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.     

Modeling non-point source pollution from rice farming in the Thachin River Basin

With the worldwide intensification of agriculture, non-point source pollution of surface waters has become a pressing issue. Conventional river water quality models consider non-point sources as accumulated entries into the rivers and do not investigate into the processes generating the pollution at its source, thus preventing the determination of effective mitigation measures. The models require extensive data inputs, which is a deficiency in many developing and emerging countries with limited data availability. The current study applies a Material Flow Model as a complementary approach to quantify non-point source pollution from agricultural areas. Rice farming in the Thachin River Basin is presented as a case study, with a focus on nutrients. The total nitrogen and phosphorus flows from rice farming to the river system are quantified, the key parameters influencing these flows are determined and potential mitigation measures are discussed. The results show that rice contributes considerable nutrient loads to the Thachin River Basin. Scenario simulations demonstrate that a significant nutrient load reduction could be achieved by following the official recommendations for fertilizer application, thus confirming the local efforts to introduce best management practice. Our results underline the importance of non-point source pollution control in intensive agricultural areas, particularly of tropical lowland delta areas such as the Central Plains of Thailand. The specific benefit of applying a Material Flow Model in this context is that with limited data availability, one can reach an understanding of the system and gain a first overview over its key pollution problems. This can serve as supportive basis for determining consecutive in-depth research requirements.     

Disentangling technological innovations: a micro-econometric analysis of their determinants

On the basis of a unique firm-level dataset from the German manufacturing sector, this paper empirically examines the determinants of environmental and non-environmental product and process innovations. The micro-econometric analysis with multivariate probit models points to an extremely high relevance of R&D activities for all technological innovation types, as well as to the relevance of a few market pull factors. The estimation results additionally reveal the importance of organisational measures for environmental product and process innovations. In this regard, not only certified environmental management systems, but also specific process- and product-related environmental organisational measures and even general organisational measures, such as the certification of a quality management system according to ISO 9001, play a crucial role. The estimation results therefore suggest the encouragement of firm-internal R&D activities and organisational measures by (environmental) policy in order to stimulate environmental technological innovations, which are able to both limit the environmental burden and contribute to the technological modernisation of the economy.     

Buchbesprechungen

The Science of Nature -     

Negotiating weights for burden sharing rules in international climate negotiations: an empirical analysis

Environmental Economics and Policy Studies - We have collected data from a world-wide survey among COP delegates to empirically investigate preferences for certain burden sharing rules among key...     

Assessment of indoor air concentrations of VOCs and their associated health risks in the library of Jawaharlal Nehru University,New Delhi

The present work investigated the levels of total volatile organic compounds (TVOC) and benzene, toluene, ethylbenzene, m/p-xylene, and o-xylene (BTEX) in different microenvironments in the library of Jawaharlal Nehru University in summer and winter during 2011–2012. Carcinogenic and non-carcinogenic health risks due to organic compounds were also evaluated using US Environmental Protection Agency (USEPA) conventional approaches. Real-time monitoring was done for TVOC using a data-logging photo-ionization detector. For BTEX measurements, the National Institute for Occupational Safety and Health (NIOSH) standard method which consists of active sampling of air through activated charcoal, followed by analysis with gas chromatography, was performed. Simultaneously, outdoor measurements for TVOC and BTEX were carried out. Indoor concentrations of TVOC and BTEX (except benzene) were higher as compared to the outdoor for both seasons. Toluene and m/p-xylene were the most abundant organic contaminant observed in this study. Indoor to outdoor (I/O) ratios of BTEX compounds were generally greater than unity and ranged from 0.2 to 8.7 and 0.2 to 4.3 in winter and summer, respectively. Statistical analysis and I/O ratios showed that the dominant pollution sources mainly came from indoors. The observed mean concentrations of TVOC lie within the second group of the Molhave criteria of indoor air quality, indicating a multifactorial exposure range. The estimated lifetime cancer risk (LCR) due to benzene in this study exceeded the value of 1?×?10^?6 recommended by USEPA, and the hazard quotient (HQ) of non-cancer risk came under an acceptable range.     

Determination of organophosphorus fire retardants and plasticizers in wastewater samples using MAE-SPME with GC-ICPMS and GC-TOFMS detection

Determination of organophosphorus fire retardants and plasticizers at trace levels in wastewater is described. In this work, microwave assisted extraction (MAE) and solid-phase microextraction (SPME) are used for sample preparation to extract and preconcentrate the analytes, followed by analysis by gas chromatography coupled to inductively coupled plasma mass spectrometry (GC-ICP-MS) for phosphorus-specific detection. Gas chromatography coupled to time of flight mass spectrometry (GC-TOF-MS) was used to confirm the organphosphorus fire retardants in wastewater. The detection limits of organophosphorus fire retardants (OPFRs) were 29 ng L(-1) for tri-n-butyl phosphate (TnBP), 45 ng for L(-1) for tris(2-butoxyethyl)phosphate (TBEP), and 50 ng L(-1) for tris(2-ethylhexyl)phosphate (TEHP). Optimized extraction conditions were performed at 65 degrees C for 30 min and with 10% NaCl. Application of MAE during the sample preparation prior to the SPME allowed the detection of tris(2-ethylhexyl) phosphate, which has been difficult to determine in previous work. Application of the method to wastewater samples resulted in detecting 3.1 microg L(-1) P from TnBP, 5.0 microg L(-1) P from TBEP, and 4.0 microg L(-1) P from TEHP. The presence of these compounds were also confirmed by SPME-GC-TOF-MS.     

Error propagation in pesticide residue measurements estimated by computational simulations and inter-laboratory sample analysis

An assessment of the error associated with conventional pesticide residue analysis has been conducted based on computer simulations and inter-laboratory residue analysis. Computational simulations were conducted based on (i) typical performance and regulatory acceptance criteria of analytical methods, and (ii) field residue distributions. In addition, field samples with incurred residues were sent to different private laboratories and the results compared. The relative difference in pesticide residues obtained when samples from the same field or produce lot are analyzed at separate laboratories was used to quantify the uncertainty associated with residue analyses performed using common analytical technology, and methods that are in compliance with current regulatory requirements. The study showed that differences of > 100% are common and should be expected when samples from the same crop are analyzed at different laboratories. The results also suggest that the error within residue measurements can be particularly detrimental when a result is reported near the maximum residue limit (MRL).     

The effect of thiacloprid formulation on DNA/chromosome damage and changes in GST activity in bovine peripheral lymphocytes

The potential genotoxic effect of thiacloprid formulation on bovine peripheral lymphocytes was evaluated using the comet assay and the cytogenetic endpoints: chromosome aberrations (CAs), sister chromatid exchanges (SCEs) and micronuclei (MNi). Whole blood cultures were treated with the insecticide at concentrations of 30, 60, 120, 240 and 480 μg mL^?1 for 24, 48 h and/or 2 h of incubation. A statistically significant increase in the frequency of DNA damage, as well as in unstable chromosome aberrations (% breaks) were found after exposure to the insecticide at concentrations ranging from 120 to 480 μg mL^?1 (P < 0.05, P < 0.01, P < 0.001). For the detection of stable structural chromosome aberrations (e.g., translocations) and numerical aberrations by the FISH method, three whole chromosome painting probes for bovine chromosomes 1, 5 and 7 (BTA1, BTA5 and BTA7) were used in our experiments. We observed numerical aberrations, but without any statistical significance. Regarding the sister chromatid exchanges, no significant elevation in the SCE frequencies was found after 24-h exposure to the insecticide. A dose-related response in the SCE induction was obtained in bovine cultures after the prolonged time of exposure (48 h) to thiacloprid formulation at concentrations ranging from 120 to 480 μg mL^?1 in each donor (P < 0.05, P < 0.01), which was associated with a reduction of the PI (P < 0.05, P < 0.01). The insecticide failed to produce MNi; however, a significant reduction of CBPI was observed. Using real-time PCR, a decrease in the expression of bovine glutathione S-transferase M3 (GSTM3) was detected at the lowest dose. The higher concentrations of thiacloprid formulation caused an increase in the mRNA expression.