Isolation and Genomic Sequence of Hepatitis A Virus from Mixed Frozen Berries in Italy

Hepatitis A virus (HAV) was detected in two samples of mixed frozen berries linked to Italian hepatitis A outbreak in April and September 2013. Both viruses were fully sequenced by next-generation sequencing and the genomes clustered with HAV complete genomes of sub-genotype IA with nucleotide identities of 95–97 %.     

Isolation of single circulating trophoblasts from maternal circulation for noninvasive fetal copy number variant profiling

Objective

To develop a multi-step workflow for the isolation of circulating extravillous trophoblasts (cEVTs) by describing the key steps enabling a semi-automated process, including a proprietary algorithm for fetal cell origin genetic confirmation and copy number variant (CNV) detection.

Methods

Determination of the limit of detection (LoD) for submicroscopic CNV was performed by serial experiments with genomic DNA and single cells from Coriell cell line biobank with known imbalances of different sizes. A pregnancy population of 372 women was prospectively enrolled and blindly analyzed to evaluate the current workflow.

Results

An LoD of 800 Kb was demonstrated with Coriell cell lines. This level of resolution was confirmed in the clinical cohort with the identification of a pathogenic CNV of 800 Kb, also detected by chromosomal microarray. The mean number of recovered cEVTs was 3.5 cells per sample with a significant reverse linear trend between gestational age and cEVT recovery rate and number of recovered cEVTs. In twin pregnanices, evaluation of zygosity, fetal sex and copy number profiling was performed in each individual cell.

Conclusion

Our semi-automated methodology for the isolation and single-cell analysis of cEVTS supports the feasibility of a cell-based noninvasive prenatal test for fetal genomic profiling.     

Participatory Bayesian network modeling to understand driving factors of land-use change decisions: insights from two case studies in northeast Madagascar

ABSTRACT

Forest frontiers worldwide reveal trade-offs that are key in mitigating global change. In the forest frontiers of northeast Madagascar, land-use changes result from decisions made by smallholder farmers. In the past, subsistence needs led to increasing shifting cultivation, resulting in forest degradation and deforestation. This study focuses on investigating the role of locally determined factors in land-use change decisions in the forest frontier context. Therefore, we developed a Bayesian network-based land-use decision model that represents the causalities between factors influencing land-use decisions and takes into account local decision-makers’ knowledge. The approach is applied in two comparative case studies in northeast Madagascar. Results show that farmers mostly aim at extending the cultivation of cash crops. These results and the causal mechanisms disentangled for the forest frontier of northeast Madagascar help understand change mechanisms and hence, support decision-making to attain the Sustainable Development Goals.     

Crown condition surveys in Italian forests: issues in reporting findings

This study examines defoliation and discoloration findings collected throughout the Italian Level I network between 1997 and 2000. Prior to this period no Quality Assurance procedures had been implemented, so that earlier findings cannot be considered reliable. The aim of the study is to compare differentindices used in reporting findings, in order to determine the full potential and limitations of each. In international surveys,findings are normally expressed in terms of individual trees presenting a defoliation level greater than 2 %; this criterion,however, has been challenged since it is not based on scientificevidence. By analysing the distribution of defoliation values(grouped in 5% classes) relating to the main species (Fagus sylvatica, Quercus pubescens, Quercus cerris, Picea abies), the study examines the behaviour of statistical indices such as the median, the mode and the mean. Instead of using the traditional 25% threshold to determine the part of the population with the highest defoliation values, a procedureis suggested whereby a different threshold can be determined foreach species. It is established based on the 90° percentile of cumulative defoliation values recorded over the four-year period. Each index used to report findings possessesits own information potential, and the findings may at times appear contradictory. The use of a combined defoliation and discoloration index (Ilce = Lacking Crown Equivalent Index) is also proposed, but the results obtained do not differin substance from the results relating to defoliation alone. Thefunctional limitations of this index are due mainly to the way the data are collected: for this reason suggestions are made onhow to improve the procedure in future surveys.     

Transport and modification of humic substances present in Antarctic snow and ancient ice

We performed a study of fulvic acids extracted from fresh and aged snow, and from recent and ancient ice in Antarctica. The fresh snow samples were collected in coastal and inland sites to evaluate the influence of the distance from the sea on organic matter transport. Moreover, in a site (Melbourne Mountain) samples were collected at different heights to study the influence of altitude on transport. The obtained results showed that dissolved fulvic acid concentrations are influenced neither by distance nor by height while particulate fulvic acid concentrations are influenced by both parameters. Moreover, the results showed that fulvic acids transported for a long distance can undergo chemical modifications. Chemical modifications are better evidenced by the analysis of samples taken in trenches at different depth, which showed structural changes attributable to the loss of nitrogen-containing compounds and to an increase in aromatic character of the structures due to reduction and/or condensation processes. With ageing, the humification process proceeds with heavy carbon losses as demonstrated by results obtained from fulvic acids isolated from ice aged between twenty-five thousand and seventy thousand years.     

Two-stage chemical fractionation method for the analysis of elements and non-volatile inorganic ions in PM10 samples: Application to ambient samples collected in Rome (Italy)

A two-stage micro-analytical scheme for the determination of metals and ions in atmospheric particulate matter collected on only one Teflon filter was developed. In the first stage the collected particles are chemically fractionated for their solubility in a pH-buffered extracting solution; in the second stage the residue is mineralised. The major non-volatile inorganic ions (Cl⁻, NO₃⁻, SO₄²⁻, Na⁺, NH₄⁺, Ca²⁺, Mg²⁺) are determined in the first fraction by ion-chromatography (IC), while metals and metalloids (Al, As, Cd, Cr, Cu, Fe, Mg, Mn, Ni, Pb, S, Sb, Se, Si, Ti, V, Zn) are determined in both the acetate extractable and the mineralised residual fractions by inductively coupled plasma optical emission spectroscopy (ICP-OES).The procedure was applied to ambient 24-h PM₁₀ samples collected on Teflon filters during two field campaigns carried out at two sites in the area of Rome (Italy). The variations in the chemical composition of the collected particles during the two periods were interpreted in the light of the dilution properties of the lower atmosphere and of the back-trajectories of the air masses. The difference in the results between the two locations was interpreted in the light of their proximity to the emission sources. It was found that the acetate extractable and the mineralised residual fraction of some metals exhibit a different temporal pattern, suggesting the existence of different emission sources of the two fractions.     

A biological and geochemical integrated approach to assess the environmental quality of a coastal lagoon (Ravenna, Italy)

The assessment of the environmental quality of coastal lagoons is rather difficult as their intrinsic high variability limits the power of analytical chemistry and ecotoxicological approaches. Aim of the present work was to integrate geochemical and biological data which were simultaneously collected from the Pialassa Baiona lagoon (Ravenna, Italy), and evaluate the usefulness of a biomonitoring strategy based on sentinel organisms and biomarkers. Geochemical analysis on suspended, surface, and subsurface sediments were performed at five different sites of the lagoon; moreover the heavy metal bioaccumulation and a battery of biomarkers was evaluated in Mytilus galloprovincialis transplanted in the same sites. Heavy metals appeared to be diffused throughout the lagoon reaching higher levels in the southernmost sites, and mainly concentrated in suspended sediments. Lysosome membrane stability, neutral lipid and lipofuscin accumulation, and metallothionein levels in mussels indicated the development of a stress syndrome in animals exposed to the polluted sites.     

Wind- and tide-induced currents in the Stagnone lagoon (Sicily)

The hydrodynamic circulation is analyzed in the coastal lagoon of Stagnone di Marsala, a natural reserve located in the north-western part of Sicily, using both experimental measurements and numerical simulations. Field measurements of velocities and water levels, carried out using an ultrasound sensor (3D), are used to validate the numerical model. A 3D finite-volume model is used to solve the Reynolds-averaged momentum and mass balance differential equations on a curvilinear structured grid, employing the k–e{\varepsilon} turbulence model for the Reynolds stresses. The numerical analysis allows to identify the relative contribution of the forces affecting the hydrodynamic circulation inside the lagoon. In the simulations only wind and tide forces are considered, neglecting the effects of water density changes. Two different conditions are considered. In the first both the wind stress over the free-surface and the tidal motion are imposed. In the second the wind action is neglected, to separately analyze the tide-induced circulation. The comparison between the two test cases highlights the fundamental role of the wind on the hydrodynamics of the Stagnone lagoon, producing a strong vertical recirculation pattern that is not observed when the flow is driven by tides only.     

Occurrence of Cryptosporidium oocysts in sewage effluents and correlation with microbial,chemical and physical water variables

Contaminated water are recognized as a potential source of Cryptosporidium oocysts. In Italy studies on the environmentalspread of the parasite are still scarce even if a high frequencyof serological responses could suggest high rates of endemic Cryptosporidium infections. In this investigation theoccurrence of the parasite in water samples from a municipalwastewater treatment plant was monitored with the aim to evaluatepossible correlation between oocysts and bacterial indicators,pathogens and physico-chemical parameters using a multivariateanalysis. Data collected showed high numbers of oocysts, with ahigh percentage of positive samples and a significant correlationwith pH, redox potential and total organic carbon. No correlationwas found between Cryptosporidium concentration and that of the other microrganisms. The results, through a probing statistical analysis, show that none of the selected microrganisms was a reliable predictor of the presence of theparasite.     

PCDD/Fs and dioxin-like PCBs in human milk and estimation of infants' daily intake: a review

This paper reviews the recent scientific literature on PCDDs, PCDFs and dioxin-like PCBs in human milk. All the papers reporting levels of these contaminants in human breast milk published from January 2000 to January 2009 and available on the www.sciencedirect.com web site were identified and included. The aim was (1) to study levels of PCDDs, PCDFs and PCBs in human milk in mothers from different geographical areas and assess infant exposure to these contaminants; (2) to study the effect of variables such as the mother’s age, number of deliveries, dietary and smoking habits and her own nutrition in infancy, and the environment, on levels of the contaminants in breast milk; (3) to study time patterns, and (4) to identify data gaps.