This report presents the highlights of the 7th European Meeting on Molecular Diagnostics held in Scheveningen, The Hague, The Netherlands, 12-14 October 2011. The areas covered included molecular diagnostics applications in medical microbiology, virology, pathology, hemato-oncology,clinical genetics and forensics. Novel real-time amplification approaches, novel diagnostic applications and new technologies, such as next-generation sequencing, PCR lectrospray-ionization TOF mass spectrometry and techniques based on the detection of proteins or other molecules, were discussed. Furthermore, diagnostic companies presented their future visions for molecular diagnostics in human healthcare.
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Phytophthora infestans, the causal agent of late blight, remains the main threat to potato production worldwide. Screening of 19 accessions of Solanum dulcamara with P. infestans isolate Ipo82001 in detached leaf assays revealed strong resistance in an individual belonging to accession A54750069-1. This plant was crossed with a susceptible genotype, and an F(1) population consisting of 63 individuals was obtained. This population segregated for resistance in 1:1 ratio, both in detached leaf assays and in an open-field experiment. Presence of the formerly mapped Rpi-dlc1 gene as the cause of the observed segregating resistance could be excluded. Subsequently, AFLP analyses using 128 primer combinations enabled identification of five markers linked to a novel resistance gene named Rpi-dlc2. AFLP markers did not show sequence similarity to the tomato and potato genomes, hampering comparative genetic positioning of the gene. For this reason we used next-generation mapping (NGM), an approach that exploits direct sequencing of DNA (in our case: cDNA) pools from bulked segregants to calculate the genetic distance between SNPs and the locus of interest. Plotting of these genetic distances on the tomato and potato genetic map and subsequent PCR-based marker analysis positioned the gene on chromosome 10, in a region overlapping with the Rpi-ber/ber1 and -ber2 loci from S. berthaultii. Pyramiding of Rpi-dlc2 and Rpi-dlc1 significantly increased resistance to P. infestans, compared with individuals containing only one of the genes, showing the usefulness of this strategy to enhance resistance against Phytophthora.
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Rioolwaterzuiveringen zijn de belangrijkste bron van geneesmiddelen en kunstmatige zoetstoffen in oppervlaktewater. De mate waarin rwzi’s deze organische microverontreinigingen verwijderen, lijkt te variëren van locatie tot locatie en/of in de tijd. Oriënterend onderzoek bij zeven rwzi’s in Groningen en Drenthe toonde aan dat de verwijdering van de zoetstof acesulfaam erg varieerde. Om het verschil in de biologische verwijderingscapaciteit voor acesulfaam en geneesmiddelen te kunnen verklaren, bieden nieuwe DNA-technieken wellicht uitkomst. Met Next Generation Sequencing (NGS) komen verschillen tussen bacteriepopulaties aan het licht die mogelijk verschillen in verwijdering van geneesmiddelen en zoetstoffen kunnen verklaren.
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To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis.
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Publicatie bij de rede, uitgesproken bij de aanvaarding van het ambt als lector Green Biotechnology aan Hogeschool Inholland te Amsterdam op 20 mei2015 door dr. C.M. Kreike
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There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil‐borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below‐ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root‐associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil‐borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species‐specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density‐dependent effects of root‐associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity‐ecosystem functioning relationships.
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Next-generation sequencing technology allows culture- independent analysis of species and genes present in a complex microbial community. Such metagenomics may overcome the inability to culture microbes in isolation. Microbial communities of interest are for example responsible for making biogas. Many applications in metagenomics focus on 16S RNA analysis. We here evaluate the possibility of whole genome analysis (WGS) as approach for metagenomics studies.Samples (Table 1) from three biogas installations fed with different feedstock were used for DNA isolation and WGS analysis. Short (75b) Illumina paired-end DNA sequence reads were generated and assembled into larger continuous stretches (contigs),AcknowledgementsResults show that WGS is feasible for complex community analysis. Large groups of organisms (for example the class Methanomicrobia) are present in all samples with a possible role in the biogas production pathway.Assemble reads into contigs•meta-velveth as metagenomics reads assemblerSequencesimilaritysearch•proteome reference database from all currently available Bacteria and Achaea genomesAssign hits to taxa•Lowest common ancestor method incorporated in MEGAN4Such studies will help to identify and use microbial species for future improvements of biogas production dependence on process parameters and feedstock.
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Abstract Background: People with severe mental illness (SMI) often suffer from long-lasting symptoms that negatively influence their social functioning, their ability to live a meaningful life, and participation in society. Interventions aimed at increasing physical activity can improve social functioning, but people with SMI experience multiple barriers to becoming physically active. Besides, the implementation of physical activity interventions in day-to-day practice is difficult. In this study, we aim to evaluate the effectiveness and implementation of a physical activity intervention to improve social functioning, mental and physical health. Methods: In this pragmatic stepped wedge cluster randomized controlled trial we aim to include 100 people with SMI and their mental health workers from a supported housing organization. The intervention focuses on increasing physical activity by implementing group sports activities, active guidance meetings, and a serious game to set physical activity goals. We aim to decrease barriers to physical activity through active involvement of the mental health workers, lifestyle courses, and a medication review. Participating locations will be divided into four clusters and randomization will decide the start of the intervention. The primary outcome is social functioning. Secondary outcomes are quality of life, symptom severity, physical activity, cardiometabolic risk factors, cardiorespiratory fitness, and movement disturbances with specific attention to postural adjustment and movement sequencing in gait. In addition, we will assess the implementation by conducting semi-structured interviews with location managers and mental health workers and analyze them by direct content analysis. Discussion: This trial is innovative since it aims to improve social functioning in people with SMI through a physical activity intervention which aims to lower barriers to becoming physically active in a real-life setting. The strength of this trial is that we will also evaluate the implementation of the intervention. Limitations of this study are the risk of poor implementation of the intervention, and bias due to the inclusion of a medication review in the intervention that might impact outcomes. Trial registration: This trial was registered prospectively in The Netherlands Trial Register (NTR) as NTR NL9163 on December 20, 2020. As the The Netherlands Trial Register is no longer available, the trial can now be found in the International Clinical Trial Registry Platform via: https:// trial search. who. int/ Trial2. aspx? Trial ID= NL9163.
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This review offers a detailed examination of the current landscape of radio frequency (RF) electromagnetic field (EMF) assessment tools, ranging from spectrum analyzers and broadband field meters to area monitors and custom-built devices. The discussion encompasses both standardized and non-standardized measurement protocols, shedding light on the various methods employed in this domain. Furthermore, the review highlights the prevalent use of mobile apps for characterizing 5G NR radio network data. A growing need for low-cost measurement devices is observed, commonly referred to as “sensors” or “sensor nodes”, that are capable of enduring diverse environmental conditions. These sensors play a crucial role in both microenvironmental surveys and individual exposures, enabling stationary, mobile, and personal exposure assessments based on body-worn sensors, across wider geographical areas. This review revealed a notable need for cost-effective and long-lasting sensors, whether for individual exposure assessments, mobile (vehicle-integrated) measurements, or incorporation into distributed sensor networks. However, there is a lack of comprehensive information on existing custom-developed RF-EMF measurement tools, especially in terms of measuring uncertainty. Additionally, there is a need for real-time, fast-sampling solutions to understand the highly irregular temporal variations EMF distribution in next-generation networks. Given the diversity of tools and methods, a comprehensive comparison is crucial to determine the necessary statistical tools for aggregating the available measurement data.
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We tested the hypothesis that in human ageing a decreased intramuscular acylcarnitine status is associated with (pre-)frailty, reduced physical performance and altered mitochondrial function. Results showed that intramuscular total carnitine levels and acetylcarnitine levels were lower in (pre-)frail old females compared to fit old females and young females, whereas no differences were observed in males. The low intramuscular acetylcarnitine levels in females correlated with low physical performance, even after correction for muscle mass (%), and were accompanied with lowered expression of genes involved in mitochondrial energy production and functionality. We concluded that in (pre-)frail old females, intramuscular total carnitine levels and acetylcarnitine levels are decreased, and this decrease is associated with reduced physical performance and low expression of a wide range of genes critical for mitochondrial function. The results stress the importance of taking sex differences into account in ageing research.
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