A new method for the identification of phytoplasmas in strawberries (Fragaria fragaria)

Motivation:Phytoplasmas are plant pathogens that generally inhabit the phloem and are transmitted from plant to plant by vector insects that feed on phloem. Their genome is small, with a high content of genes (1). The presence of extrachromosomal DNA has also been detected (2). Serological and molecular studies have shown that phytoplasmas contain a gene encoding a membrane protein and this is unique for each specie and helps to identify what type of phytoplasma is, according to its taxonomic classification (3). Different phytoplasmas had been detected and identified in strawberries plants (Fragaria fragaria). Symptoms observed on strawberries were yellow coloration of leaves, plant stunting, and reduced leaf size and the virescence were observed in the inflorescence. PCR analyses as well as sequencing of 16S ribosomal gene enabled the identification of phytoplasmas belonging to two ribosomal groups, namely stolbur and aster yellows, but the eficiency for this detection is not reliable. Here we are working to develop a new method to easily detect and identify this pathogen in plant samples before symptoms appear.Methods: 70 samples of strawberries infected with phytoplasma were tested, by,analysing leaves, crown and root in the strawberry plant to determine the most optimal zone to be sampled. The identification of phytoplasmas required a double PCRs  using phytoplasma universal primer pair P1/P7, followed by nested PCR with Fu5/Ru3 primers. Further nested PCR reactions on R16mF2/R1 amplicons were also performed with R16F2N/R2 primer pair, specific for phytoplasma belonging to aster yellow to determine their class. Asymptomatic samples were also analysed as negative controls in each PCR reaction. The amplified DNA was sequenced and the sequence analysed by Blast.Results:With this PCR method, the presence of phytoplasma was mainly detected in strawberries roots but not in leaves and crowns. This technique allowed us to detect presence of high amount of phytoplasma because a positive result in the first PCR, low amount with a positive result only in the second one, or no presence because negative result in both. Finally,, the sequencing of the amplified DNA, allowed us to determine if they belong to aster yellow or stolbur because they DNA identity.Conclusions: This new phytoplasma identification method is effective. It would be interesting to obtain a specific primer for each specie of phytoplasma and thus have a more precise method

Oxidation of CO and methanol on Pd-Ni catalysts supported on different chemically-treated carbon nanofibers

In this work, palladium-nickel nanoparticles supported on carbon nanofibers were synthesized, with metal contents close to 25 wt % and Pd:Ni atomic ratios near to 1:2. These catalysts were previously studied in order to determine their activity toward the oxygen reduction reaction. Before the deposition of metals, the carbon nanofibers were chemically treated in order to generateoxygen and nitrogen groups on their surface. Transmission electron microscopy analysis (TEM) images revealed particle diameters between 3 and 4 nm, overcoming the sizes observed for thenanoparticles supported on carbon black (catalyst Pd-Ni CB 1:2). From the CO oxidation at different temperatures, the activation energy Eact for this reaction was determined. These values indicated a high tolerance of the catalysts toward the CO poisoning, especially in the case of the catalystssupported on the non-chemically treated carbon nanofibers. On the other hand, apparent activation energy Eap for the methanol oxidation was also determined finding—as a rate determining step—the COads diffusion to the OHads for the catalysts supported on carbon nanofibers. The results here presented showed that the surface functional groups only play a role in the obtaining of lower particlesizes, which is an important factor in the obtaining of low CO oxidation activation energies

Contrasting complexing capacity of dissolved organic matter produced during the onset, development and decay of a simulated bloom of the marine diatom Skeletonema costatum

Original research articleThe capacity of natural dissolved organic matter (DOM) produced during the onset, development and decay of a simulated bloom of the marine diatom Skeletonema costatum to complex free copper has been followed for a 2 week period. Copper binding capacity of the culture was measured by anodic stripping voltammetry (ASV) with a hanging mercury drop electrode (HMDE). The concentration of dissolved organic carbon (DOC) and two fluorophores, M (humic-like, Ex/Em: 320 nm/410 nm) and T (protein-like, Ex/Em: 280 nm/350 nm), were followed during the course of the incubation. Models using DOC concentrations alone could not accurately predict the complexing capacity of the culture, especially at the end of the bloom, and better predictions were obtained when fluorescence measurements were considered. They were helpful in characterising two types of copper ligands produced in the culture. The first type, traced by the fluorescence of peak T, was related to labile DOC directly exuded by phytoplankton. The second type, traced by the fluorescence of peak M, was the refractory humic-like material presumably produced in situ as a by-product of the bacterial degradation of phytogenic materials. During the onset and development of the bloom (days 0 to 7), the fluorescence of peak T explains 60–80% of the total complexing capacity of the culture, suggesting that exuded “protein-like” compounds among other exuded complexing agents efficiently complexed free copper. On the contrary, during the decay (days 8 to 13), these ligands were replaced by humic substances as the complexing agent for copper.Financial support for this work came from the Spanish ‘Ministerio de Educación y Ciencia’ (MEC), Grant Nos. REN2000-0880-C02-01 MAR and REN2003-00958 MAR and the ‘Xunta de Galicia’, Grant No. PGIDT01MAR40201PN.Versión del editor2,75

A New Relativistic High Temperature Bose-Einstein Condensation

We discuss the properties of an ideal relativistic gas of events possessing Bose-Einstein statistics. We find that the mass spectrum of such a system is bounded by $\mu \leq m\leq 2M/\mu _K,$ where $\mu$ is the usual chemical potential, $M$ is an intrinsic dimensional scale parameter for the motion of an event in space-time, and $\mu _K$ is an additional mass potential of the ensemble. For the system including both particles and antiparticles, with nonzero chemical potential $\mu ,$ the mass spectrum is shown to be bounded by $|\mu |\leq m\leq 2M/\mu _K,$ and a special type of high-temperature Bose-Einstein condensation can occur. We study this Bose-Einstein condensation, and show that it corresponds to a phase transition from the sector of continuous relativistic mass distributions to a sector in which the boson mass distribution becomes sharp at a definite mass $M/\mu _K.$ This phenomenon provides a mechanism for the mass distribution of the particles to be sharp at some definite value.Comment: Latex, 22 page

The Pioneer Anomaly in the Light of New Data

The radio-metric tracking data received from the Pioneer 10 and 11 spacecraft from the distances between 20-70 astronomical units from the Sun has consistently indicated the presence of a small, anomalous, blue-shifted Doppler frequency drift that limited the accuracy of the orbit reconstruction for these vehicles. This drift was interpreted as a sunward acceleration of a_P = (8.74+/-1.33)x10^{-10} m/s^2 for each particular spacecraft. This signal has become known as the Pioneer anomaly; the nature of this anomaly is still being investigated. Recently new Pioneer 10 and 11 radio-metric Doppler and flight telemetry data became available. The newly available Doppler data set is much larger when compared to the data used in previous investigations and is the primary source for new investigation of the anomaly. In addition, the flight telemetry files, original project documentation, and newly developed software tools are now used to reconstruct the engineering history of spacecraft. With the help of this information, a thermal model of the Pioneers was developed to study possible contribution of thermal recoil force acting on the spacecraft. The goal of the ongoing efforts is to evaluate the effect of on-board systems on the spacecrafts' trajectories and possibly identify the nature of this anomaly. Techniques developed for the investigation of the Pioneer anomaly are applicable to the New Horizons mission. Analysis shows that anisotropic thermal radiation from on-board sources will accelerate this spacecraft by ~41 x 10^{-10} m/s^2. We discuss the lessons learned from the study of the Pioneer anomaly for the New Horizons spacecraft.Comment: 19 pages, 5 figure

Peripheral organ equivalent dose estimation procedure in proton therapy

The aim of this work is to present a reproducible methodology for the evaluation of total equivalent doses in organs during proton therapy facilities. The methodology is based on measuring the dose equivalent in representative locations inside an anthropomorphic phantom where photon and neutron dosimeters were inserted. The Monte Carlo simulation was needed for obtaining neutron energy distribution inside the phantom. The methodology was implemented for a head irradiation case in the passive proton beam of iThemba Labs (South Africa). Thermoluminescent dosimeter (TLD)-600 and TLD-700 pairs were used as dosimeters inside the phantom and GEANT code for simulations. In addition, Bonner sphere spectrometry was performed inside the treatment room to obtain the neutron spectra, some relevant neutron dosimetric quantities per treatment Gy, and a percentual distribution of neutron fluence and ambient dose equivalent in four energy groups, at two locations. The neutron spectrum at one of those locations was also simulated so that a reasonable agreement between simulation and measurement allowed a validation of the simulation. Results showed that the total out-of-field dose equivalent inside the phantom ranged from 1.4 to 0.28 mSv/Gy, mainly due to the neutron contribution and with a small contribution from photons, 10% on average. The order of magnitude of the equivalent dose in organs was similar, displaying a slow reduction in values as the organ is farther from the target volume. These values were in agreement with those found by other authors in other passive beam facilities under similar irradiation and measurement conditions

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) a-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of “extra-target” RAS suggests the need for RAS screening in all three DAA target regions

X chromosome inactivation does not necessarily determine the severity of the phenotype in Rett syndrome patients

Rett syndrome (RTT) is a severe neurological disorder usually caused by mutations in the MECP2 gene. Since the MECP2 gene is located on the X chromosome, X chromosome inactivation (XCI) could play a role in the wide range of phenotypic variation of RTT patients; however, classical methylation-based protocols to evaluate XCI could not determine whether the preferentially inactivated X chromosome carried the mutant or the wild-type allele. Therefore, we developed an allele-specific methylation-based assay to evaluate methylation at the loci of several recurrent MECP2 mutations. We analyzed the XCI patterns in the blood of 174 RTT patients, but we did not find a clear correlation between XCI and the clinical presentation. We also compared XCI in blood and brain cortex samples of two patients and found differences between XCI patterns in these tissues. However, RTT mainly being a neurological disease complicates the establishment of a correlation between the XCI in blood and the clinical presentation of the patients. Furthermore, we analyzed MECP2 transcript levels and found differences from the expected levels according to XCI. Many factors other than XCI could affect the RTT phenotype, which in combination could influence the clinical presentation of RTT patients to a greater extent than slight variations in the XCI pattern