Pathways to false positive diagnoses using molecular genetic detection methods; Phytophthora cinnamomi a case study

Phytophthora cinnamomi is one of the world's most invasive plant pathogens affecting ornamental plants, horticultural crops and natural ecosystems. Accurate diagnosis is very important to determine the presence or absence of this pathogen in diseased and asymptomatic plants. In previous studies, P. cinnamomi species-specific primers were designed and tested using various polymerase chain reaction (PCR) techniques including conventional PCR, nested PCR and quantitative real-time PCR. In all cases, the primers were stated to be highly specific and sensitive to P. cinnamomi. However, few of these studies tested their primers against closely related Phytophthora species (Phytophthora clade 7). In this study, we tested these purported P. cinnamomi-specific primer sets against 11 other species from clade 7 and determined their specificity; of the eight tested primer sets only three were specific to P. cinnamomi. This study demonstrated the importance of testing primers against closely related species within the same clade, and not just other species within the same genus. The findings of this study are relevant to all species-specific microbial diagnosis

Multiple new Phytophthora species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications

During surveys of dying vegetation in natural ecosystems and associated waterways in Australia many new taxa have been identified from Phytophthora ITS Clade 6. For representative isolates, the region spanning the internal transcribed spacer region of the ribosomal DNA, the nuclear gene encoding heat shock protein 90 and the mitochondrial cox1 gene were PCR amplified and sequenced. Based on phylogenetic analysis and morphological and physiological comparison, four species and one informally designated taxon have been described; Phytophthora gibbosa, P. gregata, P. litoralis, P. thermophila and P. taxon paludosa. Phytophthora gibbosa, P. gregata and P. taxon paludosa form a new cluster and share a common ancestor; they are homothallic and generally associated with dying vegetation in swampy or water-logged areas. Phytophthora thermophila and P. litoralis are sister species to each other and more distantly to P. gonapodyides. Both new species are common in waterways and cause scattered mortality within native vegetation. They are self-sterile and appear well adapted for survival in an aquatic environment and inundated soils, filling the niche occupied by P. gonapodyides and P. taxon salixsoil in the northern hemisphere. Currently the origin of these new taxa, their pathogenicity and their role in natural ecosystems are unknown. Following the precautionary principle, they should be regarded as a potential threat to native ecosystems and managed to minimise their further spread

Quantum Monte Carlo study of a nonmagnetic impurity in the two-dimensional Hubbard model

In order to investigate the effects of nonmagnetic impurities in strongly correlated systems, Quantum Monte Carlo (QMC) simulations have been carried out for the doped two-dimensional Hubbard model with one nonmagnetic impurity. Using a bare impurity potential which is onsite and attractive, magnetic and single-particle properties have been calculated. The QMC results show that giant oscillations develop in the Knight shift response around the impurity site due to the short-range antiferromagnetic correlations. These results are useful for interpreting the NMR data on Li and Zn substituted layered cuprates.Comment: 10 pages, 7 figure

Helicopter handling qualities: a study in pilot control compensation

The research reported in this paper is aimed at the development of a metric to quantify and predict the extent of pilot control compensation required to fly a wide range of mission task elements. To do this, the utility of a range of time- and frequency-domain measures to examine pilot control activity whilst flying hover/low-speed and forward flight tasks are explored. The tasks were performed by two test pilots using both the National Research Council (Canada)’s Bell 412 Advanced Systems Research Aircraft and the University of Liverpool’s HELIFLIGHT-R simulator. Handling qualities ratings were awarded for each of the tasks and compared with a newly developed weighted adaptive control compensation metric based on discrete pilot inputs, showing good correlation. Moreover, in combination with a time-varying frequency-domain exposure, the proposed metric is shown to be useful for understanding the relationship between the pilot’s subjective assessment, measured control activity and task performance. By collating the results from the subjective and objective metrics for a range of different mission task elements, compensation boundaries are proposed to predict and verify the subjective assessments from the Cooper-Harper Handling Qualities Rating scale.Engineering and Physical Sciences Research Council (EP/P031277/1 and EP/P030009/1

Effect of nearest neighbor repulsion on the low frequency phase diagram of a quarter-filled Hubbard-Holstein chain

We have studied the influence of nearest-neighbor (NN) repulsion on the low frequency phase diagram of a quarter-filled Hubbard-Holstein chain. The NN repulsion term induces the apparition of two new long range ordered phases (one $4k_F$ CDW for positive $U_{eff} = U-2g^2/\omega$ and one $2k_F$ CDW for negative $U_{eff}$) that did not exist in the V=0 phase diagram. These results are put into perspective with the newly observed charge ordered phases in organic conductors and an interpretation of their origin in terms of electron-molecular vibration coupling is suggested.Comment: 10 pages, 10 figure

Current and projected global distribution of Phytophthora cinnamomi, one of the world's worst plant pathogens

Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a climex model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on the presence and absence of the pathogen. The climex model captured areas of climatic suitability where P. cinnamomi occurs that is congruent with all available records. The model was validated by the collection of soil samples from asymptomatic vegetation in areas projected to be suitable by the model for which there were few records. DNA was extracted, and the presence or absence of P. cinnamomi was determined by high-throughput sequencing (HTS). While not detected using traditional isolation methods, HTS detected P. cinnamomi at higher elevations in eastern Australia and central Tasmania as projected by the climex model. Further support for the climex model was obtained using the large data set from south-west Australia where the proportion of positive records in an area is related to the Ecoclimatic Index value for the same area. We provide for the first time a comprehensive global map of the current P. cinnamomi distribution, an improved climex model of the distribution, and a projection to 2080 of the distribution with predicted climate change. This information provides the basis for more detailed regional-scale modelling and supports risk assessment for governments to plan management of this important soil-borne plant pathogen

Extreme endurance flights by landbirds crossing the Pacific Ocean: ecological corridor rather than barrier?

Mountain ranges, deserts, ice fields and oceans generally act as barriers to the movement of land-dependent animals, often profoundly shaping migration routes. We used satellite telemetry to track the southward flights of bar-tailed godwits (Limosa lapponica baueri), shorebirds whose breeding and non-breeding areas are separated by the vast central Pacific Ocean. Seven females with surgically implanted transmitters flew non-stop 8117–11 680 km (10 153±1043 s.d.) directly across the Pacific Ocean; two males with external transmitters flew non-stop along the same corridor for 7008–7390 km. Flight duration ranged from 6.0 to 9.4 days (7.8±1.3 s.d.) for birds with implants and 5.0 to 6.6 days for birds with externally attached transmitters. These extraordinary non-stop flights establish new extremes for avian flight performance, have profound implications for understanding the physiological capabilities of vertebrates and how birds navigate, and challenge current physiological paradigms on topics such as sleep, dehydration and phenotypic flexibility. Predicted changes in climatic systems may affect survival rates if weather conditions at their departure hub or along the migration corridor should change. We propose that this transoceanic route may function as an ecological corridor rather than a barrier, providing a wind-assisted passage relatively free of pathogens and predators

Frequency behavior of Raman coupling coefficient in glasses

Low-frequency Raman coupling coefficient of 11 different glasses is evaluated. It is found that the coupling coefficient demonstrates a universal linear frequency behavior near the boson peak maximum and a superlinear behavior at very low frequencies. The last observation suggests vanishing of the coupling coefficient when frequency tends to zero. The results are discussed in terms of the vibration wavefunction that combines features of localized and extended modes.Comment: 8 pages, 9 figure

A thermoresponsive and magnetic colloid for 3D cell expansion and reconfiguration

A dual thermoresponsive and magnetic colloidal gel matrix is described for enhanced stem-cell culture. The combined properties of the material allow enzyme-free passaging and expansion of mesenchymal stem cells, as well as isolation of cells postculture by the simple process of lowering the temperature and applying an external magnetic field. The colloidal gel can be reconfigured with thermal and magnetic stimuli to allow patterning of cells in discrete zones and to control movement of cells within the porous matrix during culture