De novo analysis of the haustorial transcriptome of the cucurbit powdery mildew fungus Podosphaera xanthii reveals new candidate secreted effector proteins

Backgrounds. Cucurbit crops are affected, among other pathogens, by the obligate biotrophic fungus Podosphaera xanthii, the main causal agent of powdery mildew in cucurbits. This fungus develops a specialized structure of parasitism termed haustorium. Haustoria are developed into epidermal cells and are responsible for nutrients uptake and effectors delivery. Objectives. The aim of this study was to obtain the haustorial transcriptome of P. xanthii to complete the panel of effector candidates of this fungal pathogen. Methods. To obtain the haustorial transcriptome, we have developed an effective method for isolation of haustoria without contaminants by flow cytometry. The cDNA library was built using a combination of dT primers and random primers followed by a depletion of ribosomal sequences. Sequencing was carried out by Illumina NextSeq550. Conclusions. After bioinformatic analysis, we were able to identify 25 new effector candidates secreted by the classic pathway (with signal peptide) and 269 new candidates secreted by the non-classic pathway (without signal peptide). Most proteins had no functional annotation. By protein modelling and ligand predictions, we are now being able to assign putative functions to some of these candidates to select those with potential roles in pathogenesis for subsequent functional in vivo analysis by HIGS (host-induced gene silencing). By these approaches, we are starting to shed some light into the molecular mechanisms of pathogenesis in this very important pathogen of cucurbits.This work was supported by a grant from the Ministerio de Economía y Competitividad (AGL2013-41938-R), co-financed with FEDER funds (EU). A grant form Universidad de Málaga, Campus de Excelencia Internacional Andalucía Tech, is also acknowledged

Analysis of hypervariable DNA sequences by NGS technologies: QuasiFlow

The development of Next Generation Sequencing (NGS) technologies has allowed deep characterization of highly variable sequences such as viral or mitochondrial genomes. With respect to RNA and ssDNA viruses, their low replication fidelity generates viral populations consisting of complex mutant spectra termed viral quasispecies. Their study is of special interest as they can be considered a phenotypic reservoir1. Similarly, heteroplasmy of human mitochondrial genomes, in which different sequences are found within a single individual, might have important clinical consequences. For the analysis of the mutant spectrum of such hypervariable sequences from NGS data, we have developed QuasiFlow, a workflow designed in AutoFlow2 that uses Illumina reads. QuasiFlow provides information about DNA variability, such as SNPs, indels and recombination events (Figure 1). Furthermore, it allows haplotype reconstruction of viral quasispecies and characterization of its diversity through normalized Shannon index, nucleotide diversity and mutation networks. Quasiflow performs also a comparative study among samples, based on correlation, ANOVA and PCA analysis, in order to determine which parameters are affected by the experiment and how the samples behave according to their biological origin. In this work, we have applied QuasiFlow to analyze the population structure of the begomovirus Tomato yellow leaf curl virus (TYLCV) infectious clone inoculated in Arabidopsis thaliana plants, using HiSeq or MiSeq reads. Their analysis allowed detection of minor quasispecies variants with a frequency of 10-4 to 10-5 and reconstructed the haplotypes present in the sample. In addition, QuasiFlow was used to discover variants and recombinants in mixed infections of tomato plants. These results show the fast generation of recombinant genomes in geminivirus mixed infections and demonstrate the potential of QuasiFlow for the analysis of mutant spectra using Illumina MiSeq sequencing data. We have extended the use of QuasiFlow to the analysis of highly variable sequences such as the mitochondrial DNA. For that, we have analyzed DNA Illumina Miseq reads from 47 human mitochondrial samples from different cell lines obtained from the NCBI SRA database. Quasiflow generated automatically SNPs, SNP frequencies, indels and analyzed up to 23 variables using PCA analysis and performed an hierarchical clustering of the samples. Our analysis was able to detect pathological variants presented in a frequency lower than 1%.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This research was funded by Junta de Andalucía and EU through the ERDF 2014-2020, Projects P10-CVI-6075 to M. G.C. and P10-CVI-6561 to A.G-P

Made in Europe: monetary–fiscal policy mix with financial frictions

We study the role of fiscal and monetary policies in a financially constrained economy. An active monetary–passive fiscal regime amplifies technology shocks, mitigates preference shocks, and neutralizes the expansionary effects of fiscal shocks through “debt deflation” and “real interest rate” channels, compared to an active fiscal–passive monetary policy regime. Several features of the data suggest that in the aftermath of the 2007 Financial crisis, the monetary policy in the United States was more dovish than in the Euro Area while fiscal policy seemed less concerned about the dynamics of sovereign debt, implying that the distinct post-crisis dynamics of the United States and the Euro area can be rationalized through different fiscal and monetary policy mixes

Oral health scales: design of an oral health scale of infectious potential

Objectives: In this paper we propose a new Global Oral Health Scale that will allow the infectious potential of the oral cavity, clinically manifest as local and focal infections, to be condensed into a single parameter. Study Design: Based on a number of oral health scales previously designed by our group, we designed a final version that incorporates dental and periodontal variables (some of them evaluated using corroborated objective indices) that reflect the presence of caries and periodontal disease. Results: The application of the proposed oral health scale requires the examination of 6 sites per tooth (mesio- buccal, medio-buccal, disto-buccal, disto-lingual, medio-lingual and mesio-lingual). The following variables are analysed: number of tooth surfaces with supragingival plaque, determined using the O'Leary index; number of teeth with caries and the severity of the caries; number of tooth surfaces with gingival inflammation, determined using the Ainamo and Bay index; and number of tooth surfaces with pockets >=4 mm and severity of the pockets. These variables are then grouped into 2 categories, dental and periodontal. The final grades of dental and peri - odontal health correspond to the grades assigned to a least 2 of the 3 variables analysed in each of these categories. The category (dental or periodontal) with the highest grade is the one that determines the grade of the Global Oral Health Scale. Conclusion: This scale could be particularly useful for the epidemiological studies comparing different populations and for analysis of the influence of distinct degrees of oral health on the development of certain systemic diseases

Minor salivary gland biopsy in Sjögren's syndrome: a review and introduction of a new tool to ease the procedure

Objectives: To review the existing techniques for minor salivary gland biopsy (MSGB) in the lip and to suggest a new approach to ease the procedure and reduce post-operative complications. Study Design: A comprehensive literature review and a descriptive study of a new surgical technique. Results: Diverse incisions have been suggested for MSGB with different designs (ellipse, circular, linear), different directions (parallel, oblique, vertical) and a wide range of lengths (from 1 mm up to 3 cm), but no comparative studies supporting the advantages of a particular type of incision over the others could be retrieved. A variety of features of the existing techniques for MSGB are linked to undesired events and surgical complications which could be minimized by modifying certain aspects of these procedures. The technique described, together with the use of the S forceps, represents a significant improvement over the already described chalazion forceps because it allows for a better access and positioning of the lower lip, improves the ergonomic conditions of the assistant, and facilitates the identification of lip areas with more superficial gland lobules. Conclusions: The suggested approach for lip MSGB includes a specifically designed instrument whose performance during lip biopsy may contribute to minimize post-operative complications

Available web-based teaching resources for health care professionals on screening for oral cancer

Objectives: To identify websites with adequate information on oral cancer screening for healthcare professionals (HCPs) and to assess both their quality and contents. Study Design: Websites were identified using Google and HON medical professional search engines using the terms “screening for oral cancer”. The first 100 sites retrieved by each engine were analysed using the DISCERN questionnaire (reliability), the V instrument (contents on oral cancer) and further by the Flesch-Kinkaid Reading Grade Level and the Flesch Reading Ease (readability). Results: The overall rating showed minimal shortcomings in the quality of the information in the websites. The coverage and correctness of information on “visual examination” was rated as fair/good, whereas updating of contents resulted very variable (eg: 81% for visual examination and 18.2% for molecular biomarkers). These results permitted to rank the websites housing relevant information for oral cancer. Top ranking websites were affiliated to the Oral Cancer Foundation (USA), WHO Collaborating Centre for oral cancer (UK) whose webpage is entitled “Oral Cancer Education and Research”, and the Clinical Guidelines maintained by the British Columbia Cancer Agency (Canada) and the British Dental Association (UK) respectively. Conclusions: There are web-based, HCP-addressed, resources on screening for oral cancer housing heterogeneous information both in quality and contents. The use of specific evaluation tools permits the selection of reliable websites on this topic with a potential to improve the existing educational gaps among HCPs

Simulation for training in oral cancer biopsy: a surgical model and feedback from GDPs

Objectives: To describe a new bench model for oral precancer/cancer biopsy training and to assess its effectiveness in terms of trainees' perception. Study design: Cross-sectional, descriptive, performed on 424 general dental practitioners (GDP) who undertook biopsies on a pig tongue. The participants were assessed by direct observation for 2.5 hours using specific check- lists and by means of a self-applied questionnaire. Results: The workshop was perceived as "very interesting" even by those with previous surgical experience (Xi - Xj = 0.07; 95%CI= -0.20-0.09). Most GDPs considered themselves able to undertake oral biopsies on real patients after the workshop. Those who had previously received theoretical continuous education courses on oral biopsy scored higher values within the group (Xi - Xj = 0.20; 95%CI= 0.04-0.37). Conclusions: There is a need for including clinical abilities workshops when instructing on oral biopsy techniques. More studies are needed to validate the procedure and to address cognitive and communication skills

Improved gravitational radiation time-scales: significance for LISA and LIGO-Virgo sources

We present a revised version of Peters' (1964) time-scale for the gravitational-wave (GW) induced decay of two point masses. The new formula includes the effects of the first-order post-Newtonian perturbation and additionally provides a simple fit to account for the Newtonian self-consistent evolution of the eccentricity. The revised time-scale is found by multiplying Peters' estimate by two factors, $R(e_0)= 8^{1-\sqrt{1-e_0}}$ and $Q_{\rm f}(p_0) = \exp \left(2.5 (r_{\rm S}/p_0) \right)$, where $e_0$ and $p_0$ are the initial eccentricity and periapsis, respectively, and $r_{\rm S}$ the Schwarzschild radius of the system. Their use can correct errors of a factor of 1-10 that arise from using the original Peters' formula. We apply the revised time-scales to a set of typical sources for existing ground-based laser interferometers and for the future Laser Interferometer Space Antenna (LISA), at the onset of their GW driven decay. We argue that our more accurate model for the orbital evolution will affect current event- and detection-rate estimates for mergers of compact object binaries, with stronger deviations for eccentric LISA sources, such as extreme and intermediate mass-ratio inspirals. We propose the correction factors $R$ and $Q_{\rm f}$ as a simple prescription to quantify decay time-scales more accurately in future population synthesis models. We also suggest that the corrected time-scale may be used as a computationally efficient alternative to numerical integration in other applications that include the modelling of radiation reaction for eccentric sources.Comment: Accepted for publication in MNRA

Automatic detection to inventory road slopes using open LiDAR point clouds

The transport infrastructure of a country facilitates the development and growth of its economy and improves the quality of life of its inhabitants. Increasing its resilience to different types of risks to improve performance is becoming more important. In the current context of climate change, natural hazards are more severe and frequent. In this article, we focus on rockfall as a natural hazard for roads that occurs in small areas in the vicinity of natural or cut slopes, causing road safety problems by invading part of the road. This article aims to inventory the slopes along the road, identifying the area of the road which would be invaded in case of a rockfall. A methodology divided into two blocks is proposed. First, for slope detection and inventory, an algorithm is developed based on open LiDAR point clouds analysis. The second block consists of estimating the invaded road area if a rockfall occurs on each of the inventoried slopes, using a combination of RockGIS software and the Monte Carlo method. The methodology was applied in five case studies: three sections on motorways and two sections on national roads. The results obtained for slope detection show higher rates in the case studies analyzing motorways, with a precision of 100%, a recovery rate of greater than 93.4%, and an F1 score of greater than 0.96. The results in the invaded area of the road show that 11 slopes would cause a total cut of the motorway in one of the directions if a rockfall occurs. These results are useful for infrastructure managers to remotely obtain an inventory of road slopes and know which of them would affect road safety. Also, the results can serve as input for the Intelligent Transportation System and allow the exchange of information under the Building Information Model approach.Ministerio de Ciencia, Innovación y Universidades | Ref. PID2019-108816RB-I00Ministerio de Ciencia, Innovación y Universidades | Ref. PRE2020-096222European Commission | Ref. H2020, n. 95533