Efficient In Vivo Genome Editing Using RNA-Guided Nucleases Nature Biotechnology

Abstract Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems have evolved in bacteria and archaea as a defense mechanism to silence foreign nucleic acids of viruses and plasmids. Recent work has shown that bacterial type II CRISPR systems can be adapted to create guide RNAs (gRNAs) capable of directing site-specific DNA cleavage by the Cas9 nuclease in vitro. Here we show that this system can function in vivo to induce targeted genetic modifications in zebrafish embryos with efficiencies comparable to those obtained using ZFNs and TALENs for the same genes. RNA-guided nucleases robustly enabled genome editing at 9 of 11 different sites tested, including two for which TALENs previously failed to induce alterations. These results demonstrate that programmable CRISPR/Cas systems provide a simple, rapid, and highly scalable method for altering genes in vivo, opening the door to using RNAguided nucleases for genome editing in a wide range of organisms. Bacteria and archaea have evolved an elegant adaptive defense mechanism which uses clustered regularly interspaced short palindromic repeats (CRISPR), together with CRISPRassociated (Cas) proteins, to provide acquired resistance to invading viruses and plasmids 1-3 . The type II CRISPR/Cas system relies on uptake of foreign DNA fragments into CRISPR loci 4 and subsequent transcription and processing of these CRISPR repeatspacer arrays into short CRISPR RNAs (crRNAs) 5 , which in turn anneal to a transactivating crRNA (tracrRNA) and direct sequence-specific silencing of foreign nucleic acid by Cas proteins 5-7

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Cultural Complex for Ankara New City Center

ArchitectureArchitectur

Failure prevention and restoration in power systems

In typical power system operations, failures, e.g., caused by degradation, may result in service interruption and loss of power supply. Furthermore, low-occurrence-probability but high-impact extreme events, e.g., natural disasters and cyber-attacks, may also damage the power grid. This thesis aims to develop innovative strategies for handling these two kinds of failures in power grids. In particular, we develop preventive maintenance strategies, a pre-disaster electrical vehicle charging control strategy, an accurate fault location algorithm, and an unmanned aerial vehicles routing strategy for post-disaster distribution networks....Team DeSchutte

On the powder metallurgy, additive manufacturing and welding of oxide dispersion strengthened Eurofer steel

Oxide dispersion strengthened (ODS) steels are promising candidates for use as structural materials in the next generation fission and fusion reactors. Compared to conventional ferritic or martensitic steels, ODS steels exhibit improved high-temperature creep properties and irradiation resistance. Favourable properties are mainly attributed to the fine grain features and the high number density of nanosized oxide particles in the steel matrix. These nanoparticles can act as pinning sites for dislocations and stable sinks for irradiation introduced defects, leading to significantly enhanced mechanical properties. In order to be employed in nuclear systems with large, complex structures, the fabrication and welding of ODS steels with reproducible and superior properties are inevitable and essential. However, after 10–20 years of studying since the emergence of ODS steels, these issues remain the major bottlenecks limiting further development. This thesis is concerned with ODS Eurofer steel, which is one of the representatives of ODS steels and has been the research focus in terms of promising nuclear materials within the European Union. With the aim to develop suitable and effective methods for the fabrication and welding of ODS Eurofer, the result of this study should help to extend the use of ODS steels in future nuclear applications.Team Marcel Herman

Microstructure Study of Pulsed Laser Beam Welded Oxide Dispersion-Strengthened (ODS) Eurofer Steel

Oxide dispersion-strengthened (ODS) Eurofer steel was laser welded using a short pulse duration and a designed pattern to minimise local heat accumulation. With a laser power of 2500 W and a duration of more than 3 ms, a full penetration can be obtained in a 1 mm thick plate. Material loss was observed in the fusion zone due to metal vaporisation, which can be fully compensated by the use of filler material. The solidified fusion zone consists of an elongated dual phase microstructure with a bimodal grain size distribution. Nano-oxide particles were found to be dispersed in the steel. Electron backscattered diffraction (EBSD) analysis shows that the microstructure of the heat-treated joint is recovered with substantially unaltered grain size and lower misorientations in different regions. The experimental results indicate that joints with fine grains and dispersed nano-oxide particles can be achieved via pulsed laser beam welding using filler material and post heat treatment.Team Marcel Herman

Linear instability of Poiseuille flows with highly non-ideal fluids

The objective of this work is to investigate linear modal and algebraic instability in Poiseuille flows with fluids close to their vapour-liquid critical point. Close to this critical point, the ideal gas assumption does not hold and large non-ideal fluid behaviours occur. As a representative non-ideal fluid, we consider supercritical carbon dioxide (CO 2) at a pressure of 80 bar, which is above its critical pressure of 73.9 bar. The Poiseuille flow is characterized by the Reynolds number (Re = ρ∗ wu∗ rh∗/μ∗ w), the product of the Prandtl (Pr=μ∗ wC∗ pw/κ∗ w) and Eckert numbers (Ec=u∗ 2 r/C∗ pwT∗ w) and the wall temperature that in addition to pressure determine the thermodynamic reference condition. For low Eckert numbers, the flow is essentially isothermal and no difference with the well-known stability behaviour of incompressible flows is observed. However, if the Eckert number increases, the viscous heating causes gradients of thermodynamic and transport properties, and non-ideal gas effects become significant. Three regimes of the laminar base flow can be considered: the subcritical (temperature in the channel is entirely below its pseudo-critical value), transcritical and supercritical temperature regimes. If compared to the linear stability of an ideal gas Poiseuille flow, we show that the base flow is modally more unstable in the subcritical regime, inviscid unstable in the transcritical regime and significantly more stable in the supercritical regime. Following the principle of corresponding states, we expect that qualitatively similar results will be obtained for other fluids at equivalent thermodynamic states. Energy Technolog

Micro-Doppler Period Estimation Based on Concentration Statistics of Ambiguity Function

Radar micro-Doppler (m-D) signature, which reflects the micromotion dynamic and structural characteristics of radar target with micromotion, has received increasing attention. Most of the existing m-D signature-extraction methods operate in the time domain or the time-frequency domain. Different from these methods, in this paper, an m-D period estimation approach that operates in the ambiguity domain is proposed. Although the ambiguity function (AF) has been widely used in the field of radar signal processing, its application for m-D signal is introduced for the first time. It is proved that the AF of m-D signal exhibits periodicity along the lag axis and has the best concentration when the lag equals to multiples of the m-D period. Based on this, three AF concentration statistics are employed to capture the periodicity and to provide the m-D estimate. The most important property of the AF concentration statistics is that they are (or approximately) invariant to polynomial translations with terms not larger than second order even if the signal is Doppler ambiguous. Numeric simulation and real radar experiments are used to validate the effectiveness of the proposed technique. Accepted author manuscriptAtmospheric Remote Sensin

A short-term preventive maintenance scheduling method for distribution networks with distributed generators and batteries

Preventive maintenance is applied in distribution networks to prevent failures by performing maintenance actions on components that are at risk. Distributed generators (DGs) and batteries can be used to support power to nearby loads when they are isolated due to maintenance. In this paper, a novel short-term preventive maintenance method is proposed that explicitly considers the support potential of DGs and batteries as well as uncertainties in the power generated by the DGs. Two major issues are addressed. To deal with the large-scale complexity of the network, a depth-first-search clustering method is used to divide the network into zones. Moreover, a method is proposed to capture the influence of maintenance decisions in the model of the served load from DGs and batteries via generation of topological constraints. Then a stochastic scenario-based mixed-integer non-linear programming problem is formulated to determine the short-term maintenance schedule. We show the effectiveness and efficiency of the proposed approach via a case study based on a modified IEEE-34 bus distribution network, where we also compare a branch-and-bound and a particle swarm optimization solver. The results also show that the supporting potential of DGs and batteries in preventive maintenance scheduling allows a significant reduction of load losses.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Team DeSchutterRailway Engineerin

A bidding mechanism for maintenance of generation units considering inter-ISO power exchange

To ensure the reliability of power systems, the independent system operator (ISO) manages the planning process of the maintenance of generation units for generation companies (GENCOs). This paper focuses on a widely studied two-layer long-term predictive maintenance decision making framework in a deregulated environment. In the first layer the ISO-wide maintenance schedule is optimized for the GENCOs, targeting minimal total maintenance cost and degradation statuses. In the second layer, a bidding mechanism is designed for GENCOs who are not satisfied with the time slots scheduled by the first layer, so that they can bid for their preferred time slots. A novel bidding mechanism for the host ISO (i.e., the ISO that manages the maintenance planning process) is proposed, called interchangeable bidding mechanism for maintenance (IBMM). In this mechanism, the GENCOs of the host ISO can use their bid price to purchase the supportive energy from the GENCOs of the neighbor ISOs. Furthermore, they also can pay a penalty fee for reducing the amount of energy transmitted from the host ISO to the neighbor ISO with respect to what has been stipulated in the long-term inter-ISO power exchange contract. IBMM provides more opportunities for GENCOs of the host ISO to obtain their preferred maintenance time slots. Additionally, the power system reliability can be ensured. IBMM is formulated as a mixed-integer non-linear bidding programming problem. Then, the bidding programming problem is recast into a mixed-integer second-order cone programming (MISOCP) problem that can be solved using Gurobi. In the case study, the IEEE 118-bus network is studied to illustrate the performance of the proposed bidding strategy.Team DeSchutterRailway Engineerin