Fast genomic μChIP-chip from 1,000 cells

A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells

Histone H3 Lysine 27 Methylation Asymmetry on Developmentally-Regulated Promoters Distinguish the First Two Lineages in Mouse Preimplantation Embryos

First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters of signaling and developmentally-regulated genes in the mouse ICM and TE. A genome-wide survey of promoter occupancy by H3K4me3 and H3K27me3 indicates that both compartments harbor promoters enriched in either modification, and promoters co-enriched in trimethylated H3K4 and H3K27 linked to developmental and signaling functions. The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3. Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27. Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation

Exploring methods for predicting multiple pressures on ecosystem recovery: A case study on marine eutrophication and fisheries

AbstractEfforts to attain good environmental status in the marine realm require decisions which cannot be done without knowledge of effects of different management measures. Given the wide diversity of marine ecosystems, multitude of pressures affecting it and the still poor understanding on linkages between those, there are likely no models available to give all the required answers. Hence, several separate approaches can be used in parallel to give support for management measures. We tested three completely different methods – a spatial impact index, a food web model and a Bayesian expert method. We found that a large uncertainty existed regarding the ecosystem response to the management scenarios, and that the three different modelling approaches complemented each other. The models indicated that in order to reach an improved overall state of the ecosystem nutrient reductions are the more effective of the two management variables explored, and that cumulative effects of the management of nutrient inputs and fishing mortality are likely to exist

Absorption Enhancement in Organic-Inorganic Halide Perovskite Films with Embedded Plasmonic Gold Nanoparticles

We report on the numerical analysis of solar absorption enhancement in organic-inorganic halide perovskite films embedding plasmonic gold nanoparticles. The effect of particle size and concentration is analyzed in realistic systems in which random particle location within the perovskite film and the eventual formation of dimers are also taken into account. We find a maximum integrated solar absorption enhancement of ∼10% in perovskite films of 200 nm thickness and ∼6% in 300 nm films, with spheres of radii 60 and 90 nm, respectively, in volume concentrations of around 10% in both cases. We show that the presence of dimers boosts the absorption enhancement up to ∼12% in the thinnest films considered. Absorption reinforcement arises from a double contribution of plasmonic near-field and scattering effects, whose respective weight can be discriminated and evaluated from the simulations.Peer Reviewe

Haut parleur tout aimant guidé sur joint ferrofluide : caractérisation dynamique du guidage

Une étude expérimentale sur le comportement visqueux de ferrofluides, au sein d'une goutte insérée entre deux plans parallèles, en condition de cisaillement oscillatoire et sous champ magnétique homogène et stationnaire, permet d'alimenter un modèle pour les pertes d'un haut-parleur tout aimant guidé sur joint ferrofluide. Ces joints sont localisés dans les zones de fort gradient de champs magnétique. Le modèle de perte, fonction du volume, de la viscosité et de la saturation magnétique du ferrofluide, est alors validé par confrontation avec une expérience

Forage fish interactions: A symposium on creating the tools for ecosystem-based management of marine resources

Forage fish (FF) have a unique position within marine foodwebs and the development of sustainable harvest strategies for FF will be a critical step in advancing and implementing the broader, ecosystem-based management of marine systems. In all, 70 scientists from 16 nations gathered for a symposium on 12–14 November 2012 that was designed to address three key questions regarding the effective management of FF and their ecosystems: (i) how do environmental factors and predator–prey interactions drive the productivity and distribution of FF stocks across ecosystems worldwide, (ii) what are the economic and ecological costs and benefits of different FF management strategies, and (iii) do commonalities exist across ecosystems in terms of the effective management of FF exploitation

Insights from two decades of the Student Conference on Conservation Science

Conservation science is a crisis-oriented discipline focused on reducing human impacts on nature. To explore how the field has changed over the past two decades, we analyzed 3245 applications for oral presentations submitted to the Student Conference on Conservation Science (SCCS) in Cambridge, UK. SCCS has been running every year since 2000, aims for global representation by providing bursaries to early-career conservationists from lower-income countries, and has never had a thematic focus, beyond conservation in the broadest sense. We found that the majority of projects submitted to SCCS were based on primary biological data collected from local scale field studies in the tropics, contrary to established literature which highlights gaps in tropical research. Our results showed a small increase over time in submissions framed around how nature benefits people as well as a small increase in submissions integrating social science. Our findings suggest that students and early-career conservationists could provide pathways to increase availability of data from the tropics and address well-known biases in the published literature towards wealthier countries. We hope this research will motivate efforts to support student projects, ensuring data and results are published and data made publicly available.The project was made possible through funding from: JG: EUs Horizon 2020 Marie Skłodowska-Curie program (No 676108) and VILLUM FONDEN (VKR023371), HA-P; National Council for Scientific and Technological Development (CNPq) (203407/2017-2), TA: The Australian Research Council Future Fellowship (FT180100354), The Grantham Foundation for the Protection of the Environment and The Kenneth Miller Trust, APC: the Natural Environment Research Council (NERC DTP [NE/L002507/1]), LC: Cambridge International Scholarship from the Cambridge Trust, FH: the Newton International Fellowship of the Royal Society, DM: the Australian Government, Endeavor Postgraduate Scholarhip, HM: Branco Weiss Fellowship Administered by the ETH Zürich and Drapers' Company Fellowship, Pembroke College BIS: the Natural Environment Research Council (NERC DTP[NE/L002507/1 and NE/S001395/1]) and the Royal Commission for the Exhibition of 1851 Research Fellowship, HW: Cambridge Trust Cambridge-Australia Poynton Scholarship and Cambridge Department of Zoology J. S. Gardiner Scholarship

Quick-scan on different scenarios relating to the ACFM 2003 advice: biological and economic consequences

In dit rapport worden de resultaten beschreven van een quick-scan die in het najaar van 2003 is uitgevoerd door het Nederlands Instituut voor Visserijonderzoek en het Landbouw Economisch Instituut op verzoek van de Directie Visserij van het ministerie van Landbouw, Natuurbeheer en Voedselveiligheid. Naar aanleiding van de biologische adviezen van ICES in oktober 2003 ten aanzien van het beheer een aantal visbestanden in de Noordzee, heeft het ministerie een lijst van vragen en scenario’s geformuleerd waar zij aanvullende biologische en economische analyses van wilde om de consequenties van verschillende beleidsopties te kunnen wegen

Site-specific chromatin immunoprecipitation: a selective method to individually analyze neighboring transcription factor binding sites in vivo

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) and their binding sites (TFBSs) play a central role in the regulation of gene expression. It is therefore vital to know how the allocation pattern of TFBSs affects the functioning of any particular gene in vivo. A widely used method to analyze TFBSs in vivo is the chromatin immunoprecipitation (ChIP). However, this method in its present state does not enable the individual investigation of densely arranged TFBSs due to the underlying unspecific DNA fragmentation technique. This study describes a site-specific ChIP which aggregates the benefits of both EMSA and in vivo footprinting in only one assay, thereby allowing the individual detection and analysis of single binding motifs.</p> <p>Findings</p> <p>The standard ChIP protocol was modified by replacing the conventional DNA fragmentation, i. e. via sonication or undirected enzymatic digestion (by MNase), through a sequence specific enzymatic digestion step. This alteration enables the specific immunoprecipitation and individual examination of occupied sites, even in a complex system of adjacent binding motifs in vivo. Immunoprecipitated chromatin was analyzed by PCR using two primer sets - one for the specific detection of precipitated TFBSs and one for the validation of completeness of the enzyme digestion step. The method was established exemplary for Sp1 TFBSs within the <it>egfr </it>promoter region. Using this site-specific ChIP, we were able to confirm four previously described Sp1 binding sites within <it>egfr </it>promoter region to be occupied by Sp1 in vivo. Despite the dense arrangement of the Sp1 TFBSs the improved ChIP method was able to individually examine the allocation of all adjacent Sp1 TFBS at once. The broad applicability of this site-specific ChIP could be demonstrated by analyzing these SP1 motifs in both osteosarcoma cells and kidney carcinoma tissue.</p> <p>Conclusions</p> <p>The ChIP technology is a powerful tool for investigating transcription factors in vivo, especially in cancer biology. The established site-specific enzyme digestion enables a reliable and individual detection option for densely arranged binding motifs in vivo not provided by e.g. EMSA or in vivo footprinting. Given the important function of transcription factors in neoplastic mechanism, our method enables a broad diversity of application options for clinical studies.</p

Attributes of climate resilience in fisheries: from theory to practice

In a changing climate, there is an imperative to build coupled social-ecological systems—including fisheries—that can withstand or adapt to climate stressors. Although resilience theory identifies system attributes that supposedly confer resilience, these attributes have rarely been clearly defined, mechanistically explained, nor tested and applied to inform fisheries governance. Here, we develop and apply a comprehensive resilience framework to examine fishery systems across (a) ecological, (b) socio-economic and (c) governance dimensions using five resilience domains: assets, flexibility, organization, learning and agency. We distil and define 38 attributes that confer climate resilience from a coupled literature- and expert-driven approach, describe how they apply to fisheries and provide illustrative examples of resilience attributes in action. Our synthesis highlights that the directionality and mechanism of these attributes depend on the specific context, capacities, and scale of the focal fishery system and associated stressors, and we find evidence of interdependencies among attributes. Overall, however, we find few studies that test resilience attributes in fisheries across all parts of the system, with most examples focussing on the ecological dimension. As such, meaningful quantification of the attributes’ contributions to resilience remains a challenge. Our synthesis and holistic framework represent a starting point for critical application of resilience concepts to fisheries social-ecological systems