The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G + C and the dinucleotide CpG. CGIs often include transcription initiation sites and display ‘active’ histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a ‘bivalent’ chromatin state bearing simultaneous ‘active’ and ‘inactive’ chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G + C-rich DNA. A high CpG density alone is not sufficient for this effect, as A + T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G + C-richness are required for induction of signature chromatin structures at CGIs.DOI: http://dx.doi.org/10.7554/eLife.03397.001

Key message The QTL Fhb1 was successfully introgressed and validated in three durum wheat populations. The novel germplasm and the QTL detected will support improvement of Fusarium resistance in durum wheat. AbstractDurum wheat (Triticum durum Desf.) is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is hampered by limited genetic variation within this species. To date, resistant sources are mainly available in a few wild relative tetraploid wheat accessions. In this study, the effect of the well-known hexaploid wheat (Triticum aestivum L.) quantitative trait locus (QTL) Fhb1 was assessed for the first time in durum wheat. Three F7-RIL mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, which carries an Fhb1 introgression from Sumai-3, and the European T. durum cultivars Karur, Durobonus and SZD1029K. The RILs were evaluated in field experiments for FHB resistance in three seasons using spray inoculation and genotyped with SSR as well as genotyping-by-sequencing markers. QTL associated with FHB resistance were identified on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS at which the resistant parent DBC-480 contributed the positive alleles. The QTL on 3BS was detected in all three populations centered at the Fhb1 interval. The Rht-B1 locus governing plant height was found to have a strong effect in modulating FHB severity in all populations. The negative effect of the semi-dwarf allele Rht-B1b on FHB resistance was compensated by combining with Fhb1 and additional resistance QTL. The successful deployment of Fhb1 in T. durum was further substantiated by assessing type 2 resistance in one population. The efficient introgression of Fhb1 represents a significant step forward for enhancing FHB resistance in durum wheat.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2785-0) contains supplementary material, which is available to authorized users.

Dendritic cells (DCs) direct CD4+ T cell differentiation into diverse helper (Th) subsets that are required for protection against varied infections. However, the mechanisms used by DCs to promote Th2 responses, which are important both for immunity to helminth infection and in allergic disease, are currently poorly understood. We demonstrate a key role for the protein methyl-CpG-binding domain-2 (Mbd2), which links DNA methylation to repressive chromatin structure, in regulating expression of a range of genes that are associated with optimal DC activation and function. In the absence of Mbd2, DCs display reduced phenotypic activation and a dramatically impaired capacity to initiate Th2 immunity against helminths or allergens. These data identify an epigenetic mechanism that is central to activation of CD4+ T cell responses by DCs, particularly in Th2 settings, and reveal methyl-CpG-binding proteins and the genes under their control as possible therapeutic targets for type-2 inflammation.

A fast track "Hot Start" process was implemented to launch the European Bank for Induced Pluripotent Stem Cells (EBiSC) to provide early release of a range of established control and disease linked human induced pluripotent stem cell (hiPSC) lines. Established practice amongst consortium members was surveyed to arrive at harmonised and publically accessible Standard Operations Procedures (SOPs) for tissue procurement, bio-sample tracking, iPSC expansion, cryopreservation, qualification and distribution to the research community. These were implemented to create a quality managed foundational collection of lines and associated data made available for distribution. Here we report on the successful outcome of this experience and work flow for banking and facilitating access to an otherwise disparate European resource, with lessons to benefit the international research community. ETOC: The report focuses on the EBiSC experience of rapidly establishing an operational capacity to procure, bank and distribute a foundational collection of established hiPSC lines. It validates the feasibility and defines the challenges of harnessing and integrating the capability and productivity of centres across Europe using commonly available resources currently in the field.

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Inter-rows in vineyards are commonly tilled in order to control weeds and/or to conserve water. While impacts of tillage on earthworms are well studied in arable systems, very little is known from vineyards. In an experimental vineyard, the impact of four reduced tillage methods on earthworms was examined: rotary hoeing, rotary harrowing, grubbing and no tillage. According to an erosion prevention programme, tillage was applied every other inter-row only while alternating rows retained vegetated. Earthworms were extracted from the treated inter-rows 10, 36, 162 and 188 days after tillage. Across dates, tillage methods had no effect on overall earthworm densities or biomass. Considering each sampling date separately, earthworm densities were affected only at day 36 after tillage leading to lower densities under rotary hoeing (150.7 ± 42.5 worms/m²) and no tillage (117.3 ± 24.8 worms/m²) than under rotary harrowing (340.0 ± 87.4 worms/m²) and grubbing (242.7 ± 43.9 worms/m²). Time since tillage significantly increased earthworm densities or biomass, and affected soil moisture and temperature. Across sampling dates, earthworm densities correlated positively with soil moisture and negatively with soil temperature; individual earthworm mass increased with increasing time since tillage. It was concluded that reduced tillage in vineyards has little impact on earthworms when applied in spring under dry soil conditions.

Wood is one of the most important sustainable natural resources. Throughout centuries, large cities as well as regions of very high wood demand (for example, areas of salt production and iron processing) had to be supplied with wood for building and burning. One of the largest forests in Austria can be found in the National Park covering the range of mountains called “Limestone Alps.” Within this region, a wide network of dams was set up to transport single logs (“Holztrift”). Due to the dendrochronological dating of the surviving dams, regional chronologies spanning a length of almost 600 years for Norway spruce, Silver fir and European larch were set up. These chronologies serve as the background for dendro-provenancing timber. Dendro-provenancing checks the similarities between samples and different regional chronologies. The highest statistical figures give hints of the origins of the wood. Archival analyses show that many logs were transported to Vienna as rafts. For example, in 1865, more than 1504 rafts arrived in Vienna, all from different origins. The logs were used as building material as well as for burning. Further archival analyses showed that logs from this region were also used for building the roof of the Hofburg Castle in Vienna. Several hundred samples from the roof construction were dendrochronologically dated and used for dendro-provenancing. The origin of the logs was confirmed to be the wider region of the Northern alpine foothills. This meant that rafts from the rivers Alm and Traun as well as from the rivers Steyr and Enns had floated down to Vienna.

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