Comprehensive prenatal diagnostics: Exome versus genome sequencing

Objective

This study aimed to assess the diagnostic yield of prenatal genetic testing using trio whole exome sequencing (WES) and trio whole genome sequencing (WGS) in pregnancies with fetal anomalies by comparing the results with conventional chromosomal microarray (CMA) analysis.

Methods

A total of 40 pregnancies with fetal anomalies or increased nuchal translucency (NT ≥ 5 mm) were included between the 12th and 21st week of gestation. Trio WES/WGS and CMA were performed in all cases.

Results

The trio WES/WGS analysis increased the diagnostic yield by 25% in cases with negative CMA results. Furthermore, all six chromosomal aberrations identified by CMA were independently detected by WES/WGS analysis. In total, 16 out of 40 cases obtained a genetic sequence variant, copy number variant, or aneuploidy explaining the phenotype, resulting in an overall WES/WGS diagnostic yield of 40%. WES analysis provided a more reliable identification of mosaic sequence variants than WGS because of its higher sequencing depth.

Conclusions

Prenatal WES/WGS proved to be powerful diagnostic tools for fetal anomalies, surpassing the diagnostic yield of CMA. They have the potential to serve as standalone methods for prenatal diagnosis. The study highlighted the limitations of WGS in accurately detecting mosaic variants, which is particularly relevant when analyzing chorionic villus samples.     

Inactivation of Viruses and Bacteriophages as Models for Swine Hepatitis E Virus in Food Matrices

Hepatitis E virus has been recognised as a food-borne virus hazard in pork products, due to its zoonotic properties. This risk can be reduced by adequate treatment of the food to inactivate food-borne viruses. We used a spectrum of viruses and bacteriophages to evaluate the effect of three food treatments: high pressure processing (HPP), lactic acid (LA) and intense light pulse (ILP) treatments. On swine liver at 400 MPa for 10 min, HPP gave log₁₀ reductions of ≥4.2, ≥5.0 and 3.4 for feline calicivirus (FCV) 2280, FCV wildtype (wt) and murine norovirus 1 (MNV 1), respectively. Escherichia coli coliphage ?X174 displayed a lower reduction of 1.1, while Escherichia coli coliphage MS2 was unaffected. For ham at 600 MPa, the corresponding reductions were 4.1, 4.4, 2.9, 1.7 and 1.3 log₁₀. LA treatment at 2.2 M gave log₁₀ reductions in the viral spectrum of 0.29–2.1 for swine liver and 0.87–3.1 for ham, with ?X174 and MNV 1, respectively, as the most stable microorganisms. The ILP treatment gave log₁₀ reductions of 1.6–2.8 for swine liver, 0.97–2.2 for ham and 1.3–2.3 for sausage, at 15–60 J cm^?2, with MS2 as the most stable microorganism. The HPP treatment gave significantly (p < 0.05) greater virus reduction on swine liver than ham for the viruses at equivalent pressure/time combinations. For ILP treatment, reductions on swine liver were significantly (p < 0.05) greater than on ham for all microorganisms. The results presented here could be used in assessments of different strategies to protect consumers against virus contamination and in advice to food producers. Conservative model indicators for the pathogenic viruses could be suggested.     

Development of Tools for Integrated Monitoring and Assessment of Hazardous Substances and Their Biological Effects in the Baltic Sea

The need to develop biological effects monitoring to facilitate a reliable assessment of hazardous substances has been emphasized in the Baltic Sea Action Plan of the Helsinki Commission. An integrated chemical–biological approach is vitally important for the understanding and proper assessment of anthropogenic pressures and their effects on the Baltic Sea. Such an approach is also necessary for prudent management aiming at safeguarding the sustainable use of ecosystem goods and Services. The BEAST project (Biological Effects of Anthropogenic Chemical Stress: Tools for the Assessment of Ecosystem Health) set out to address this topic within the BONUS Programme. BEAST generated a large amount of quality-assured data on several biological effects parameters (biomarkers) in various marine species in different sub-regions of the Baltic Sea. New indicators (biological response measurement methods) and management tools (integrated indices) with regard to the integrated monitoring approach were suggested.     

Imposex occurrence in marine whelks at a military facility in the high Arctic

Imposex was found in the Arctic whelk Buccinum finmarkianum at several marine stations off Thule Air Base, an US military facility in Northwest Greenland. This indicates a widespread contamination with the antifouling agents, tributyltin (TBT) or triphenyltin (TPhT) in the area, but such contamination was not supported by the organotin analyses in sediments, whelks and clams, which in general was below the analytical detection limit. Organotin concentrations above the detection limit were found only at one station close to a quay, where the highest frequency of imposex also occurred. This suggests that imposex in B. finmarkianum is a biomarker of TBT more sensitive than the detection limits, which the analytical chemistry could achieve in this study.     

Carbon, nitrogen, and phosphorus distribution in particle size-fractionated separated pig and cattle slurry

Solid liquid separation of animal slurry is a method to reduce the excess nutrient loads from intensive livestock production. Five different separation technologies (sedimentation, centrifugation, pressurized filtration, polymer flocculation and drainage, and iron chloride addition + polymer flocculation and drainage) were applied to pig and cattle slurry in a laboratory study. Separation efficiencies of mass, dry matter (DM), N, and P were measured. Particle size fractionation of the solid fractions was performed by subjecting them to wet fractionation and C, organic N (N(org)), and P contents were subsequently measured. Chemical pretreatment with polymer before gravity drainage separated DM, total N, and P from raw pig and cattle slurry with the highest efficiencies. Sedimentation and centrifugation separated P from pig and cattle slurries with higher simple separation efficiencies (0.77 and 0.70, respectively) compared with pressurized filtration (0.15 and 0.37). Pressurized filtration transferred the lowest masses (14 and 18%) to the solid fractions. Solid fractions from pig slurry generally contained higher concentrations of P and C compared with cattle slurry solid fractions. The majority of C in solid fractions was present in particles > 25 microm, whereas N and P were present in larger proportions in particles < 25 microm. Chemical pretreatment increased the capture of smaller N(org)- and P-rich particles into larger particles between 25 and 1000 microm.     

Comparative goal-oriented assessment of conventional and alternative sewage sludge treatment options

Phosphorous (P) is a limited and non-substitutable resource. Sewage sludge contains significant amounts of P and is therefore a widely applied fertilizer. Due to its organic and inorganic contaminants, sewage sludge is also combusted in industrial facilities as well as in waste incinerators. This study compares five common methods and one novel alternative based on a thermo-chemical process to treat and dispose of sewage sludge with regard to environmental impact, resource recovery, and materials dissipation. The comparison is based on material flow analysis, energy balances, selected LCA impact analysis, and statistical entropy analysis. This work shows that the novel technology combines both advantages of the established practices: organic and inorganic pollutants are either destroyed or removed from the P containing material, and the P returned to the soil exhibits high plant-availability. The novel method also has low emissions. The additional energy requirements should be reduced. However, with regards to sewage sludge P recovery is more important than energy recovery.     

Butyltin compounds in sediment and molluscs from the shipping strait between Denmark and Sweden

The distribution of tributyltin (TBT) contamination in the subtidal zone of the waters between Denmark and Sweden was investigated in relation to major international shipping lanes. Sediment and different benthic molluscs were sampled in transects along and perpendicularly to the shipping lanes in the Sound (?resund) and the Kattegat/Skagerrak region. The samples were analysed for TBT and its degradation products, dibutyltin (DBT) and monobutyltin (MBT), using GC-PFPD. In sediments, the TBT concentration ranged from <1 to 19 ng g(-1) dry weight (dw) with a strong correlation between the TBT concentration and the organic fraction in sediment (r(2)=0.90) in the samples collected in the Sound, where the highest concentrations were found. This relationship was not observed in the samples from the Kattegat because the TBT concentration in most sediment samples was below the limit of detection. In the molluscs, TBT and its degradation products were detected in all samples from the entire area with concentrations ranging from 8.1 ng g(-1) dw in Buccinum undatum to 1316 ng g(-1) dw in Nuculana pernula. The deposit-feeding bivalve N. pernula was found to have a particularly high accumulation potential for TBT. In addition, a strong correlation between TBT concentrations in sediment and N. pernula was found. Therefore this species seems to be an ideal organism for monitoring sediment contamination. The TBT concentration in N. pernula was found to decrease gradually along the shipping lanes from the Sound, through the Kattegat and into the Skagerrak.     

Exposure to inhalable dust and endotoxin among Danish livestock farmers: results from the SUS cohort study

Studies on personal dust and endotoxin concentrations among animal farmers have been either small or limited to a few sectors in their investigations. The present study aimed to provide comparable information on the levels and variability of exposure to personal dust and endotoxin in different types of animal farmers. 507 personal inhalable dust samples were collected from 327 farmers employed in 54 pig, 26 dairy, 3 poultry, and 3 mink farms in Denmark. Measurements in pig and dairy farmers were full-shift and performed during summer and winter, while poultry and mink farmers were monitored during 4 well-defined production stages. The collected samples were measured for dust gravimetrically and analyzed for endotoxin by the Limulus amebocyte lysate assay. Simple statistics and random-effect analysis were used to describe the levels and the variability in measured dust and endotoxin exposure concentrations. Measured inhalable dust levels had an overall geometric mean of 2.5 mg m(-3) (range 相似文献   

How oxygen deficiency in the Baltic Sea proper has spread and worsened: The role of ammonium and hydrogen sulphide

Even large inflows of oxygen-rich seawater to the Baltic Proper have in recent decades given only short-lived relief from oxygen deficiency below the halocline. We analyse long-term changes in oxygen deficiency, and calculate the “total oxygen debt” ΣOD, the oxygen required to oxidize the hydrogen sulphide (H₂S) and ammonium (NH₄) that builds up during stagnation periods. Since the early 1990s, oxygen below 65m has gradually decreased during successive stagnation periods, and the ΣOD has increased, with NH₄ more important than previously recognised. After the major inflow in 2014, the Baltic Proper ΣOD has reached its highest level so far. The gradual shift of the ΣOD to shallower sub-halocline waters in the western and northern basins has increased the risk of periodic coastal hypoxia and export of hypoxic water to the Bothnian Sea. The potential for inflows large enough to more than eliminate the ΣOD seems limited in the near term.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13280-022-01738-8.     

Insecticide residues in bats along a land use-gradient dominated by cotton cultivation in northern Benin,West Africa

Many regions in Africa are currently being converted from subsistence to cash crop farming such as cotton. Agricultural intensification is usually accompanied by increased use of pesticides, which can have an impact on non-target organisms. Bats are particularly sensitive to insecticide loads while providing substantial ecosystem services as predators of herbivorous insects. In this study, pesticide residues in bats in a landscape in northern Benin were investigated, which spanned a land use gradient from an agricultural zone dominated by cotton farms, through a buffer zone, and into a national park. Insecticides used in cotton cultivation, such as endosulfan, chlorpyrifos, flubendiamide, and spirotetramat, as well as persistent insecticides such as bis(4-chlorophenyl)-1,1,1-trichloroethane (DDT), lindane, and aldrine, were analysed. Insecticide residues detected in bats comprised DDT, endosulfan, and their corresponding transformation products. Maximum concentrations in the sampled bats were 11.2 mg/kg lipid of p,p′-DDE (median: 0.0136 mg/kg lipid) and 0.797 mg/kg lipid of β-endosulfan (median: below detection limit [DL]). While insecticide concentrations were below lethal concentrations our data suggest that DDT had probably been recently used in the study region, and larger scale use would pose an increased risk for bat populations due to the high biomagnification of DDT.