caused strong local hydromorphological modification of the river ecosystem transforming it into a sub-lacustrine habitat, it has also led to the formation of wetlands of considerable naturalistic importance. Indeed, in these man-made wetlands, optimal hydrological conditions have been created by favouring both the expansion of pre-existing riparian communities and the rooting of new aquatic communities, albeit typical of lacustrine ecosystems. Some of these plant communities have become an important food resource, refuge or nesting habitats for aquatic fauna, while others fall into category of Natura 2000 habitats. Therefore, river damming seems to have indirectly had a “favourable” effect for habitat conservation and local biodiversity.     

Hydractinia echinata test system. II. SAR toxicity study of some anilide derivatives of Naphthol-AS type

In this paper, a toxicity study for a series of anilides of Naphthol-AS type is presented. The toxicity of the model compounds was determined by using the Hydractinia echinata (Hydrozoa) test system. Conformational analysis of Naphthol-AS derivatives was performed to elucidate the possible enzymatic hydrolysis mechanism of these compounds. This mechanism occurs with different rates and always leads to a stoichiometric mixture of reaction products, consisting in the substituted amine and the corresponding α-hydroxy-carboxylic acid. With one exception, the toxicities of the reaction products are subadditive. Quite similar measured toxicity values, log(1/MRC₅₀), led to their average calculated values, and thus to the establishment of class isotoxicity. This method represents a practical alternative useful for the reduction of experimental tests on animals to the lowest possible level, in accordance to the ‘3Rs’ (reduction, refinement and replacement) concept.