Twelve years of assessing the quality of preimplantation genetic testing for monogenic disorders

Objective

Genomics Quality Assessment has provided external quality assessments (EQAs) for preimplantation genetic testing (PGT) for 12 years for eight monogenic diseases to identify sub-optimal PGT strategies, testing and reporting of results, which can be shared with the genomics community to aid optimised standards of PGT services for couples.

Method

The EQAs were provided in two stages to mimic end-to-end protocols. Stage 1 involved DNA feasibility testing of a couple undergoing PGT and affected proband. Participants were required to report genotyping results and outline their embryo testing strategy. Lymphoblasts were distributed for mock embryo testing for stage 2. Submitted clinical reports and haplotyping results were assessed against peer-ratified criteria. Performance was monitored to identify poor performance.

Results

The most common testing methodology was short tandem repeat linkage analysis (59%); however, the adoption of single nucleotide polymorphism-based platforms was observed and a move from blastomere to trophectoderm testing. There was a variation in testing strategies, assigning marker informativity and understanding test limitations, some clinically unsafe. Critical errors were reported for genotyping and interpretation.

Conclusion

EQA provides an overview of the standard of preimplantation genetic testing-M clinical testing and identifies areas of improvement for accurate detection of high-risk embryos.     

Degradation of methyl-phenanthrene isomers during bioremediation of soil contaminated by residual fuel oil

Phenanthrene and methyl-phenanthrenes are major aromatic pollutants originating in particular from fuel oil. Phenanthrene is usually degraded faster than methyl-phenanthrenes under geological and environmental conditions. Here, we report a preferential and accelerated biodegradation of methyl-phenanthrenes versus phenanthrene in soil contaminated by fuel oil. The polluted soil was mixed with sawdust and sand to form a homogenized biopile. The biopile was continuously sprayed with microbial consortia isolated from crude oil?Ccontaminated soil and treated by biosurfactants and nutritive substances for biostimulation. During a 6-month bioremediation experiment, a steady increase in the relative abundance of phenanthrene compared to methyl-phenathrenes was observed by gas chromatography?Cmass spectrometry. The increase was the highest for trimethyl-phenanthrenes, with a phenanthrene/trimethyl-phenanthrenes ratio increasing from 0.42 to 2.45. By contrast, the control, non-stimulated samples showed a ratio decrease from 0.85 to 0.11. Moreover, the results showed that the level of degradability depends on the number of methyl groups.     

The influence of air flow on maximum explosion characteristics of dust–air mixtures

A standard spherical apparatus for measuring explosion characteristics was modified to give increased and controlled turbulence within a dust–air mixture. This was intended to mimic the local effects which may occur during industrial dust explosions, particularly secondary ones which may develop in ducts or mine galleries where the initial explosion causes an increased air velocity and suspension of further quantities of dust.The results show that there may be a doubling of the maximum explosion pressure and of the rate of pressure rise during the explosion under more turbulent conditions. This is significant for modelling of dust explosions and suggests that explosion relief may be inadequate if this factor is not taken into consideration.The modified apparatus therefore gives a laboratory method for assessing the effect of turbulence in dust explosions.     

Atmospheric aerosol growth rates at different background station types

Environmental Science and Pollution Research - Highly time-resolved particle number size distributions (PNSDs) were evaluated during 5 years (2013–2017) at four background stations in the...     

Oxidation state specific analysis of arsenic species in tissues of wild-type and arsenic (+ 3 oxidation state) methyltransferase-knockout mice

Arsenic methyltransferase(As3mt) catalyzes the conversion of inorganic arsenic(i As) to its methylated metabolites, including toxic methylarsonite(MAs~Ⅲ) and dimethylarsinite(DMAs~Ⅲ). Knockout(KO) of As3 mt was shown to reduce the capacity to methylate i As in mice. However, no data are available on the oxidation states of As species in tissues of these mice. Here, we compare the oxidation states of As species in tissues of male C57BL/6 As3mt-KO and wild-type(WT) mice exposed to arsenite(iA s~Ⅲ) in drinking water. WT mice were exposed to50 mg/L As and As3mt-KO mice that cannot tolerate 50 mg/L As were exposed to 0, 15, 20, 25 or30 mg/L As. iA s~Ⅲaccounted for 53% to 74% of total As in liver, pancreas, adipose, lung, heart, and kidney of As3mt-KO mice; tri- and pentavalent methylated arsenicals did not exceed 10% of total As. Tissues of WT mice retained iA s and methylated arsenicals: iA s~Ⅲ, MAs~Ⅲand DMAs~Ⅲ represented 55%‐68% of the total As in the liver, pancreas, and brain. High levels of methylated species, particularly MAs~Ⅲ, were found in the intestine of WT, but not As3mt-KO mice,suggesting that intestinal bacteria are not a major source of methylated As. Blood of WT mice contained significantly higher levels of As than blood of As3mt-KO mice. This study is the first to determine oxidation states of As species in tissues of As3mt-KO mice. Results will help to design studies using WT and As3mt-KO mice to examine the role of iA s methylation in adverse effects of iA s exposure.     

Effect of Compatibilizing Agent on the Properties of Highly Crystalline Composites Based on Poly(lactic acid) and Wood Flour and/or Mica

This article contains a concept of the mechanical properties improvement of the highly crystalline poly(lactic acid) (PLA) and filled composites. PLA as a semi-crystalline thermoplastic polymer was plasticized with poly(ethylene glycol) and filled with 30 vol% of organic and/or inorganic filler. The degree of crytallinity was intentionally increased by annealing. The filler/polymer matrix interphase was modified with the addition of 4, 4′-Methylenediphenyl diisocyanate (MDI). The effect of compatibilizing as well as plasticizing agent on the thermal and mechanical properties, the water-absorption behaviour and crystallization characteristics were studied. The results indicated that high content of filler and crystallites have a strong influence on the composite′s mechanical properties despite of the plasticizer content, showing a high Young modulus. The MDI seems to react in preference easy with plasticizing agent and then alternatively with filler due to the low functionality of commercial PLA grade.     

Screening for Stockholm Convention persistent organic pollutants in the Bosna River (Bosnia and Herzogovina)

The Stockholm Convention, which aspires to manage persistent organic pollutants (POPs) at the international level, was recently ratified in Bosnia and Herzegovina (BiH). Despite this fact, there is in general a paucity of data regarding the levels of POPs in the environment in BiH. In the present study, screening for POPs was conducted in one of the country’s major rivers, the Bosna. A two-pronged approach was applied using passive samplers to detect the freely dissolved and bioavailable concentrations in the water phase and sediment analysis to provide an integrated measure of historical contamination. At several places along the river, the concentrations of polycyclic aromatic hydrocarbons (PAH) were high and exhibited potential for both chronic and acute effects to biota. River water also showed elevated concentrations of PAH, up to 480 ng L^?1 near the city of Doboj, and diagnostic ratios suggested combustion sources for the contamination present in both types of sample. The levels of the other contaminants measured—polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) and polybrominated diphenyl ethers—were generally low in the water phase. However, PCBs and some OCPs were present in river sediments at levels which breach the international criteria and thus suggest potential for ecological damage. Additionally, the levels of heptachlor breached these criteria in many of the sites investigated. This study presents the first screening data for some of these Stockholm Convention relevant compounds in BiH and reveals both low concentrations of some chemical groups, but significant point sources and historic contamination for others.     

Dispersion of Pollutants in Street Canyon under Traffic Induced Flow and Turbulence

A 3-D Eulerian-Lagrangian approach to moving vehicles is presented that takes into account the traffic induced flow rate and turbulence. The method is applied to pollutants dispersion in a street canyon. The approach is based on CFD calculations using Eulerian approach to the continuous phase and Lagrangian approach to the "discrete phase" of moving objects - vehicles. A commercial CFD code StarCD was used into which the Lagrangian model was integrated. As an example a street canyon is taken into consideration. It has the length of 50 m and the aspect ratio of 1.27. The speed of wind was assigned values of 4, 7 and 12 m/s at the altitude of 300 m. The total height of the domain is 115 m. In the study different traffic situations are considered, namely one-way and two-way traffic with different traffic rates per lane. The predictions show that different traffic situations affect pollutants dispersion in the street canyon and that there are also differences in the pollutants dispersion in case of one- and two-way traffic.