Global Egr1-miRNAs Binding Analysis in PMA-Induced K562 Cells Using ChIP-Seq

Although much is known about microRNAs' regulation in gene expression and their contributions in cell fate, to date, globally lineage-(cell-) specific identification of the binding events between a transcription factor and its targeting microRNA genes is still waiting for elucidation. In this paper, we performed a ChIP-Seq experiment to find the targeting microRNA genes of a transcription factor, Egr1, in human erythroleukemia cell line K562. We found Egr1 binding sites near the promoters of 124 distinct microRNA genes, accounting for about 42% of the miRNAs which have high-confidence predicted promoters (294). We also found EGR1 bind to another 63 pre-miRNAs. We chose 12 of the 187 microRNAs with Egr1 binding sites to perform ChIP-PCR assays and the positive binding signal from ChIP-PCR confirmed the ChIP-Seq results. Our experiments provide the first global binding profile between Egr1 and its targeting microRNA genes in PMA-treated K562 cells, which may facilitate the understanding of pathways controlling microRNA biology in this specific cell line

On the Suitability of Estelle for Multimedia Systems

Formal Description Techniques have been widely used for the specification of traditional networked applications. They have not been applied to the specification of new applications such as multimedia systems yet. In this paper, we examine the FDT Estelle with respect to its suitability for multimedia system specification and automatic derivation of efficient implementations. We show that it is possible to specify certain aspects of multimedia systems, but that Estelle is not sufficient for others. The derived implementations often perform badly. We show the reasons and propose to use a slightly modified Estelle syntax and semantics to solve the problems. The implemented solution was tested successfully

Implementing water protection policy at farm level in the European Union: lessons from the N-Toolbox case studies

In 2008 the European Commission released a call for proposals under the workprogramme topic: novel approaches for reducing nitrogen losses. The objective of the programme was to improve uptake of the Nitrates Directive at the farm level. The consortium (Newcastle University, Louis Bolk Institute, Technical University of Madrid, and Aarhus University) responded to the call by developing a project that combined a review of the state of the art in technologies to reduce losses of N to water, with the upgrading of a user-friendly software package for simulating field-scale N dynamics, and the testing of strategies with farmers. N-Toolbox will lay the foundations for improved implementation of water protection policy at the farm level throughout the EU. This document is a short summary of key findings and experiences from the on-farm case study component of the project in Spain, United Kingdom, The Netherlands and Denmark

Biosafety education relevant to genetically engineered crops for academic and non-academic stakeholders in East Africa

Development and deployment of genetically engineered crops requires effective environmental and food safety assessment capacity. In-country expertise is needed to make locally appropriate decisions. In April 2007, biosafety and biotechnology scientists, regulators, educators, and communicators from Kenya, Tanzania, and Uganda, met to examine the status and needs of biosafety training and educational programs in East Africa. Workshop participants emphasized the importance of developing biosafety capacity within their countries and regionally. Key recommendations included identification of key biosafety curricular components for university students; collaboration among institutions and countries; development of informational materials for non-academic stakeholders and media; and organization of study tours for decision makers. It was emphasized that biosafety knowledge is important for all aspects of environmental health, food safety, and human and animal hygiene. Thus, development of biosafety expertise, policies and procedures can be a stepping stone to facilitate improved biosafety for all aspects of society and the environment

Strategies for GHG mitigation in Mediterranean cropping systems. A review

In this review we aimed to synthetize and analyze the most promising GHGs mitigation strategies for Mediterranean cropping systems. A description of most relevant measures, based on the best crop choice and management by farmers (i.e., agronomical practices), was firstly carried out. Many of these measures can be also efficient in other climatic regions, but here we provide particular results and discussion of their efficiencies for Mediterranean cropping systems. An integrated assessment of management practices on mitigating each component of the global warming potential (N2O and CH4 emissions and C sequestration) of production systems considering potential side-effects of their implementation allowed us to propose the best strategies to abate GHG emissions, while sustaining crop yields and mitigating other sources of environmental pollution (e.g. nitrate leaching and ammonia volatilization)

Strategies for greenhouse gas emissions mitigation in Mediterranean agriculture: A review

[EN] An integrated assessment of the potential of different management practices for mitigating specific components of the total GHG budget (N2O and CH4 emissions and C sequestration) of Mediterranean agrosystems was performed in this study. Their suitability regarding both yield and environmental (e.g. nitrate leaching and ammonia volatilization) sustainability, and regional barriers and opportunities for their implementation were also considered. Based on its results best strategies to abate GHG emissions in Mediterranean agro-systems were proposed. Adjusting N fertilization to crop needs in both irrigated and rain-fed systems could reduce N2O emissions up to 50% compared with a non-adjusted practice. Substitution of N synthetic fertilizers by solid manure can be also implemented in those systems, and may abate N2O emissions by about 20% under Mediterranean conditions, with additional indirect benefits associated to energy savings and positive effects in crop yields. The use of urease and nitrification inhibitors enhances N use efficiency of the cropping systems and may mitigate N2O emissions up to 80% and 50%, respectively. The type of irrigation may also have a great mitigation potential in the Mediterranean region. Drip-irrigated systems have on average 80% lower N2O emissions than sprinkler systems and drip-irrigation combined with optimized fertilization showed a reduction in direct N2O emissions up to 50%. Methane fluxes have a relatively small contribution to the total GHG budget of Mediterranean crops, which can mostly be controlled by careful management of the water table and organic inputs in paddies. Reduced soil tillage, improved management of crop residues and agro-industry by-products, and cover cropping in orchards, are the most suitable interventions to enhance organic C stocks in Mediterranean agricultural soils. The adoption of the proposed agricultural practices will require farmers training. The global analysis of life cycle emissions associated to irrigation type (drip, sprinkle and furrow) and N fertilization rate (100 and 300 kg N ha(-1) yr(-1)) revealed that these factors may outweigh the reduction in GHG emissions beyond the plot scale. The analysis of the impact of some structural changes on top-down mitigation of GHG emissions revealed that 3-15% of N2O emissions could be suppressed by avoiding food waste at the end-consumer level. A 40% reduction in meat and dairy consumption could reduce GHG emissions by 20-30%. Reintroducing the Mediterranean diet (i.e. similar to 35% intake of animal protein) would therefore result in a significant decrease of GHG emissions from agricultural production systems under Mediterranean conditions. (C) 2016 Elsevier B.V. All rights reserved.The authors would like to thank the Spanish National R+D+i Plan (AGL2012-37815-C05-01, AGL2012-37815-C05-04) and very specifically the workshop held in December 2016 in Butron (Bizkaia) to synthesize the most promising measures to reduce N2O emissions from Spanish agricultural soils. BC3 is sponsored by the Basque Government. M. L. Cayuela thanks Fundacion Seneca for financing the project 19281/PI/14.Sanz-Cobeña, A.; Lassaletta, L.; Aguilera, E.; Del Prado, A.; Garnier, J.; Billen, G.; Iglesias, A.... (2017). Strategies for greenhouse gas emissions mitigation in Mediterranean agriculture: A review. Agriculture Ecosystems & Environment. 238:5-24. https://doi.org/10.1016/j.agee.2016.09.038S52423

Avalanche behavior in yield stress fluids

We show that, above a critical stress, typical yield stress fluids (gels and clay suspensions) and soft glassy materials (colloidal glasses) start flowing abruptly and subsequently accelerate, leading to avalanches that are remarkably similar to those of granular materials. Rheometrical tests reveal that this is associated with a bifurcation in rheological behavior: for small stresses, the viscosity increases in time; the material eventually stops flowing. For slightly larger stresses the viscosity decreases continuously in time; the flow accelerates. Thus the viscosity jumps discontinuously to infinity at the critical stress. We propose a simple physical model capable of reproducing these effects.Philippe Coussot, Q. D. Nguyen, H.T. Huynh, and Daniel Bon