siRNA carrying an (E)-vinylphosphonate moiety at the 5' end of the guide strand augments gene silencing by enhanced binding to human Argonaute-2

Efficient gene silencing by RNA interference (RNAi) in vivo requires the recognition and binding of the 5'- phosphate of the guide strand of an siRNA by the Argonaute protein. However, for exogenous siRNAs it is limited by the rapid removal of the 5'- phosphate of the guide strand by metabolic enzymes. Here, we have determined the crystal structure of human Argonaute-2 in complex with the metabolically stable 5'-(E)-vinylphosphonate (5'-E-VP) guide RNA at 2.5-A resolution. The structure demonstrates how the 5' binding site in the Mid domain of human Argonaute-2 is able to adjust the key residues in the 5'-nucleotide binding pocket to compensate for the change introduced by the modified nucleotide. This observation also explains improved binding affinity of the 5'-E-VP -modified siRNA to human Argonaute-2 in-vitro, as well as the enhanced silencing in the context of the trivalent N-acetylgalactosamine (GalNAc)-conjugated siRNA in mice relative to the un-modified siRNA

Esociformes: Esocidae, Pikes, and Umbridae (Mudminnows)

The order Esociformes (Pikes and Mudminnows) comprises two families, Esocidae (Pikes) and Umbridae (Mudminnows). The Pikes are a small Holarctic (Northern Hemisphere) family, that includes large, elongate predators with duckbill-like snouts full of sharp teeth. Popular with sport fishers, the largest Pikes fight fiercely on hook and line. As piscivorous, voracious, ambush predators, the Pikes play an important functional role in the trophic ecology and fish assemblage structure of many aquatic systems, especially in northern lakes. Other esocids, such as the Olympic Mudminnow, Novumbra hubbsi, and Blackfishes, genus Dallia, are interesting because of their tolerance of low dissolved oxygen and pH. The Alaska Blackfish, Dallia pectoralis, and the Northern Pike, Esox lucius, can also withstand the extremely cold conditions of the Arctic and subarctic waters of Canada, Alaska, and Siberia. The name Esocidae is derived from Linnaeus’s (1758) generic name for Pike, Esox, from the Latin word esox meaning Pike, which came originally from the Greek isox or possibly the Gaelic eog, ehawe (salmon) (Boschung & Mayden 2004)

Alternative infill strategies for expensive multi-objective optimisation

This is the author accepted manuscript. The final version is available from ACM via the DOI in this record.Many multi-objective optimisation problems incorporate computationally or financially expensive objective functions. State-of-the-art algorithms therefore construct surrogate model(s) of the parameter space to objective functions mapping to guide the choice of the next solution to expensively evaluate. Starting from an initial set of solutions, an infill criterion — a surrogate-based indicator of quality — is extremised to determine which solution to evaluate next, until the budget of expensive evaluations is exhausted. Many successful infill criteria are dependent on multi-dimensional integration, which may result in infill criteria that are themselves impractically expensive. We propose a computationally cheap infill criterion based on the minimum probability of improvement over the estimated Pareto set. We also present a range of set-based scalarisation methods modelling hypervolume contribution, dominance ratio and distance measures. These permit the use of straightforward expected improvement as a cheap infill criterion. We investigated the performance of these novel strategies on standard multi-objective test problems, and compared them with the popular SMS-EGO and ParEGO methods. Unsurprisingly, our experiments show that the best strategy is problem dependent, but in many cases a cheaper strategy is at least as good as more expensive alternatives.This research was supported by the Engineering and Physical Sciences Research Council [grant number EP/M017915/1]

Stochastic motion of test particle implies that G varies with time

The aim of this letter is to propose a new description to the time varying gravitational constant problem, which naturally implements the Dirac's large numbers hypothesis in a new proposed holographic scenario for the origin of gravity as an entropic force. We survey the effect of the Stochastic motion of the test particle in Verlinde's scenario for gravity\cite{Verlinde}. Firstly we show that we must get the equipartition values for $t\rightarrow\infty$ which leads to the usual Newtonian gravitational constant. Secondly,the stochastic (Brownian) essence of the motion of the test particle, modifies the Newton's 2'nd law. The direct result is that the Newtonian constant has been time dependence in resemblance as \cite{Running}.Comment: Accepted in International Journal of Theoretical Physic

The potential of marginal coastal nursery habitats for the conservation of a culturally important Caribbean marine species

Aim: Identifying the potential of marginal habitats for species conservation is of key importance when their core high-quality habitats are under substantial disturbances and threats. However, there is currently a knowledge gap on how useful marine marginal habitats may be for conserving endangered marine species. Here, we investigate the potential of groundwater-fed coastal areas for the conservation of the queen conch, an economically and culturally important marine gastropod. Location: The inlet of Xel-Ha, typical of groundwater-fed coastal areas widely distributed along the Yucatan Peninsula coast in Mexico and partially protected by a network of marine protected areas. Methods: We tracked 66 queen conchs (Lobatus gigas) using acoustic telemetry over a period of 3.5 years. We investigated for ontogenetic niche shift using a network analysis and by modelling their growth. Results: The queen conchs exhibited the same ontogenetic niche shift required to complete their life cycle in this marginal habitat as they do in offshore core habitats. A total of 33 individuals departed the inlet and migrated from shallow groundwater-affected nursery grounds to deeper marine habitats more suitable for breeding aggregation. Main conclusions: As the broad-scale movement behaviour of queen conch in this inlet is similar to that observed on the overfished core habitats, our findings suggest that groundwater-fed coastal areas should be included in conservation planning for an effective management of this species within a network of marine protected areas

In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation

In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington’s disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find tha

Sodium channel slow inactivation interferes with open channel block

Mutations in the voltage-gated sodium channel Nav1.7 are linked to inherited pain syndromes such as erythromelalgia (IEM) and paroxysmal extreme pain disorder (PEPD). PEPD mutations impair Nav1.7 fast inactivation and increase persistent currents. PEPD mutations also increase resurgent currents, which involve the voltage-dependent release of an open channel blocker. In contrast, IEM mutations, whenever tested, leave resurgent currents unchanged. Accordingly, the IEM deletion mutation L955 (ΔL955) fails to produce resurgent currents despite enhanced persistent currents, which have hitherto been considered a prerequisite for resurgent currents. Additionally, ΔL955 exhibits a prominent enhancement of slow inactivation (SI). We introduced mutations into Nav1.7 and Nav1.6 that either enhance or impair SI in order to investigate their effects on resurgent currents. Our results show that enhanced SI is accompanied by impaired resurgent currents, which suggests that SI may interfere with open-channel block

Slingshot: a PiggyBac based transposon system for tamoxifen-inducible ‘self-inactivating’ insertional mutagenesis

We have developed a self-inactivating PiggyBac transposon system for tamoxifen inducible insertional mutagenesis from a stably integrated chromosomal donor. This system, which we have named ‘Slingshot’, utilizes a transposon carrying elements for both gain- and loss-of-function screens in vitro. We show that the Slingshot transposon can be efficiently mobilized from a range of chromosomal loci with high inducibility and low background generating insertions that are randomly dispersed throughout the genome. Furthermore, we show that once the Slingshot transposon has been mobilized it is not remobilized producing stable clonal integrants in all daughter cells. To illustrate the efficacy of Slingshot as a screening tool we set out to identify mediators of resistance to puromycin and the chemotherapeutic drug vincristine by performing genetrap screens in mouse embryonic stem cells. From these genome-wide screens we identified multiple independent insertions in the multidrug resistance transporter genes Abcb1a/b and Abcg2 conferring resistance to drug treatment. Importantly, we also show that the Slingshot transposon system is functional in other mammalian cell lines such as human HEK293, OVCAR-3 and PE01 cells suggesting that it may be used in a range of cell culture systems. Slingshot represents a flexible and potent system for genome-wide transposon-mediated mutagenesis with many potential applications