Structural and functional characterisation of novel bacterial Toll/Interleukin-1 receptor (TIR)-like proteins.

The extracellular domain of Toll-like receptors (TLRs) recognises highly specific pathogen-associated molecular patterns in innate immunity. This causes molecular rearrangement of the intracellular Toll/Interleukin-1 (TIR) domains of the TLRs allowing recruitment of downstream adaptor proteins via heterotypic TIR-TIR protein interactions. This in turn initiates a signalling cascade leading to proinflammatory immune responses. Recent work has indicated that TIR-like proteins (TLPs)from pathogenic bacteria contain TIR domains and interfere with host TLR signalling. Bacterial TLPs are suggested to bind to the TIR domains of host TLRs and/or adaptor proteins, thereby inhibiting intracellular signalling. This project focuses on characterisation of the TLPs from the highly pathogenic bacteria Yersinia pestis (YpTLP) and Burkholderia pseudomallei (BpTLP). The aim of the project was to produce soluble, pure and stable TLPs of yields suitable for functional and structural studies. Bacterial TLPs were expressed in E. coli. Expression of the full-length YpTLP and BpTLP using pWaldo-GFPe yielded 2.78 mg/l and 2.52 mg/l respectively. Protein purification steps were complicated by protein precipitation, possible degradation and misfolding. Subsequent efforts focused on the expression of the TIR only domain/homologue regions: YpTIR and BpTIR. Soluble YpTIR and BpTIR were expressed using pET26b. GST pull down assays indicated positive interactions between His-tagged YpTIR/BpTIR and GST-tagged human MyD88-TIR, a major adaptor protein, revealing MyD88 as a potential target of the bacterial TLPs. However expression yields of pure protein were too low to allow further studies. YpTIR and BpTIR were then expressed as fusions with an N-terminal GB1 tag using GEV2. Subsequent purification produced highly pure GB1-YpTIR (5 mg/l). NMR analysis indicated that the protein was folded and likely to be in a dimeric form, a finding confirmed by gel filtration. Native and derivative crystals of YpTIR were obtained, and native diffraction datasets collected to 2.95 A. Further work includes obtaining the phase information. It is anticipated that the crystal structure of YpTIR will provide insight into the molecular basis of TIR signalling and evidence of evolutionary conservation among TIR domains

Farmers' management of rice varietal diversity in the mid-hills of Nepal: implications for on-farm conservation and crop improvement

Season-long monitoring of on-farm rice (Oryza sativa, L.) plots in Nepal explored farmers' decision-making process on the deployment of varieties to agroecosystems, application of production inputs to varieties, agronomic practices and relationship between economic return and area planted per variety. Farmers deploy varieties [landraces (LRs) and modern varieties (MVs)] to agroecosystems based on their understanding of characteristics of varieties and agroecosystems, and the interaction between them. In marginal growing conditions, LRs can compete with MVs. Within an agroecosystem, economic return and area planted to varieties have positive relationship, but this is not so between agroecosystems. LRs are very diverse on agronomic and economic traits; therefore, they cannot be rejected a priori as inferior materials without proper evaluation. LRs have to be evaluated for useful traits and utilized in breeding programmes to generate farmer-preferred materials for marginal environments and for their conservation on-farm

Effect of Irrigation and Potash Levels on Keeping Quality of Potato

Irrigation and fertilizer are the most dominating factors, in deciding the keeping quality of potato. It is, therefore, essential to formulate the efficient, reliable and economically viable irrigation management strategy with the use of potassium nutrient in order to produce better keeping quality. The investigation comprising four levels of irrigation (25, 30, 35 and 40 mm CPE (Cumulative pan evaporation) and four levels of potash (0, 100, 125 and 150 kg/ha) was carried out at Research Farm of the Department of Vegetable Science, CCS Haryana Agricultural University, (Haryana) Hisar, India during two years to find out the optimum level of irrigation and potash for obtaining higher yield of potatoes with better keeping quality at ambient room temperature. The potato variety used for the investigation was Kufri Bahar. The treatments were laid out in a split plot design with three replications. The increasing levels of irrigation and potash showed significant improvement in keeping quality parameters of potato. Likewise, the values for physiological loss in weight and decay loss of potato tubers (%) at 15, 30, 45 and 60 days after harvest were the lowest with irrigation level 40 mm CPE and application of potash @ 150 kg/ha. The two years results suggest that the irrigation level 40 mm CPE along with potash @ 150 kg/ha has shown the best treatment combination for the storage of potato at ambient room temperature under semiarid conditions of Hisar (Haryana)

Performance Modelling and Analysis of a New CoMP-based Handover Scheme for Next Generation Wireless Networks. Performance Modelling and Analysis for the Design and Development of a New Handover Scheme for Cell Edge Users in Next Generation Wireless Networks (NGWNs) Based on the Coordinated Multi-Point (CoMP) Joint Transmission (JT) Technique

Inter-Cell Interference (ICI) will be one of main problems for degrading the performance of future wireless networks at cell edge. This adverse situation will become worst in the presence of dense deployment of micro and macro cells. In this context, the Coordinated Multi-Point (CoMP) technique was introduced to mitigate ICI in Next Generation Wireless Networks (NGWN) and increase their network performance at cell edge. Even though the CoMP technique provides satisfactory solutions of various problems at cell edge, nevertheless existing CoMP handover schemes do not prevent unnecessary handover initialisation decisions and never discuss the drawbacks of CoMP handover technique such as excessive feedback and resource sharing among UEs. In this research, new CoMP-based handover schemes are proposed in order to minimise unnecessary handover decisions at cell edge and determine solution of drawbacks of CoMP technique in conjunction with signal measurements such as Reference Signal Received Power (RSRP) and Received Signal Received Quality (RSRQ). A combination of calculations of RSRP and RSRQ facilitate a credible decision making process of CoMP mode and handover mode at cell edge. Typical numerical experiments indicate that by triggering the CoMP mode along with solutions of drawbacks, the overall network performance is constantly increase as the number of unnecessary handovers is progressively reduced

Angular instability due to radiation pressure in the LIGO gravitational-wave detector

We observed the effect of radiation pressure on the angular sensing and control system of the Laser Interferometer Gravitational-Wave Observatory (LIGO) interferometer’s core optics at LIGO Hanford Observatory. This is the first measurement of this effect in a complete gravitational-wave interferometer. Only one of the two angular modes survives with feedback control, because the other mode is suppressed when the control gain is sufficiently large. We developed a mathematical model to understand the physics of the system. This model matches well with the dynamics that we observe

Probing microplasticity in small scale FCC crystals via Dynamic Mechanical Analysis

In small-scale metallic systems, collective dislocation activity has been correlated with size effects in strength and with a step-like plastic response under uniaxial compression and tension. Yielding and plastic flow in these samples is often accompanied by the emergence of multiple dislocation avalanches. Dislocations might be active pre-yield, but their activity typically cannot be discerned because of the inherent instrumental noise in detecting equipment. We apply Alternate Current (AC) load perturbations via Dynamic Mechanical Analysis (DMA) during quasi-static uniaxial compression experiments on single crystalline Cu nano-pillars with diameters of 500 nm, and compute dynamic moduli at frequencies 0.1, 0.3, 1, and 10 Hz under progressively higher static loads until yielding. By tracking the collective aspects of the oscillatory stress-strain-time series in multiple samples, we observe an evolving dissipative component of the dislocation network response that signifies the transition from elastic behavior to dislocation avalanches in the globally pre-yield regime. We postulate that microplasticity, which is associated with the combination of dislocation avalanches and slow viscoplastic relaxations, is the cause of the dependency of dynamic modulus on the driving rate and the quasi-static stress. We construct a continuum mesoscopic dislocation dynamics model to compute the frequency response of stress over strain and obtain a consistent agreement with experimental observations. The results of our experiments and simulations present a pathway to discern and quantify correlated dislocation activity in the pre-yield regime of deforming crystals.Comment: 5 pages, 3 figure

Leveraging legacy codes to distributed problem solving environments: A web service approach

This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer