Real-time reverse transcription polymerase chain reaction development for rapid detection of Tomato brown rugose fruit virus and comparison with other techniques

Background: Tomato brown rugose fruit virus (ToBRFV) is a highly infectious tobamovirus that causes severe disease in tomato (Solanum lycopersicum L.) crops. In Italy, the first ToBRFV outbreak occurred in 2018 in several provinces of the Sicily region. ToBRFV outbreak represents a serious threat for tomato crops in Italy and the Mediterranean Basin. Methods: Molecular and biological characterisation of the Sicilian ToBRFV ToB-SIC01/19 isolate was performed, and a sensitive and specific Real-time RT-PCR TaqMan minor groove binder probe method was developed to detect ToBRFV in infected plants and seeds. Moreover, four different sample preparation procedures (immunocapture, total RNA extraction, direct crude extract and leaf-disk crude extract) were evaluated. Results: The Sicilian isolate ToB-SIC01/19 (6,391 nt) showed a strong sequence identity with the isolates TBRFV-P12-3H and TBRFV-P12-3G from Germany, Tom1-Jo from Jordan and TBRFV-IL from Israel. The ToB-SIC01/19 isolate was successfully transmitted by mechanical inoculations in S. lycopersicum L. and Capsicum annuum L., but no transmission occurred in S. melongena L. The developed real-time RT-PCR, based on the use of a primer set designed on conserved sequences in the open reading frames3, enabled a reliable quantitative detection. This method allowed clear discrimination of ToBRFV from other viruses belonging to the genus Tobamovirus, minimising false-negative results. Using immunocapture and total RNA extraction procedures, the real-time RT-PCR and end-point RT-PCR gave the same comparable results. Using direct crude extracts and leaf-disk crude extracts, the end-point RT-PCR was unable to provide a reliable result. This developed highly specific and sensitive real-time RT-PCR assay will be a particularly valuable tool for early ToBRFV diagnosis, optimising procedures in terms of costs and time

Public Health England's recovery tools: potential teaching resources?

The file attached to this record is the author's final peer reviewed version.Training to combat chemical and radiation accidents, incidents or attacks is critical for health professionals due to recent events involving these hazards or their use as unconventional weapons, such as the use of the nerve agent novichok in Salisbury, UK. Health professionals need to have appropriate knowledge and skills to effectively respond to future events involving any of these substances, which requires a rapid and coordinated response from different professionals to protect the environment and minimise the number of people exposed and reduce morbidity and mortality. However, despite chemical and radiation incidents becoming increasingly prevalent, literature reviews have shown that there is a lack of teaching of appropriate competences to face future crises in Europe, particularly amongst clinicians and other health professionals that would be part of the initial response. Thus, De Montfort University (DMU, UK) in collaboration with different academics from the University of Alcalá (Spain) and researchers from Public Health England (PHE) with comprehensive experience in environmental decontamination and restoration, have created a short training course for providing undergraduate/postgraduate students with basic skills to respond to chemical incidents, basic skills that are based on the major competences recently identified by the European Commission [1]. This novel training has been tested with students from different backgrounds in various European universities, recording high degrees of acquisition of the various basic competences that we developed to initially respond to chemical events [2]. To develop the practical part of this chemical training, we have incorporated the novel guidance and methodology developed by PHE to successfully tailor a protection and recovery response to any incident involving chemical substances, which is available in the “UK Recovery Handbook for Chemical Incidents” [3] and its web-based tools: “Chemical Recovery Navigation Tool” (CRNT, [4]) and “Chemical Recovery Record Form” (CRRF, [5]). These innovative resources aid the user to select effective protection, decontamination and restoration techniques or strategies from a pool of up-to-date options applicable to different environments according to the physicochemical properties of the chemical(s) involved and the area affected. The CRNT is accompanied by the CRRF, which facilitates collection and analysis of the necessary data to inform decisions, and an e-learning resource named “Chemical Recovery: Background” (CRB, [6]), which could facilitate the learning of environmental decontamination and restoration. We are currently developing a short training course to cover minor radiation incidents; this radiation training will follow the same methods used to develop the chemical training, but with the specific PHE recovery tools to tackle such events, specifically the “UK Recovery Handbooks for Radiation Incidents” [7] and its associated web-based tools “Radiation Recovery Navigation Tool” (Rad RNT, [8]), one for each environment: food production systems, inhabited areas and drinking water supplies. This communication will explore the use of the PHE’s Recovery Navigation Tools as potential resources to facilitate the acquisition of basic knowledge to tailor protection and recovery interventions for minor chemical and radiation incidents to protect the public

Probabilistic Bounds on the Length of a Longest Edge in Delaunay Graphs of Random Points in d-Dimensions

Motivated by low energy consumption in geographic routing in wireless networks, there has been recent interest in determining bounds on the length of edges in the Delaunay graph of randomly distributed points. Asymptotic results are known for random networks in planar domains. In this paper, we obtain upper and lower bounds that hold with parametric probability in any dimension, for points distributed uniformly at random in domains with and without boundary. The results obtained are asymptotically tight for all relevant values of such probability and constant number of dimensions, and show that the overhead produced by boundary nodes in the plane holds also for higher dimensions. To our knowledge, this is the first comprehensive study on the lengths of long edges in Delaunay graphsComment: 10 pages. 2 figures. In Proceedings of the 23rd Canadian Conference on Computational Geometry (CCCG 2011). Replacement of version 1106.4927, reference [5] adde

The largest oxigen bearing organic molecule repository

We present the first detection of complex aldehydes and isomers in three typical molecular clouds located within 200pc of the center of our Galaxy. We find very large abundances of these complex organic molecules (COMs) in the central molecular zone (CMZ), which we attribute to the ejection of COMs from grain mantles by shocks. The relative abundances of the different COMs with respect to that of CH3OH are strikingly similar for the three sources, located in very different environments in the CMZ. The similar relative abundances point toward a unique grain mantle composition in the CMZ. Studying the Galactic center clouds and objects in the Galactic disk having large abundances of COMs, we find that more saturated molecules are more abundant than the non-saturated ones. We also find differences between the relative abundance between COMs in the CMZ and the Galactic disk, suggesting different chemical histories of the grain mantles between the two regions in the Galaxy for the complex aldehydes. Different possibilities for the grain chemistry on the icy mantles in the GC clouds are briefly discussed. Cosmic rays can play an important role in the grain chemistry. With these new detections, the molecular clouds in the Galactic center appear to be one of the best laboratories for studying the formation of COMs in the Galaxy.Comment: 20 pages, 4 figures, accepted in Ap

A Resonant soft x-ray powder diffraction study to determine the orbital ordering in A-site ordered SmBaMn2O6

Soft X-ray resonant powder diffraction has been performed at the Mn L2,3 edges of A-site ordered SmBaMn2O6. The energy and polarization dependence of the (1/2 1/2 0) reflection provide direct evidence for a (x2-z2)/(y2-z2) type orbital ordering in contrast to the single layer manganite. The temperature dependence of the reflection indicates an orbital reorientation transition at 210 K, below which the charge and orbital ordered MnO2 sheets show AAAA type of stacking. The concurring reduction of the ferromagnetic super exchange correlations leads to further charge localization

Facing the wind of the pre-FUor V1331 Cyg

The mass outflows in T Tauri stars (TTS) are thought to be an effective mechanism to remove angular momentum during the pre-main-sequence contraction of a low-mass star. The most powerful winds are observed at the FUor stage of stellar evolution. V1331 Cyg has been considered as a TTS at the pre-FUor stage. We analyse high-resolution spectra of V1331 Cyg collected in 1998-2007 and 20-d series of spectra taken in 2012. For the first time the photospheric spectrum of the star is detected and stellar parameters are derived: spectral type G7-K0 IV, mass 2.8 Msun, radius 5 Rsun, vsini < 6 km/s. The photospheric spectrum is highly veiled, but the amount of veiling is not the same in different spectral lines, being lower in weak transitions and much higher in strong transitions. The Fe II 5018, Mg I 5183, K I 7699 and some other lines of metals are accompanied by a `shell' absorption at radial velocity of about -240 km/s. We show that these absorptions form in the post-shock gas in the jet, i.e. the star is seen though its jet. The P Cyg profiles of H-alpha and H-beta indicate the terminal wind velocity of about 500 km/s, which vary on time-scales from several days to years. A model of the stellar wind is developed to interpret the observations. The model is based on calculation of hydrogen spectral lines using the radiative transfer code TORUS. The observed H-alpha and H-beta line profiles and their variability can be well reproduced with a stellar wind model, where the mass-loss rate and collimation (opening angle) of the wind are variable. The changes of the opening angle may be induced by small variability in magetization of the inner disc wind. The mass-loss rate is found to vary within (6-11)x10^{-8} Msun/yr, with the accretion rate of 2.0x10^{-6} Msun/yr.Comment: 11 pages, 12 figures; accepted for publication in MNRAS. Typographical errors have been corrected after the proof stag