ALBERT

Description: Aggressive tax planning has become a sustainability problem, as governments have to cope with less tax revenue, which is crucial for investments in sustainable development goals. The OECD and the EU authorities have taken several initiatives against aggressive tax planning, such as the Action Plan against BEPS. However, these initiatives lack effectiveness, and aggressive tax planning is still omnipresent. We analyze the fight against aggressive corporate tax planning from a Real Option Theory perspective, in order to find an explanation for the difficult shift of companies’ aggressive tax planning strategies to more sustainable tax behavior. The Real Option Theory shows that, as long as the option to ‘delay’ the investment in sustainable tax behavior has too much value because the benefits of such investment are uncertain, companies will wait. Based on this new understanding, we suggest additional public policy interventions against aggressive tax planning. These interventions aim directly at reducing this real option value (of waiting).

Description: Background: Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments. Results: The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads. Conclusions: We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies.

Description: Article The protein factors that bind to regulatory regions in the genome have not been systematically mapped. Here the authors performed chromatin immunoprecipitations for histone modifications associated with promoters, enhancers or heterochromatin in mouse embryonic stem cells and assigned a genome location to many factors important for pluripotency. Nature Communications doi: 10.1038/ncomms8155 Authors: Erik Engelen, Johannes H. Brandsma, Maaike J. Moen, Luca Signorile, Dick H. W. Dekkers, Jeroen Demmers, Christel E. M. Kockx, Zehila Ozgür, Wilfred F. J. van IJcken, Debbie L. C. van den Berg, Raymond A. Poot

Description: Background: Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various rRNA removal and cDNA synthesis methods have been applied in published microbial metatranscriptomic studies, making comparisons arduous. Whereas efficiency and biases introduced by rRNA removal methods have been relatively well explored, the impact of cDNA synthesis and library preparation on transcript abundance remains poorly characterized. The evaluation of potential biases introduced at this step is challenging for metatranscriptomic samples, where data analyses are complex, for example because of the lack of reference genomes. Results: Herein, we tested four cDNA synthesis and Illumina library preparation protocols on a simplified mixture of total RNA extracted from four bacterial species. In parallel, RNA from each microbe was tested individually. cDNA synthesis was performed on rRNA depleted samples using the TruSeq Stranded Total RNA Library Preparation, the SMARTer Stranded RNA-Seq, or the Ovation RNA-Seq V2 System. A fourth experiment was made directly from total RNA using the Encore Complete Prokaryotic RNA-Seq. The obtained sequencing data were analyzed for: library complexity and reproducibility; rRNA removal efficiency and bias; the number of genes detected; coverage uniformity; and the impact of protocols on expression biases. Significant variations, especially in organism representation and gene expression patterns, were observed among the four methods. TruSeq generally performed best, but is limited by its requirement of hundreds of nanograms of total RNA. The SMARTer method appears the best solution for smaller amounts of input RNA. For very low amounts of RNA, the Ovation System provides the only option; however, the observed biases emphasized its limitations for quantitative analyses. Conclusions: cDNA and library preparation methods may affect the outcome and interpretation of metatranscriptomic data. The most appropriate method should be chosen based on the available quantity of input RNA and the quantitative or non-quantitative objectives of the study. When low amounts of RNA are available, as in most metatranscriptomic studies, the SMARTer method seems to be the best compromise to obtain reliable results. This study emphasized the difficulty in comparing metatranscriptomic studies performed using different methods.

Description: Sustainability, Vol. 10, Pages 2133: Does Access Trump Ownership? Exploring Consumer Acceptance of Access-Based Consumption in the Case of Smartphones Sustainability doi: 10.3390/su10072133 Authors: Flora Poppelaars Conny Bakker Jo van Engelen Value creation in a circular economy is based on products being returned after use. In the case of smartphones, most are never returned and tend to be kept in drawers. Smartphone access services (e.g., leasing or upgrade) have been experimented with in the Netherlands but have been largely unsuccessful. This study explores the reasons why consumers rejected these access-based smartphone services and is one of the very few to address this topic. The findings are compared with the case of car access services, which are socially better accepted, to identify potential areas for improvement. The qualitative study consists of in-depth interviews with consumers (n = 18) who either adopted and used a smartphone or car access service, or had considered a new smartphone or car but did not choose access-based consumption. The findings of this small-scale study suggest that the main reasons for the rejection of smartphone access services are a lack of awareness, misunderstanding of terms and conditions, and unsatisfactory compensation for their sacrifice of not owning. Smartphone access providers could thus clearly communicate customers’ rights and responsibilities, offer an excellent service experience (especially during repair) by taking over the burdens of ownership, and stimulate the societal logic shift from ownership to access.

Description: Hierarchical control of enzymatic actuators using DNA-based switchable memories Nature Communications, Published online: 24 October 2017; doi:10.1038/s41467-017-01127-w Naturally evolved regulatory circuits have hierarchical layers of signal generation and processing. Here, the authors emulate these networks using feedback-controlled DNA circuits that convert upstream signaling to downstream enzyme activity in a switchable memories circuit.

Description: High-coherence electron bunches produced by femtosecond photoionization Nature Communications 4, 1693 (2013). doi:10.1038/ncomms2700 Authors: W. J. Engelen, M. A. van der Heijden, D. J. Bakker, E. J. D. Vredenbregt & O. J. Luiten

Description: Millions of people worldwide die prematurely or suffer from severe health ailments due to cooking equipment that causes unhealthy doses of (household) air pollution. Many attempts to address this have fallen short because technology was not improved sufficiently or the way it was introduced constituted an ill fit with the broader “cooking eco-system”. In terms of technology, (biomass) gasifier stoves look promising on all three sustainability dimensions (people, planet, profit) but have not been adopted on a substantial scale across cultures and regions either. We therefore used a design approach that takes multiple contexts (target groups) into account and compared the performance of a gasifier stove that was developed following this multi-context approach with four previous gasifier versions. With the comparative assessment using criteria well beyond mere technological performance we found that it performed better than these versions as well as than what could be expected based on historical learning, while providing additional systemic advantages. These results encourage verification of the value of the multi-context approach in more settings while providing clues for refinement of the assessment method.

Description: EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes Nature Communications, Published online: 5 April 2017; doi:10.1038/ncomms14806 In Drosophila , ecdysone-regulated genes are bound by a heterodimer of ecdysone receptor (EcR) and Ultraspiracle. Here, the authors provide evidence of a non-canonical complex containing EcR and the nucleosome remodeller dMi-2 that limits transcription of ecdysone-regulated genes.

Description: This paper explicitly incorporated the impact that realized investments in new transportation infrastructure have on adoption speed in a real option framework for taking sustainable investment decisions under uncertainty and analyzed the consequences of this dependence for optimal business investment strategies. We used a modified Generalized Bass Model to shape the adoption diffusion process and incorporate this approach into an N-fold compound real option framework. We applied the combined model to the case study of the introduction of hydrogen fuel stations for hydrogen cars in the Netherlands. We performed a scenario analysis for six different transportation infrastructure investment strategies combined with four different parameterizations. The results show the risk of ignoring the potential interaction between the adoption process and the speed with which the required transportation infrastructure will become available. This may lead to suboptimal decisions with respect to the optimal timing of corporate investment spending, as well as with respect to the assessment of the overall feasibility of the project.