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.     

On the Design of Computer-Based Models for Integrated Environmental Science

The current research agenda in environmental science is dominated by calls to integrate science and policy to better understand and manage links between social (human) and natural (nonhuman) processes. Freshwater resource management is one area where such calls can be heard. Designing computer-based models for integrated environmental science poses special challenges to the research community. At present it is not clear whether such tools, or their outputs, receive much practical policy or planning application. It is argued that this is a result of (1) a lack of appreciation within the research modeling community of the characteristics of different decision-making processes including policy, planning, and (2) participation, (3) a lack of appreciation of the characteristics of different decision-making contexts, (4) the technical difficulties in implementing the necessary support tool functionality, and (5) the socio-technical demands of designing tools to be of practical use. This article presents a critical synthesis of ideas from each of these areas and interprets them in terms of design requirements for computer-based models being developed to provide scientific information support for policy and planning. Illustrative examples are given from the field of freshwater resources management. Although computer-based diagramming and modeling tools can facilitate processes of dialogue, they lack adequate simulation capabilities. Component-based models and modeling frameworks provide such functionality and may be suited to supporting problematic or messy decision contexts. However, significant technical (implementation) and socio-technical (use) challenges need to be addressed before such ambition can be realized.     

Mercury in wild mushrooms and underlying soil substrate from Koszalin, North-central Poland

Concentrations of total mercury were determined by cold-vapour atomic absorption spectroscopy (CV-AAS) in 221 caps and 221 stalks of 15 species of wild growing higher fungi/mushrooms and 221 samples of corresponding soil substrate collected in 1997-98 in Manowo County, near the city of Koszalin in North-central Poland. Mean mercury concentrations in caps and stalks of the mushroom species examined and soils varied between 30+/-31 and 920+/-280, 17+/-11 and 560+/-220, and 10+/-9 and 170+/-110 ng/g dry matter, respectively. Cap to stalk mercury concentration quotients were from 1.0+/-0.4 in poison pax (Paxillus involutus) to 2.8+/-0.7 in slippery jack (Suillus luteus). Brown cort (Cortinarius malicorius), fly agaric (Amanita muscaria), orange-brown ringless amanita (A. fulva), red-aspen bolete (Leccinum rufum) and mutagen milk cap (Lactarius necator) contained the highest concentrations of mercury both in caps and stalks, and mean concentrations varied between 600+/-750 and 920+/-280 and 370+/-470 and 560+/-220 ng/g dry matter, respectively. An estimate of daily intake of mercury from mushroom consumption indicated that the flesh of edible species of mushrooms may not pose hazards to human health even at a maximum consumption rate of 28 g/day. However, it should be noted that mercury intake from other foods will augment the daily intake rates. Species such as the sickener (Russula emetica), Geranium-scented russula (R. fellea) and poison pax (P. involutus) did not concentrate mercury as evidenced from the bioconcentration factors (BCFs: concentrations in mushroom/concentration in soil substrate), which were less than 1. Similarly, red-hot milk cap (L. rufus), rickstone funnel cap (Clitocybe geotropa) and European cow bolete (S. bovinus) were observed to be weak accumulators of mercury. Fly agaric (A. muscaria) accumulated great concentrations of mercury with BCFs reaching 73+/-42 and 38+/-22 in caps and stalks, respectively. Mercury BCFs of between 4.0+/-2.3 and 23+/-25 (caps) and 2.6+/-1.9 and 14+/-12 (stalks) were noted for the other mushroom species. Relatively great concentrations of mercury in fly agaric (A. muscaria) were due to preferential uptake of this element by this species.     

Land cover composition determinants in the Uckermark (NE Germany) over a 220-year period

There is broad consensus that land use/cover has changed in central Europe over millennia. However, few studies have addressed the roles of the anthropogenic (socio-economic) and natural (biophysical) factors driving these changes over shorter periods (e.g., 100 years). In this study, we analyse the determinants of land cover composition at three discrete time periods (c. 1780, 1890, and 2000). We hypothesise that different anthropogenic and natural factors are the determinants of the main land cover types (arable fields, grasslands, and forests) and that the effects of natural and anthropogenic factors on the main land cover types differ among landscapes with highly dynamic and more stable forest-open land distributions. The study was carried out in the Uckermark region located in northeastern Germany. We compiled data on natural and anthropogenic factors (e.g. forest cover and number of inhabitants) of 65 municipalities in four landscape sections of equal size (10 × 10 km). Landscape sections were selected to reflect different dynamics (high/low) in conversion from forest to arable fields or grasslands and vice versa from 1780 to 2000. Averaged linear mixed-effect models explained between 7.5 and 81.2 % of the variance. The unique effect of anthropogenic factors varied from 2.1 to 18.7 % and that of natural factors varied from 0.2 to 43.4 %. In four of six models that included both types of factors, the natural factors were more influential than the anthropogenic factors. Except in three cases, anthropogenic and natural factors showed opposite effects on land cover types in more dynamic and more stable windows. Though the Uckermark region has been influenced by human activity for thousands of years, natural factors were a major determinant of land cover composition during all time periods, whereas anthropogenic factors became more important only during the latest time period under investigation.     

Chemical characteristics of trace metals in PM10 and their concentrated weighted trajectory analysis at Central Delhi, India

Trace metals associated with PM₁₀ aerosols and their variation during day and nighttime as well as during different seasons have been studied for the year 2012. PCA analysis suggested 5 PCs, which accounted for 86.8% cumulative variance. PC1 accounted for 30% with a significant loading of metals of anthropogenic origin, while PC2 showed 28% variance with the loading of metals of crustal origin. These trace metals showed seasonal distinct day and night time characteristics. The concentrations of Cu, Pb, and Cd were found to be higher during nighttime in all the seasons. Only Fe was observed with significantly higher mean concentrations during daytime of all seasons except monsoon. The highest mean values of Cu, Cd, Zn, and Pb during post-monsoon might be attributed to winds advection over the regions of waste/biomass burning and industrial activities in Punjab and Haryana regions. Furthermore, concentration weighted trajectory analysis suggested that metals of crustal origin were contributed by long-range transport while metals of anthropogenic and industrial activities were contributed by regional/local source regions.     

Photosensitized Oxidation of Cyanide in Aqueous Solutions of Photoactive Modified Hydroxyethylcellulose

Novel water-soluble polymeric photosensitizers based on a natural polymer, naphthalene-modified hydroxyethylcellulose (HENC), were obtained and used for the photooxidation of cyanide. The reaction leads to the formation of cyanate. The process occurs via photoinduced electron transfer from CN⁻ to the naphthalene or naphthoquinone polymeric chromophores. The kinetics of the reaction depend on the degree of substitution of HENC, its concentration, and pH of the solution. The polymers can be easily removed after reaction as prolonged irradiation leads to their photodegradation.     

Water quality in rice-growing watersheds in a Mediterranean climate

Rice (Oryza sativa L.) agriculture is estimated to cover 161 million ha of land on Earth, with 10% grown in temperate regions. Currently there are strong concerns about surface water nutrient pollution, and the purpose of this study was to determine the impacts of temperate rice cultivation on nutrient dynamics at the small watershed scale. Over the course of the 2008 growing season (May through September), bi-weekly grab samples were collected from outlets of 11 agricultural subwatersheds in California. Samples were analyzed for NO₃-N, NH₄-N, PO₄-P, K, and dissolved organic nitrogen (DON) concentrations, and the average values across all subwatersheds and sampling dates were 0.22, 0.031, 0.047, 1.36, and 0.32 mg L⁻¹, respectively. Linear mixed effects analysis was used to evaluate the magnitude of relationships between nutrient concentration and flux and subwatershed characteristics (i.e. percent soil clay and organic matter, percent rice area, irrigation water reuse, subwatershed discharge, irrigated area, and time, measured as the day in the growing season). For all nutrients, flux decreased over time and increased with discharge. Concentrations of K and DON were highest at the start and end of the growing season. Concentrations of NH₄-N were near non-detect levels, with the exception of a peak in mid-July, which corresponds to when many growers top-dress rice fields with N fertilizer. Nitrate-N concentration and flux decreased with percent rice area, whereas PO₄-P concentrations increased with percent rice area, indicating that rice area should be considered in future watershed-scale studies of nutrient discharge. In all subwatersheds, the discharge loads of K were smaller than surface water input loads, while NO₃-N, NH₄-N, PO₄-P, and DON discharge loads exceeded input loads when total growing season discharge was greater than 3500-6600 m³ ha⁻¹. This implies that the management of subwatershed discharge can be used to control nutrient export from rice-growing areas.     

The response of temperate aquatic ecosystems to global warming: novel insights from a multidisciplinary project

This article serves as an introduction to this special issue of Marine Biology, but also as a review of the key findings of the AQUASHIFT research program which is the source of the articles published in this issue. AQUASHIFT is an interdisciplinary research program targeted to analyze the response of temperate zone aquatic ecosystems (both marine and freshwater) to global warming. The main conclusions of AQUASHIFT relate to (a) shifts in geographic distribution, (b) shifts in seasonality, (c) temporal mismatch in food chains, (d) biomass responses to warming, (e) responses of body size, (f) harmful bloom intensity, (f), changes of biodiversity, and (g) the dependence of shifts to temperature changes during critical seasonal windows.