Effects of low-frequency noise and temperature on copepod and amphipod performance

Offshore wind farms (OWF) are bound to increase as a mitigation strategy to reduce the emission of greenhouse gases, it is crucial to address all of their potential impacts on key ecosystem components in detail. Especially, the chronic effect of noise created during OWF turbine operations (duration 20-25 years) must be understood. As sensitive receptors cover the whole body of crustaceans to detect their surroundings, those low frequency noises may disrupt basic ecological (prey detection and predator avoidance) and physiological (metabolism) functions. Here we present an investigation designed to understand the joint effect of noise and increased temperature on copepod. The pelagic copepod Acartia tonsa is commonly used as a proxy for a range of fundamental processes that relate to marine planktonic crustaceans. Given that higher temperatures increase metabolic demands, the experiment was conducted at three different temperature levels (18, 21, 24°C) combined with silent and noise treatments. We assessed the combined effects on energetic balance, and oxidative stress indicators. The outputs of the project will provide important information on the potential impact of low-frequency noise on marine invertebrate key organisms with implications for secondary production and ecosystem functioning

Characterization and differentiation of sublittoral sandbanks in the southeastern North Sea

Marine sublittoral sandbanks are essential offshore feeding grounds for larger crustaceans, fish and seabirds. In the southern North Sea, sandbanks are characterized by considerable natural sediment dynamics and are subject to chronic bottom trawling. However, except for the Dogger Bank, sandbanks in the southeastern North Sea have been only poorly investigated until now. We used an extensive, multi-annual dataset covering ongoing national monitoring programmes, environmental impact assessments, and basic research studies to analyse benthic communities on sublittoral sandbanks, evaluating their ecological value against the backdrop of similar seafloor habitats in this region. The analysis revealed complex spatial structuring of sandy seafloor habitats of the southeastern North Sea. Different infauna clusters were identified and could be specified by their composition of characteristic species. The sandbanks shared common structural features in their infauna community composition although they were not necessarily characterized by particularly high biodiversity compared to other sandy habitats. A close association of one of the main bioturbators in the southern North Sea, the sea urchin Echinocardium cordatum, with sandbanks was detected, which may promote the sediment-bound biogeochemical activity in this particular seafloor habitat. This would corroborate the status of sandbanks as sites of high ecological value calling for consideration in marine conservation

Individual epigenetic status of the pathogenic D4Z4 macrosatellite correlates with disease in facioscapulohumeral muscular dystrophy

BACKGROUND: Both forms of facioscapulohumeral muscular dystrophy (FSHD) are associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite. Chromatin changes due to large deletions of heterochromatin (FSHD1) or mutations in chromatin regulatory proteins (FSHD2) lead to relaxation of epigenetic repression and increased expression of the deleterious double homeobox 4 (DUX4) gene encoded within the distal D4Z4 repeat. However, many individuals with the genetic requirements for FSHD remain asymptomatic throughout their lives. Here we investigated family cohorts of FSHD1 individuals who were either affected (manifesting) or without any discernible weakness (nonmanifesting/asymptomatic) and their unaffected family members to determine if individual epigenetic status and stability of repression at the contracted 4q35 D4Z4 array in myocytes correlates with FSHD disease. RESULTS: Family cohorts were analyzed for DNA methylation on the distal pathogenic 4q35 D4Z4 repeat on permissive A-type subtelomeres. We found DNA hypomethylation in FSHD1-affected subjects, hypermethylation in healthy controls, and distinctly intermediate levels of methylation in nonmanifesting subjects. We next tested if these differences in DNA methylation had functional relevance by assaying DUX4-fl expression and the stability of epigenetic repression of DUX4-fl in myogenic cells. Treatment with drugs that alter epigenetic status revealed that healthy cells were refractory to treatment, maintaining stable repression of DUX4, while FSHD1-affected cells were highly responsive to treatment and thus epigenetically poised to express DUX4. Myocytes from nonmanifesting subjects had significantly higher levels of DNA methylation and were more resistant to DUX4 activation in response to epigenetic drug treatment than cells from FSHD1-affected first-degree relatives containing the same contraction, indicating that the epigenetic status of the contracted D4Z4 array is reflective of disease. CONCLUSIONS: The epigenetic status of the distal 4qA D4Z4 repeat correlates with FSHD disease; FSHD-affected subjects have hypomethylation, healthy unaffected subjects have hypermethylation, and nonmanifesting subjects have characteristically intermediate methylation. Thus, analysis of DNA methylation at the distal D4Z4 repeat could be used as a diagnostic indicator of developing clinical FSHD. In addition, the stability of epigenetic repression upstream of DUX4 expression is a key regulator of disease and a viable therapeutic target

Basic Hallmarks of Urothelial Cancer Unleashed in Primary Uroepithelium by Interference with the Epigenetic Master Regulator ODC1

Urothelial carcinoma (UC) is a common disease causing significant morbidity and mortality as well as considerable costs for health systems. Extensive aberrant methylation of DNA is broadly documented in early UC, contributing to genetic instability, altered gene expression and tumor progression. However the triggers initiating aberrant methylation are unknown. Recently we discovered that several genes encoding key enzymes of methyl group and polyamine metabolism, including Ornithine Decarboxylase 1 (ODC1), are affected by DNA methylation in early stage UC. In this study, we investigated the hypothesis that these epigenetic alterations act in a feed-forward fashion to promote aberrant DNA methylation in UC. We demonstrate that siRNA-mediated knockdown of ODC1 expression elicits genome-wide LINE-1 demethylation, induction of LINE-1 transcripts and double-strand DNA breaks and decreases viability in primary cultured uroepithelial cells. Similarly, following siRNA-mediated knockdown of ODC1, UC cells undergo double-strand DNA breaks and apoptosis. Collectively, our findings provide evidence that ODC1 gene hypermethylation could be a starting point for the onset of genome-wide epigenetic aberrations in urothelial carcinogenesis. Furthermore, LINE-1 induction enabled by ODC1 interference provides a new experimental model to study mechanisms and consequences of LINE-1 activation in the etiology and progression of UC as well as presumably other cancers

CRITTERBASE, a science-driven data warehouse for marine biota

Data on marine biota exist in many formats and sources, such as published literature, data repositories, and unpublished material. Due to this heterogeneity, information is difficult to find, access and combine, severely impeding its reuse for further scientific analysis and its long-term availability for future generations. To address this challenge, we present CRITTERBASE, a publicly accessible data warehouse and interactive portal that currently hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data for 18,644 samples and 3,664 benthic taxa (2,824 of which at species level). These samples were collected by grabs, underwater imaging or trawls in Arctic, North Sea and Antarctic regions between the years 1800 and 2014. Data were collated from literature, unpublished data, own research and online repositories. All metadata and links to primary sources are included. We envision CRITTERBASE becoming a valuable and continuously expanding tool for a wide range of usages, such as studies of spatio-temporal biodiversity patterns, impacts and risks of climate change or the evidence-based design of marine protection policies

Characterization of Fluorescent Eye Markers for Mammalian Transgenic Studies

Genotyping mice by DNA based methods is both laborious and costly. As an alternative, we systematically examined fluorescent proteins expressed in the lens as transgenic markers for mice. A set of eye markers has been selected such that double and triple transgenic animals can be visually identified and that fluorescence intensity in the eyes can be used to distinguish heterozygous from homozygous mice. Taken together, these eye markers dramatically reduce the time and cost of genotyping transgenics and empower analysis of genetic interaction

Analysis of Myogenic and Candidate Disease Biomarkers in FSHD Muscle Cells

The UMMS Wellstone Program is a foundation and NIH-funded cooperative research center focusing on identifying biomarkers for facioscapulohumeral muscular dystrophy (FSHD) to gain insight into the molecular pathology of the disease and to develop potential therapies. FSHD is characterized by progressive wasting of skeletal muscles, with weakness often initiating in facial muscles and muscles supporting the scapula and upper arms. While the genetics associated with FSHD are complex, the major form of the disease, FSHD1, is linked to contraction of the D4Z4 repeat region located at chromosome 4q. Recently, a transcript encoded at the distal end of the repeat region, Dux4-fl, normally expressed in embryonic stem cells and germ cells, was also detected in differentiated muscle cells and biopsies from FSHD subjects, giving rise to the hypothesis that DUX4-FL function contributes to muscle weakness. We established a repository of high quality, well-characterized primary and immortalized muscle cell strains from FSHD and control subjects in affected families to provide biomaterials for cell and molecular studies to the FSHD research community. qPCR and immunostaining analyses demonstrate similar growth and differentiation characteristics in cells from FSHD and control subjects within families. We detected Dux4-fl transcript and protein in FSHD cells as recently described; interestingly, we also detected Dux4-fl in muscle cells from a subset of control individuals, suggesting that any Dux4-fl-mediated myopathy would require additional modifying elements. Microarray analysis of FSHD and control muscle cells demonstrated that several genes were upregulated in FSHD cells, including genes that were concurrently identified as downstream targets of Dux4-fl and as candidate FSHD disease genes. Future studies will further characterize the RNA and protein expression of candidate disease genes in cells from FSHD and control subjects, including nonmanifesting subjects with the D4Z4 lesion but no muscle weakness, and utilizing whole transcriptome sequencing (RNAseq) to identify additional candidates

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13