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Session B1: German Participatory Forum on Fish Protection and Downstream Migration
Abstract
Fish protection and downstream fish migration has been an item of intensive and often controversial discussions in recent years in Germany, both from an environmental policy perspective and a technical point of view. In response, the Federal Environment Agency, with support from Ecologic Institute, initiated a Forum on Fish Protection and Downstream Fish Migration in 2012.
The Forum includes participants from federal and regional water resource management authorities, nature and angler NGOs, consultancies, water managers and hydropower. More than 200 stakeholders have engaged in a dialogue process on the following jointly-identified key topics: environmental policy and legal framework; river basin-related strategies; applied behavioral and population biology; technical measures for fish protection and downstream migration; monitoring.
The Forum has hosted a series of interactive workshops and conferences to foster dialogue and has achieved the exchange of information and experiences on the various topics put on the table. To increase acceptability and engagement of participants in the process, the Forum has not actively sought to reach consensus. In the outcomes of discussion on conflicting topics, both common and differing opinions have been taken on board. In addition, a common understanding has been developed on the current state of knowledge and technology that needs to be taken into account for fish protection, downstream fish migration and the conservation and establishment of fish populations. Next to the identification of key problem areas, the Forum experts proposed initial solutions and identified needs for further research and practical action.
In 2014, the Forum produced a synthesis as a result of the discussions taking place so far during the workshops. The Forum participants have highlighted the improvement that has taking place in the debate culture on the topic of fish protection and downstream migration within Germany due to the Forum events. The participants highly recommended continuing this type of dialogue process
Completeness of Information Sources
Information quality plays a crucial role in every application that integrates data from autonomous sources. However, information quality is hard to measure and complex to consider for the tasks of information integration, even if the integrating sources cooperate. We present a systematic and formal approach to the measurement of information quality and the combination of such measurements for information integration. Our approach is based on a value model that incorporates both extensional value (coverage) and intensional value (density) of information. For both aspects we provide merge functions for adequately scoring integrated results. Also, we combine the two criteria to an overall completeness criterion that formalizes the intuitive notion of completeness of query results. This completeness measure is a valuable tool to assess source size and to predict result sizes of queries in integrated information systems. We propose this measure as an important step towards the usage of information quality for source selection, query planning, query optimization, and quality feedback to users.Peer Reviewe
High frequency, cell type-specific visualization of fluorescent-tagged genomic sites in interphase and mitotic cells of living Arabidopsis plants
<p>Abstract</p> <p>Background</p> <p>Interphase chromosome organization and dynamics can be studied in living cells using fluorescent tagging techniques that exploit bacterial operator/repressor systems and auto-fluorescent proteins. A nuclear-localized Repressor Protein-Fluorescent Protein (RP-FP) fusion protein binds to operator repeats integrated as transgene arrays at defined locations in the genome. Under a fluorescence microscope, the tagged sites appear as bright fluorescent dots in living cells. This technique has been used successfully in plants, but is often hampered by low expression of genes encoding RP-FP fusion proteins, perhaps owing to one or more gene silencing mechanisms that are prevalent in plant cells.</p> <p>Results</p> <p>We used two approaches to overcome this problem. First, we tested mutations in four factors involved in different types of gene silencing and/or epigenetic modifications for their effects on nuclear fluorescence. Only mutations in DDM1, a chromatin remodelling ATPase involved in repeat-induced heterochromatin formation and DNA methylation, released silencing of the RP-FP fusion protein. This result suggested that the operator repeats can trigger silencing of the adjacent gene encoding the RP-FP fusion protein. In the second approach, we transformed the tagged lines with a second T-DNA encoding the RP-FP fusion protein but lacking operator repeats. This strategy avoided operator repeat-induced gene silencing and increased the number of interphase nuclei displaying fluorescent dots. In a further extension of the technique, we show that green fluorescent-tagged sites can be visualized on moving mitotic chromosomes stained with red fluorescent-labelled histone H2B.</p> <p>Conclusions</p> <p>The results illustrate the propensity of operator repeat arrays to form heterochromatin that can silence the neighbouring gene encoding the RP-FP fusion protein. Supplying the RP-FP fusion protein in <it>trans </it>from a second T-DNA largely alleviates this problem. Depending on the promoter used to drive expression of the RP-FP fusion protein gene, the fluorescent tagged sites can be visualized at high frequency in different cell types. The ability to observe fluorescent dots on both interphase and mitotic chromosomes allows tagged sites to be tracked throughout the cell cycle. These improvements enhance the versatility of the fluorescent tagging technique for future studies of chromosome arrangement and dynamics in living plants.</p
Impact of a Major Inflow Event on the Composition and Distribution of Bacterioplankton Communities in the Baltic Sea
Major Baltic inflow (MBI) events carry highly saline water from the North Sea to
the central Baltic Sea and thereby affect both its environmental conditions and its
biota. While bacterioplankton communities in the Baltic Sea are strongly structured by
salinity, how MBIs impact the composition and distribution of bacteria is unknown.
The exceptional MBI in 2014, which brought saline and oxygenated water into the
basins of the central Baltic Sea, enabled the linkage of microbiological investigations
to hydrographic and modeling studies of this MBI. Using sequence data of 16S
ribosomal RNA (rRNA) and 16S rRNA genes (rDNA), we analyzed bacterioplankton
community composition in the inflowing water and in the uplifted former bottomwater at stations reached by the MBI. Bacterial diversity data were compared with
respective data obtained from previous, non-inflow conditions. Changes in bacterial
community composition following the 2014 MBI were mainly apparent at the genus level.
A number of specific taxa were enriched in the inflowing water, with large changes in the
rRNA/rDNA ratios indicating the different activity levels between of the water masses.
The relative similarity of the bacterial communities in the inflowing and uplifted waters as
well as the results from an inflow-simulating numerical model showed that the inflowing
water did not originate directly from the North Sea but mostly from adjacent areas in
the Baltic Sea. This suggested that the inflow event led to a series of shifts in Baltic Sea
water masses among the Baltic Sea basins and a gradual mixing of the water bodies.
Dramatic changes in the bacterial community composition occurred when the bottomwater inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the
formerly anoxic bacterial community, dominated by Epsilonproteobacteria. Our study of
the impact of MBIs on bacterioplankton communities therefore highlights two relevant
underlying mechanisms that impact the distribution and possibly also the activities of
planktonic bacteria in the Baltic Sea: (1) the successive dilution of inflowing North Sea
water with ambient waters and (2) the uplifting of former bottom-water communities to
higher water strata.This work was funded by the Deutsche Forschungsgemeinschaft (DFG) (projects JU367/15-1, JU367/16-1 to KJ and LA1466/8- 1 to ML). DH was supported by the European Regional Development Fund and the Estonian Research Council Mobilitas Plus Top Researcher grant âMOBTT24.â UG was supported by the BMBF project âHydrodynamic observations and simulations of munition in the sea,â a subproject of the collaborative project âEnvironmental monitoring for the delaboration of munitions in the seaâ (Grant No. #03F0747C).This work was funded by the Deutsche Forschungsgemeinschaft
(DFG) (projects JU367/15-1, JU367/16-1 to KJ and LA1466/8-
1 to ML). DH was supported by the European Regional Development Fund and the Estonian Research Council Mobilitas
Plus Top Researcher grant âMOBTT24.â UG was supported by
the BMBF project âHydrodynamic observations and simulations
of munition in the sea,â a subproject of the collaborative project
âEnvironmental monitoring for the delaboration of munitions in
the seaâ (Grant No. #03F0747C)
AGO6 Functions in RNA-Mediated Transcriptional Gene Silencing in Shoot and Root Meristems in Arabidopsis thaliana
RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points
Distinct and concurrent pathways of Pol II-and Pol IV- dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana
SUMMARY Short interfering RNAs (siRNAs) homologous to transcriptional regulatory regions can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of target genes. In our system, siRNAs are produced by transcribing an inverted DNA repeat (IR) of enhancer sequences, yielding a hairpin RNA that is processed by several Dicer activities into siRNAs of 21-24 nt. Primarily 24-nt siRNAs trigger RdDM of the target enhancer in trans and TGS of a downstream GFP reporter gene. We analyzed siRNA accumulation from two different structural forms of a trans-silencer locus in which tandem repeats are embedded in the enhancer IR and distinguished distinct RNA polymerase II (Pol II)-and Pol IV-dependent pathways of siRNA biogenesis. At the original silencer locus, Pol-II transcription of the IR from a 35S promoter produces a hairpin RNA that is diced into abundant siRNAs of 21-24 nt. A silencer variant lacking the 35S promoter revealed a normally masked Pol IV-dependent pathway that produces low levels of 24-nt siRNAs from the tandem repeats. Both pathways operate concurrently at the original silencer locus. siRNAs accrue only from specific regions of the enhancer and embedded tandem repeat. Analysis of these sequences and endogenous tandem repeats producing siRNAs revealed the preferential accumulation of siRNAs at GC-rich regions containing methylated CG dinucleotides. In addition to supporting a correlation between base composition, DNA methylation and siRNA accumulation, our results highlight the complexity of siRNA biogenesis at repetitive loci and show that Pol II and Pol IV use different promoters to transcribe the same template
Peptide microarray based analysis of antibody responses to SARS-CoV-2 identifies unique epitopes with potential for diagnostic test development
Humoral immunity to the Severe Adult Respiratory Syndrome (SARS) Coronavirus (CoV)â2 is not fully understood yet but is a crucial factor of immune protection. The possibility of antibody crossâreactivity between SARSâCoVâ2 and other human coronaviruses (HCoVs) would have important implications for immune protection but also for the development of specific diagnostic ELISA tests. Using peptide microarrays, n = 24 patient samples and n = 12 control samples were screened for antibodies against the entire SARSâCoVâ2 proteome as well as the Spike (S), Nucleocapsid (N), VME1 (V), R1ab, and Protein 3a (AP3A) of the HCoV strains SARS, MERS, OC43 and 229E. While widespread crossâreactivity was revealed across several immunodominant regions of S and N, IgG binding to several SARSâCoVâ2âderived peptides provided statistically significant discrimination between COVIDâ19 patients and controls. Selected target peptides may serve as capture antigens for future, highly COVIDâ19âspecific diagnostic antibody tests
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