Characterization of soluble forms of NCAM

AbstractNeural cell adhesion molecule (NCAM) has been described as a family of membrane glycoproteins. However, soluble NCAM immunoreactivity has long been recognized. We here show that soluble NCAM is composed of two quantitatively major polypeptides of Mr 180 000 and 115 000 and two minor components of Mr 160 000 and 145 000. Soluble NCAM was immunochemically identical to membrane NCAM, was polysialylated and carried the HNK-1 epitope. It only constituted 0.8% of total NCAM in newborn rat brain. Soluble NCAM appeared in neuronal cell culture medium 15–30 min after the start of synthesis preceding accumulation of membrane-associated NCAM on the cell surface. This indicates that soluble NCAM contains a secreted component

Pixel classification methods for identifying and quantifying leaf surface injury from digital images

Plants exposed to stress due to pollution, disease or nutrient deficiency often develop visible symptoms on leaves such as spots, colour changes and necrotic regions. Early symptom detection is important for precision agriculture, environmental monitoring using bio-indicators and quality assessment of leafy vegetables. Leaf injury is usually assessed by visual inspection, which is labour-intensive and to a consid- erable extent subjective. In this study, methods for classifying individual pixels as healthy or injured from images of clover leaves exposed to the air pollutant ozone were tested and compared. RGB images of the leaves were acquired under controlled conditions in a laboratory using a standard digital SLR camera. Different feature vectors were extracted from the images by including different colour and texture (spa- tial) information. Four approaches to classification were evaluated: (1) Fit to a Pattern Multivariate Image Analysis (FPM) combined with T2 statistics (FPM-T2) or (2) Residual Sum of Squares statistics (FPM-RSS), (3) linear discriminant analysis (LDA) and (4) K-means clustering. The predicted leaf pixel classifications were trained from and compared to manually segmented images to evaluate classification performance. The LDA classifier outperformed the three other approaches in pixel identification with significantly higher accuracy, precision, true positive rate and F-score and significantly lower false positive rate and computation time. A feature vector of single pixel colour channel intensities was sufficient for capturing the information relevant for pixel identification. Including neighbourhood pixel information in the feature vector did not improve performance, but significantly increased the computation time. The LDA classifier was robust with 95% mean accuracy, 83% mean true positive rate and 2% mean false positive rate, indicating that it has potential for real-time applications.Opstad Kruse, OM.; Prats Montalbán, JM.; Indahl, UG.; Kvaal, K.; Ferrer Riquelme, AJ.; Futsaether, CM. (2014). Pixel classification methods for identifying and quantifying leaf surface injury from digital images. Computers and Electronics in Agriculture. 108:155-165. doi:10.1016/j.compag.2014.07.010S15516510

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

Using peptide arrays and binding to native histone proteins, we show that the ADD domain of Dnmt3a specifically interacts with the H3 histone 1–19 tail. Binding is disrupted by di- and trimethylation of K4, phosphorylation of T3, S10 or T11 and acetylation of K4. We did not observe binding to the H4 1–19 tail. The ADD domain of Dnmt3b shows the same binding specificity, suggesting that the distinct biological functions of both enzymes are not related to their ADD domains. To establish a functional role of the ADD domain binding to unmodified H3 tails, we analyzed the DNA methylation of in vitro reconstituted chromatin with Dnmt3a2, the Dnmt3a2/Dnmt3L complex, and the catalytic domain of Dnmt3a. All Dnmt3a complexes preferentially methylated linker DNA regions. Chromatin substrates with unmodified H3 tail or with H3K9me3 modification were methylated more efficiently by full-length Dnmt3a and full-length Dnmt3a/3L complexes than chromatin trimethylated at H3K4. In contrast, the catalytic domain of Dnmt3a was not affected by the H3K4me3 modification. These results demonstrate that the binding of the ADD domain to H3 tails unmethylated at K4 leads to the preferential methylation of DNA bound to chromatin with this modification state. Our in vitro results recapitulate DNA methylation patterns observed in genome-wide DNA methylation studies

EURAD EC project – overview of the routes work package: identified key issues and open questions about waste management routes in Europe, from cradle to grave

The ROUTES Work Package (WP) is one of the two strategic studies being conducted as part of the European Joint Programme on Radioactive Waste Management (EURAD). ROUTES’ objectives are (i) to provide a framework for European Union’s member states (MS) to share methodologies, experiences, and knowledge in situations in which a waste management strategy is difficult to define as well as to (ii) to compare national approaches and strategies of waste management. The work considers national programmes at different stages of their development and deals with different amounts and types of radioactive waste. The expected output is identifying Research & Development (R&D) needs and opportunities for collaboration between MS, which need not be confined to ROUTES or EURAD frameworks. This work has enabled ROUTES partners to identify key issues such as retrieving poorly characterised legacy waste from a predisposal or disposal facility, implementing specific waste management solutions in the absence of well-defined WAC or developing innovative or shared solutions for MS that have only limited amounts of waste to manage. Discussion of these questions is illustrated through some of the case studies identified and analysed under the ROUTES WP

Pipeline for Large-Scale Microdroplet Bisulfite PCR-Based Sequencing Allows the Tracking of Hepitype Evolution in Tumors

Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into “hepitypes” and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe