Extraction of DNA from Choline Chloride Feed Additive (CC) and from derived Pre-Mixes (PMCC) and Screening of CC and PMCC for (a) presence of rice and (b) presence of Bt63

Choline Chloride 60% (CC) is a feed additive that is imported in significant quantities from China. In a number of cases GM rice, harbouring the event Bt63, has been found in imported CC batches but not in derived pre-mixes. The Member States were asked to provide positive CC samples and derived pre-mixes to the EU-RL GMFF in order to allow the EU-RL GMFF establishing practical approaches to DNA extraction and the subsequent testing for presence of (a) rice and (b) the Bt63 rice event. This technical note has been derived based on data provided from National Control Laboratories and experience made by the EU-RL GMFF when re-testing nine feed additive samples and ten pre-mixes samples. The EU-RL GMFF found that the extraction of DNA from the feed additive Choline Chloride (CC) does not normally pose specific problems. It can be carried out following the available protocols or using available standard DNA extraction kits. The extraction of DNA from derived pre-mixes (PMCC) is, however, posing problems because of observed strong inhibition and the presence of DNA from additional sources than those present in the CC. The EU-RL GMFF has tried a number of protocols and extraction kits on PMCC samples. On this basis it is concluded that it is advisable to carefully purify the DNA, to verify the possible presence of inhibition effects and eventually to try to reduce any inhibition observed. Concerning testing the extracted DNA for rice and Bt63 rice event presence, this does not pose a problem in case of the CC while for PMCC rice was not anymore detectable or was detected in trace amounts. In any case testing for Bt63 presence was impossible. A possible explanation could be that much of the extracted DNA is from other plants than rice and hence the concentration of rice DNA is below the LOD of the rice-taxon specific method. In order to verify this, the EU-RL GMFF has analysed the available rice (taxon-) specific methods by means of bio-informatics and (partly) in the laboratory and concludes that they all should be suitable for specifically and reliably detecting rice from the Oryza sativa species. The re-testing by the EU-RL GMFF of CC and PMCC samples has confirmed the results of the initial tests.JRC.I.3-Molecular Biology and Genomic

A novel mutation in SPART gene causes a severe neurodevelopmental delay due to mitochondrial dysfunction with complex I impairments and altered pyruvate metabolism

Funding: Royal Society grant RG110387 (S.P.)Loss-of-function mutations in the SPART gene cause Troyer syndrome, a recessive form of spastic paraplegia resulting in muscle weakness, short stature, and cognitive defects. SPART encodes for Spartin, a protein linked to endosomal trafficking and mitochondrial membrane potential maintenance. Here, we identified with whole exome sequencing (WES) a novel frameshift mutation in the SPART gene in 2 brothers presenting an uncharacterized developmental delay and short stature. Functional characterization in an SH-SY5Y cell model shows that this mutation is associated with increased neurite outgrowth. These cells also show a marked decrease in mitochondrial complex I (NADH dehydrogenase) activity, coupled to decreased ATP synthesis and defective mitochondrial membrane potential. The cells also presented an increase in reactive oxygen species, extracellular pyruvate, and NADH levels, consistent with impaired complex I activity. In concordance with a severe mitochondrial failure, Spartin loss also led to an altered intracellular Ca2+ homeostasis that was restored after transient expression of wild-type Spartin. Our data provide for the first time a thorough assessment of Spartin loss effects, including impaired complex I activity coupled to increased extracellular pyruvate. In summary, through a WES study we assign a diagnosis of Troyer syndrome to otherwise undiagnosed patients, and by functional characterization we show that the novel mutation in SPART leads to a profound bioenergetic imbalance.PreprintPeer reviewe

Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes

While numerous studies have implicated copy number variants (CNVs) in a range of neurological phenotypes, the impact relative to disease severity has been difficult to ascertain due to small sample sizes, lack of phenotypic details, and heterogeneity in platforms used for discovery. Using a customized microarray enriched for genomic hotspots, we assayed for large CNVs among 1,227 individuals with various neurological deficits including dyslexia (376), sporadic autism (350), and intellectual disability (ID) (501), as well as 337 controls. We show that the frequency of large CNVs (>1 Mbp) is significantly greater for ID–associated phenotypes compared to autism (p = 9.58×10−11, odds ratio = 4.59), dyslexia (p = 3.81×10−18, odds ratio = 14.45), or controls (p = 2.75×10−17, odds ratio = 13.71). There is a striking difference in the frequency of rare CNVs (>50 kbp) in autism (10%, p = 2.4×10−6, odds ratio = 6) or ID (16%, p = 3.55×10−12, odds ratio = 10) compared to dyslexia (2%) with essentially no difference in large CNV burden among dyslexia patients compared to controls. Rare CNVs were more likely to arise de novo (64%) in ID when compared to autism (40%) or dyslexia (0%). We observed a significantly increased large CNV burden in individuals with ID and multiple congenital anomalies (MCA) compared to ID alone (p = 0.001, odds ratio = 2.54). Our data suggest that large CNV burden positively correlates with the severity of childhood disability: ID with MCA being most severely affected and dyslexics being indistinguishable from controls. When autism without ID was considered separately, the increase in CNV burden was modest compared to controls (p = 0.07, odds ratio = 2.33)

Mapping and Assessment of Ecosystems and their Services: An EU ecosystem assessment

This report presents an ecosystem assessment covering the total land area of the EU as well as the EU marine regions. The assessment is carried out by Joint Research Centre, European Environment Agency, DG Environment, and the European Topic Centres on Biological Diversity and on Urban, Land and Soil Systems. This report constitutes a knowledge base which can support the evaluation of the 2020 biodiversity targets. It also provides a data foundation for future assessments and policy developments, in particular with respect to the ecosystem restoration agenda for the next decade (2020-2030). The report presents an analysis of the pressures and condition of terrestrial, freshwater and marine ecosystems using a single, comparable methodology based on European data on trends of pressures and condition relative to the policy baseline 2010. The following main conclusions are drawn: - Pressures on ecosystems exhibit different trends. - Land take, atmospheric emissions of air pollutants and critical loads of nitrogen are decreasing but the absolute values of all these pressures remain too high. - Impacts from climate change on ecosystems are increasing. - Invasive alien species of union concern are observed in all ecosystems, but their impact is particularly high in urban ecosystems and grasslands. - Pressures from overfishing activities and marine pollution are still high. - In the long term, air and freshwater quality is improving. - In forests and agroecosystems, which represent over 80% of the EU territory, there are improvements in structural condition indicators (biomass, deadwood, area under organic farming) relative to the baseline year 2010 but some key bio-indicators such as tree-crown defoliation continue to increase. This indicates that ecosystem condition is not improving. - Species-related indicators show no progress or further declines, particularly in agroecosystems. The analysis of trends in ecosystem services concluded that the current potential of ecosystems to deliver timber, protection against floods, crop pollination, and nature-based recreation is equal to or lower than the baseline value for 2010. At the same time, the demand for these services has significantly increased. A lowered potential in combination with a higher demand risks to further decrease the condition of ecosystems and their contribution to human well-being. Despite the wide coverage of environmental legislation in the EU, there are still large gaps in the legal protection of ecosystems. On land, 76% of the area of terrestrial ecosystems, mainly forests, agroecosystems and urban ecosystems, are excluded from a legal designation under the Bird and Habitat Directives. Freshwater and marine ecosystems are subject to specific protection measures under the Water Framework and Marine Strategy Framework Directives. The condition of ecosystems that are under legal designation is unfavourable. More efforts are needed to bend the curve of biodiversity loss and ecosystem degradation and to put ecosystems on a path to recovery. The progress that is made in certain areas such as pollution reduction, increasing air and water quality, increasing share of organic farming, the expansion of forests, and the efforts to maintain marine fish stocks at sustainable levels show that a persistent implementation of policies can be effective. These successes should encourage us to act now and to put forward an ambitious plan for the restoration of Europe’s ecosystems.JRC.D.3-Land Resource

Visual Search of multiple objects from a single query

Hundreds of millions of images are uploaded to the cloud every day. Innovative applications able to analyze and extract efficiently information from such a big database are needed nowadays more than ever. Visual search is an application able to retrieve information of a query image comparing it against a large image database. In this paper a Visual Search pipeline implementation is presented able to retrieve multiple objects depicted in a single query image. Quantitative and qualitative precision results are shown on both real and synthetic datasets

Resistivity measurements in superconducting Ba1-xKxBiO3

The electrical resistance R in a superconducting Ba1-xKxBiO3 single crystal is studied as a function of the temperature T and the current I. The measurements performed without applied magnetic field indicate that the flux lines are generated by the self-field and that several transitions contribute independently to the R(T) and R(I) characteristics. A phenomenological expression of the R(T, I) dependence is proposed