Packaging signals in single-stranded RNA viruses: nature’s alternative to a purely electrostatic assembly mechanism

The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA–coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology

Best practices for time-resolved serial synchrotron crystallography

With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments

The influence of surface hardness on the fretting wear of steel pairs: its role in debris retention in the contact

The influence of specimen hardness (between 275 kgf mm−2 and 835 kgf mm−2) in an AISI Type O1 steel-on-steel fretting contact was examined. In equal-hardness pairs, a variation in the wear volume of around 20% across the range of hardnesses examined was observed. However, in pairs where the two specimens in the couple had different hardnesses, a critical hardness differential threshold existed, above which the wear was predominantly associated with the harder specimen (with debris embedment on the softer specimen surface). This retention of debris provides protection of that surface from further wear and also results in accelerated wear of the harder counterface due to abrasion by the oxide debris bed which has built up on the opposing specimen

The Detectability of Departures from the Inflationary Consistency Equation

We study the detectability, given CMB polarization maps, of departures from the inflationary consistency equation, r \equiv T/S \simeq -5 n_T, where T and S are the tensor and scalar contributions to the quadrupole variance, respectively. The consistency equation holds if inflation is driven by a slowly-rolling scalar field. Departures can be caused by: 1) higher-order terms in the expansion in slow-roll parameters, 2) quantum loop corrections or 3) multiple fields. Higher-order corrections in the first two slow-roll parameters are undetectably small. Loop corrections are detectable if they are nearly maximal and r \ga 0.1. Large departures (|\Delta n_T| \ga 0.1) can be seen if r \ga 0.001. High angular resolution can be important for detecting non-zero r+5n_T, even when not important for detecting non-zero r.Comment: 7 pages, 4 figures, submitted to PR

Dynamical effects induced by long range activation in a nonequilibrium reaction-diffusion system

We both show experimentally and numerically that the time scales separation introduced by long range activation can induce oscillations and excitability in nonequilibrium reaction-diffusion systems that would otherwise only exhibit bistability. Namely, we show that the Chlorite-Tetrathionate reaction, where autocatalytic species diffuses faster than the substrates, the spatial bistability domain in the nonequilibrium phase diagram is extended with oscillatory and excitability domains. A simple model and a more realistic model qualitatively account for the observed behavior. The latter model provides quantitative agreement with the experiments.Comment: 19 pages + 9 figure

Constraining slow-roll inflation with WMAP and 2dF

We constrain slow-roll inflationary models using the recent WMAP data combined with data from the VSA, CBI, ACBAR and 2dF experiments. We find the slow-roll parameters to be $0 < \epsilon_1 < 0.032$ and $\epsilon_2 + 5.0 \epsilon_1 = 0.036 \pm 0.025$. For inflation models $V \propto \phi^{\alpha}$ we find that $\alpha< 3.9, 4.3$ at the 2$\sigma$ and $3\sigma$ levels, indicating that the $\lambda\phi^4$ model is under very strong pressure from observations. We define a convergence criterion to judge the necessity of introducing further power spectrum parameters such as the spectral index and running of the spectral index. This criterion is typically violated by models with large negative running that fit the data, indicating that the running cannot be reliably measured with present data.Comment: 8 pages RevTeX4 file with six figures incorporate

Synthetic Nitrogen Fertiliser in South Asia: Production, Import, Export, and Use for Crops, South Asia Nitrogen Hub (SANH) Policy Brief

This policy brief is produced by the UKRI GCRF South Asian Nitrogen Hub (SANH). It provides an overview of the patterns and trends in synthetic nitrogen (N) fertiliser use in crop production, import, export and emission in the South Asian Region (SAR) and its member countries; Afghanistan, Bangladesh, Bhutan, Nepal, India, Maldives, Pakistan, and Sri Lanka. In summary, reactive nitrogen (Nr) in fertilisers is essential for meeting global food and animal feed demands, but Nr pollution has become a major environmental issue across all scales. For SAR, inefficient use of synthetic N fertiliser is a key factor contributing to water pollution, air pollution, climate change, biodiversity loss and soil degradation. Further insights are provided on major fertiliser products, as well as in crop production, import and export. These data are essential for informing and promoting sustainable nitrogen management. Evidence based policy is more important than ever. The SANH is supported by UK Research and Innovation (UKRI) through its Global Challenge Research Fund (GCRF) to gather evidence on nitrogen issues to support countries in the South Asian Region (SAR) comprising eight countries (Nepal, Bangladesh, Pakistan, India, Bhutan, Sri Lanka, Afghanistan, and Maldives) to identify solutions and reduce nitrogen waste. SANH is pioneering a UK-SAR research partnership to catalyse transformational change in SAR to tackle the nitrogen challenge, benefi ting the economy, people’s health and the environment. SANH brings together 32 leading research organisations with governments and other partners. This policy brief provides key insights into national fertiliser trends for all eight SAR countries

Synthetic Nitrogen Fertiliser in South Asia: Production, Import, Export, and Use for Crops, South Asia Nitrogen Hub (SANH) Policy Brief

This policy brief is produced by the UKRI GCRF South Asian Nitrogen Hub (SANH). It provides an overview of the patterns and trends in synthetic nitrogen (N) fertiliser use in crop production, import, export and emission in the South Asian Region (SAR) and its member countries; Afghanistan, Bangladesh, Bhutan, Nepal, India, Maldives, Pakistan, and Sri Lanka. In summary, reactive nitrogen (Nr) in fertilisers is essential for meeting global food and animal feed demands, but Nr pollution has become a major environmental issue across all scales. For SAR, inefficient use of synthetic N fertiliser is a key factor contributing to water pollution, air pollution, climate change, biodiversity loss and soil degradation. Further insights are provided on major fertiliser products, as well as in crop production, import and export. These data are essential for informing and promoting sustainable nitrogen management. Evidence based policy is more important than ever. The SANH is supported by UK Research and Innovation (UKRI) through its Global Challenge Research Fund (GCRF) to gather evidence on nitrogen issues to support countries in the South Asian Region (SAR) comprising eight countries (Nepal, Bangladesh, Pakistan, India, Bhutan, Sri Lanka, Afghanistan, and Maldives) to identify solutions and reduce nitrogen waste. SANH is pioneering a UK-SAR research partnership to catalyse transformational change in SAR to tackle the nitrogen challenge, benefi ting the economy, people’s health and the environment. SANH brings together 32 leading research organisations with governments and other partners. This policy brief provides key insights into national fertiliser trends for all eight SAR countries

Visual Analysis of a Cold Rolling Process Using Data-Based Modeling

International Conference on Engineering Applications of Neural Networks (13th. 2012. Coventry Univ, Otaniemi, Finland

Operation of an optoelectronic crossbar switch containing a terabit-per-second free-space optical interconnect

The experimental operation of a terabit-per-second scale optoelectronic connection to a silicon very-large-scale-integrated circuit is described. A demonstrator system, in the form of an optoelectronic crossbar switch, has been constructed as a technology test bed. The assembly and testing of the components making up the system, including a flip-chipped InGaAs-GaAs optical interface chip, are reported. Using optical inputs to the electronic switching chip, single-channel routing of data through the system at the design rate of 250 Mb/s (without internal fan-out) was achieved. With 4000 optical inputs, this corresponds to a potential aggregate data input of a terabit per second into the single 14.6 /spl times/ 15.6 mm CMOS chip. In addition 50-Mb/s data rates were switched utilizing the full internal optical fan-out included in the system to complete the required connectivity. This simultaneous input of data across the chip corresponds to an aggregate data input of 0.2 Tb/s. The experimental system also utilized optical distribution of clock signals across the CMOS chip