The cell-free DNA virome of 108,349 Dutch pregnant women

Objective

Viral infections during pregnancy are a major health concern to mother and fetus. By repurposing cell-free Non Invasive Prenatal Testing (NIPT) sequencing data, we investigated prevalence and abundance of viral DNA in a cohort of 108,349 pregnant women.

Method

Cell-free DNA (cfDNA) sequencing reads that did not map to any of the human chromosomes or mitochondrial DNA of the human reference genome build GRCh38 were aligned to 224 DNA viruses selected from the NCBI refseq viral database.

Results

In total 443,665 reads of viral origin were detected across 42,273 samples representing 165 viral species. Several are known to be potentially harmful during pregnancy and/or childbirth, including Cytomegalovirus, Parvovirus B19 and Hepatitis B. Viral sequences were mostly detected at very low abundance. However, several cases had exceptionally high viral loads for Parvovirus B19, Hepatitis B and others. We found statistically significant associations between presence of viral DNA and gestational age, maternal age, fetal fraction, cfDNA concentration and others.

Conclusion

We demonstrate the feasibility to detect viral DNA from typical genome-wide NIPT cfDNA sequencing and describe the main characteristics of the viral DNA in our cohort. Our dataset of detected viral sequence reads is made publicly available to guide future clinical implementations.     

Ecosystem engineering potential of the gastropod Terebralia palustris (Linnaeus, 1767) in mangrove wastewater wetlands - A controlled mesocosm experiment

The effect of different sewage concentrations (0, 20, 60 and 100%), vegetation (Bare, Avicennia marina or Rhizophora mucronata) and immersion periods (immersion/emersion period of 12/12 h or 3/3 days just for 100%) conditions were studied for 6 months on survival and growth rates of Terebralia palustris (Linnaeus, 1767). Gastropods' activity and ecosystem engineering preformed at bare and A. marina planted cells and 3 sewage conditions (0, 20 and 60%) were determined. Survival rates were higher than 70% in all treatments. Growth rate decreased significantly with increasing sewage concentrations (mainly at unplanted conditions) and longer immersion periods. A complete shift (from immersion to emersion periods) and a significant decrease in mobility and consequently its engineer potential, due to sewage contamination, lead to a 3-4 fold decrease in the amount of sediment disturbed. Sewage contamination, primary producers' abundance and environmental conditions may have influenced the gastropods survival, growth and its ecosystem engineering potential.     

Learning About the History of Landscape Use for the Future: Consequences for Ecological and Social Systems in Swedish Bergslagen

Barriers and bridges to implement policies about sustainable development and sustainability commonly depend on the past development of social–ecological systems. Production of metals required integration of use of ore, streams for energy, and wood for bioenergy and construction, as well as of multiple societal actors. Focusing on the Swedish Bergslagen region as a case study we (1) describe the phases of natural resource use triggered by metallurgy, (2) the location and spatial extent of 22 definitions of Bergslagen divided into four zones as a proxy of cumulative pressure on landscapes, and (3) analyze the consequences for natural capital and society. We found clear gradients in industrial activity, stream alteration, and amount of natural forest from the core to the periphery of Bergslagen. Additionally, the legacy of top-down governance is linked to today’s poorly diversified business sector and thus municipal vulnerability. Comparing the Bergslagen case study with other similar regions in Russia and Germany, we discuss the usefulness of multiple case studies.     

Solving Problems in Social–Ecological Systems: Definition, Practice and Barriers of Transdisciplinary Research

Translating policies about sustainable development as a social process and sustainability outcomes into the real world of social–ecological systems involves several challenges. Hence, research policies advocate improved innovative problem-solving capacity. One approach is transdisciplinary research that integrates research disciplines, as well as researchers and practitioners. Drawing upon 14 experiences of problem-solving, we used group modeling to map perceived barriers and bridges for researchers’ and practitioners’ joint knowledge production and learning towards transdisciplinary research. The analysis indicated that the transdisciplinary research process is influenced by (1) the amount of traditional disciplinary formal and informal control, (2) adaptation of project applications to fill the transdisciplinary research agenda, (3) stakeholder participation, and (4) functional team building/development based on self-reflection and experienced leadership. Focusing on implementation of green infrastructure policy as a common denominator for the delivery of ecosystem services and human well-being, we discuss how to diagnose social–ecological systems, and use knowledge production and collaborative learning as treatments.     

Protected Area as an Indicator of Ecological Sustainability? A Century of Development in Europe’s Boreal Forest

Protected area (PA) is an indicator linked to policies on ecological sustainability. We analyzed area, size, and categories of PAs in the European boreal forest biome in Norway, Sweden, Finland, and Russia from 1900 to 2010. The PA increased from 1.5 × 10³ ha in 1909 to 2.3 × 10⁷ ha in 2010. While the total PA in the boreal biome was 10.8 %, the figures ranged from 17.2 % in the northern, 7.9 % of the middle, and 8.7 % of the southern boreal sub-regions. The median size of PAs varied from 10 to 124 ha among countries. The categories of less strictly PAs increased over time. The proportion of area occupied by PAs is an important response indicator for conservation efforts. However, the use of PA as an indicator of ecological sustainability needs to consider ecosystem representation, functional connectivity and management categories.     

Spatial & temporal variations of PM10 and particle number concentrations in urban air

The size of particles in urban air varies over four orders of magnitude (from 0.001 μm to 10 μm in diameter). In many cities only particle mass concentrations (PM10, i.e. particles <10 μm diameter) is measured. In this paper we analyze how differences in emissions, background concentrations and meteorology affect the temporal and spatial distribution of PM10 and total particle number concentrations (PNC) based on measurements and dispersion modeling in Stockholm, Sweden. PNC at densely trafficked kerbside locations are dominated by ultrafine particles (<0.1 μm diameter) due to vehicle exhaust emissions as verified by high correlation with NOx. But PNC contribute only marginally to PM10, due to the small size of exhaust particles. Instead wear of the road surface is an important factor for the highest PM10 concentrations observed. In Stockholm, road wear increases drastically due to the use of studded tires and traction sand on streets during winter; up to 90% of the locally emitted PM10 may be due to road abrasion. PM10 emissions and concentrations, but not PNC, at kerbside are controlled by road moisture. Annual mean urban background PM10 levels are relatively uniformly distributed over the city, due to the importance of long range transport. For PNC local sources often dominate the concentrations resulting in large temporal and spatial gradients in the concentrations. Despite these differences in the origin of PM10 and PNC, the spatial gradients of annual mean concentrations due to local sources are of equal magnitude due to the common source, namely traffic. Thus, people in different areas experiencing a factor of 2 different annual PM10 exposure due to local sources will also experience a factor of 2 different exposure in terms of PNC. This implies that health impact studies based solely on spatial differences in annual exposure to PM10 may not separate differences in health effects due to ultrafine and coarse particles. On the other hand, health effect assessments based on time series exposure analysis of PM10 and PNC, should be able to observe differences in health effects of ultrafine particles versus coarse particles.     

Soil pollution in day-care centers and playgrounds in Norway: national action plan for mapping and remediation

Systematic geochemical mapping based on sampling and analysis of surface soils (0–2 cm) has been carried out in several Norwegian cities. The soils in the oldest parts of the cities are contaminated with metals (especially Pb) and polycyclic aromatic hydrocarbons (PAH). Due to the fact that children are often in contact with surface soil, it was realized that special focus had to be directed towards soils in day-care centers and playgrounds. The first mapping and remedy program was initiated in Trondheim in 1996. Here, the importance of copper–chromium–arsenic (CCA)-pressure-impregnated wood in playing equipment as a pollution source for soils was documented, and a process was started with the aim to ban this product. Soils from day-care centers in the inner city of Bergen were polluted to a degree that required remediation in 45% out of 87 centers, mainly due to high concentrations of Pb and benzo(a)pyrene. In Oslo, 38% of 700 day-care centers needed remediation due to soil pollution by Pb, BaP, Cd, Hg, Ni and PCB. Removal of CCA-impregnated wood was necessary in more than half of the day-care centers The Norwegian parliament has decided to investigate all outdoor playing areas in day-care centers, playgrounds and schoolyards in Norway, starting in 2007 with day-care centers in the ten largest cities and five most important industrial areas. The Norwegian Institute of Public Health has developed quality criteria for soils in day-care centers and playgrounds for As, Cd, Cr⁶⁺, Hg, Ni, Pb, zinc, PAH_sum16, benzo(a)pyrene, and PCB_sum7. The Geological Survey of Norway has developed guidance for mapping of soil pollution (sampling, chemical analysis and reporting) in day-care centers. Especially the sampling strategy has been developed in the period 1996–2007, and the preferred sampling strategy is to collect at least 10 samples of surface soil (0–2 cm) from (1) “original soil” on the site, (2) artificial man-made “hills”, and (3) soils used for growing vegetables. A total number of 2,000 day-care-centres are to be investigated, and necessary remediation should be completed before the end of 2010.     

Assessing ecological function in the context of species recovery

Species interactions matter to conservation. Setting an ambitious recovery target for a species requires considering the size, density, and demographic structure of its populations such that they fulfill the interactions, roles, and functions of the species in the ecosystems in which they are embedded. A recently proposed framework for an International Union for Conservation of Nature Green List of Species formalizes this requirement by defining a fully recovered species in terms of representation, viability, and functionality. Defining and quantifying ecological function from the viewpoint of species recovery is challenging in concept and application, but also an opportunity to insert ecological theory into conservation practice. We propose 2 complementary approaches to assessing a species’ ecological functions: confirmation (listing interactions of the species, identifying ecological processes and other species involved in these interactions, and quantifying the extent to which the species contributes to the identified ecological process) and elimination (inferring functionality by ruling out symptoms of reduced functionality, analogous to the red-list approach that focuses on symptoms of reduced viability). Despite the challenges, incorporation of functionality into species recovery planning is possible in most cases and it is essential to a conservation vision that goes beyond preventing extinctions and aims to restore a species to levels beyond what is required for its viability. This vision focuses on conservation and recovery at the species level and sees species as embedded in ecosystems, influencing and being influenced by the processes in those ecosystems. Thus, it connects and integrates conservation at the species and ecosystem levels.