Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems

We thank all members of the NTG laboratory for helpful discussions during the development of this project. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Supplementary Data are available at NAR Online: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkaa1149#supplementary-dataBacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.Spanish Ministerio de Ciencia, Innovacion y UniversidadesEuropean Commission BIO2017-82244-PFPU predoctoral fellowship grant from the Ministerio de Economia y Competitividad FPU15/02714FPU predoctoral fellowship grant from the Ministerio de Ciencia, Innovacion y Universidades FPU17/0508

Potential biological control pseudomonas sp. PCI2 against damping-off of tomato caused by Sclerotium Rolfsii

Fluorescent Pseudomonas spp. isolated from the roots of healthy tomato plants were screened for their antagonistic activities against Sclerotium rolfsii, Alternaria alternata and Fusarium solani, three phytopathogenic fungi of tomato and pepper. They were tested for phosphate solubilization ability and production of siderophores, hydrolytic enzymes, indole 3-acetic acid and hydrogen cyanid. The isolates were also characterized based on biochemical (API 20NE test) and genotypic (ERIC-PCR fingerprinting) features. A Pseudomonas sp. strain denoted PCI2 was chosen as a potential candidate for controlling tomato damping-off caused by Sclerotium rolfsii. PCI2 was identified at the genus level with a 16S rDNA partial sequence analysis and its phylogenetic relationship with previously characterized Pseudomonas species was determined. PCI2 clustered with the P. putida species. Growth chamber studies resulted in statistically significant increases in plant stand (29%) as well as in root dry weight (58%). PCI2 was able to establish itself and survive in tomato rhizosphere after 40 days, following planting of bacterized seeds. PCI2 is a potential biological control agent that may contribute to the protection of tomato plants against damping-off caused by S. rolfsii.Fil: Pastor, Nicolás Alejandro. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Reynoso, Maria Marta. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Tonelli, Maria Laura. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Masciarelli, Oscar Alberto. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Rosas, Susana Beatriz. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Rovera, Marisa. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentin

Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils

To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils. Methods and Results: Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H′), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields. Conclusions: Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils. Significance and Impact of the Study: Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.Fil: Ganuza, Mauricio Roque. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pastor, Nicolás Alejandro. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigación en Micología y Micotoxicología. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación en Micología y Micotoxicología; ArgentinaFil: Boccolini, Maricel Fatima. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Erazo, Jessica Gabriela. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigación en Micología y Micotoxicología. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación en Micología y Micotoxicología; ArgentinaFil: Palacios, Sofia Alejendra. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Oddino, Claudio Marcelo. Universidad Nacional de Río Cuarto. Facultad de Agronomía y Veterinaria; ArgentinaFil: Reynoso, Maria Marta. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigación en Micología y Micotoxicología. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación en Micología y Micotoxicología; ArgentinaFil: Rovera, Marisa. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; ArgentinaFil: Torres, Adriana Monica. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Vulnerabilidad territorial: indicadores para su medición desde los servicios sociales

El informe da respuesta a una de las líneas de trabajo del Laboratorio de Servicios Sociales para 2019, consistente en producir conocimiento sobre los indicadores específicos que permiten considerar un territorio como "espacio vulnerable", en la línea establecida por el artículo 25 de la Ley 3/2019, de 18 de febrero, de la Generalitat, de Servicios Sociales Inclusivos de la Comunitat Valenciana, y también sobre las fuentes de datos disponibles sobre estos indicadores. Para ello, el trabajo se estructura en 4 partes y 6 anexos: (1) La primera parte consiste en una aproximación al concepto de vulnerabilidad aplicada al territorio y a otros conceptos cercanos, realizada mediante la revisión bibliográfica de la literatura científica al respecto. (2) La segunda parte contiene un análisis comparado del tratamiento que las Leyes autonómicas de Servicios Sociales en vigor dan a los territorios singulares. (3) La tercera parte consiste en, por un lado, la identificación de áreas, dimensiones e indicadores que permiten caracterizar a un territorio como "vulnerable", y, por otro lado, la identificación de las principales fuentes de datos disponibles, de alcance autonómico, para nutrir de datos los indicadores. (4) La cuarta parte presenta las conclusiones y propuestas que surgen del trabajo realizado. (5) Los anexos recogen el detalle de los resultados obtenidos en las diferentes fases del trabajo explicitados a lo largo del texto.Informe elaborado en el marco del Convenio para el fomento de la investigación sobre los indicadores sociales en Servicios Sociales de la Comunitat Valenciana (Ref. CONSELLERIAIGUALDAD1-19I), suscrito entre la Vicepresidència i Conselleria d’Igualtat i Polítiques Inclusives (Generalitat Valenciana) y la Universitat d’Alacant (Grup d’Investigació sobre Treball Social i Serveis Socials – GITSS)

TransLectures

transLectures (Transcription and Translation of Video Lectures) is an EU STREP project in which advanced automatic speech recognition and machine translation techniques are being tested on large video lecture repositories. The project began in November 2011 and will run for three years. This paper will outline the project¿s main motivation and objectives, and give a brief description of the two main repositories being considered: VideoLectures.NET and poliMedia. The first results obtained by the UPV group for the poliMedia repository will also be provided.The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 287755. Funding was also provided by the Spanish Government (iTrans2 project, TIN2009-14511; FPI scholarship BES-2010-033005; FPU scholarship AP2010-4349)Silvestre Cerdà, JA.; Del Agua Teba, MA.; Garcés Díaz-Munío, GV.; Gascó Mora, G.; Giménez Pastor, A.; Martínez-Villaronga, AA.; Pérez González De Martos, AM.... (2012). TransLectures. IberSPEECH 2012. 345-351. http://hdl.handle.net/10251/3729034535

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Potential of Pseudomonas putida PCI2 for the Protection of Tomato Plants Against Fungal Pathogens

Tomato is one of the most economically attractive vegetable crops due to its high yields. Diseases cause significant losses in tomato production worldwide. We carried out Polymerase Chain Reaction studies to detect the presence of genes encoding antifungal compounds in the DNA of Pseudomonas putida strain PCI2. We also used liquid chromatography-electrospray tandem mass spectrometry to detect and quantify the production of compounds that increase the resistance of plants to diseases from culture supernatants of PCI2. In addition, we investigated the presence of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase in PCI2. Finally, PCI2 was used for inoculation of tomato seeds to study its potential biocontrol activity against Fusarium oxysporum MR193. The obtained results showed that no fragments for the encoding genes of hydrogen cyanide, pyoluteorin, 2,4-diacetylphloroglucinol, pyrrolnitrin, or phenazine-1-carboxylic acid were amplified from the DNA of PCI2. On the other hand, PCI2 produced salicylic acid and jasmonic acid in Luria–Bertani medium and grew in a culture medium containing ACC as the sole nitrogen source. We observed a reduction in disease incidence from 53.33 % in the pathogen control to 30 % in tomato plants pre-inoculated with PCI2 as well as increases in shoot and root dry weights in inoculated plants, as compared to the pathogenicity control. This study suggests that inoculation of tomato seeds with P. putida PCI2 increases the resistance of plants to root rot caused by F. oxysporum and that PCI2 produces compounds that may be involved at different levels in increasing such resistance. Thus, PCI2 could represent a non-contaminating management strategy potentially applicable in vegetable crops such as tomato.Fil: Pastor, Nicolás Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; ArgentinaFil: Masciarelli, Oscar Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Ciencias Naturales; ArgentinaFil: Fischer, Sonia Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Ciencias Naturales; ArgentinaFil: Luna, Maria Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Ciencias Naturales; ArgentinaFil: Rovera, Marisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentin

Inoculation with Pseudomonas putida PCI2, a phosphate solubilizing rhizobacterium, stimulates the growth of tomato plants

The use of phosphate solubilizing plant growth-promoting microorganisms as inoculants assists in the hydrolysis of insoluble forms of phosphorus leading to increased plant growth. Pseudomonas putida PCI2 was evaluated for phosphatase activity and solubilization of AlPO4 and FePO4. The effect of different incubation temperatures, concentrations of NaCl and different pH on growth of PCI2 and P solubilization was studied. PCI2 proved to be positive for phosphatase activity, solubilized AlPO4 and hydrolyzed Ca3(PO4)2 even in medium with 5 % NaCl. In addition, PCI2 produced 45 % units of siderophores. The production of IAA by PCI2 was stimulated in vitro by the addition of different concentrations of L-tryptophan to the culture medium. Assays with tomato seedlings showed that the length of the root was reduced as the concentration of IAA increased. On the other hand, inoculation with PCI2 caused a clear growth-promoting effect on shoot growth in the presence of L-tryptophan. P. putida PCI2 is adapted to different environmental conditions and has potential to be developed and used as an inoculant for increasing the growth of tomato plants.Fil: Pastor, Nicolás Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; ArgentinaFil: Rosas, Susana Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; ArgentinaFil: Luna, Maria Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto; ArgentinaFil: Rovera, Marisa. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; Argentin

Evaluation of Pseudomonas chlororaphis subsp. aurantiaca SR1 for growth promotion of soybean and for control of Macrophomina phaseolina

Pseudomonas chlororaphis subsp. aurantiaca SR1 was evaluated for control of Macrophomina phaseolina in vitro and in soybean plants, for growth promotion of soybean plants and for production of antifungal compounds. Strain SR1 caused a significant inhibition of M. phaseolina in vitro and reduced damping-off in the in vivo assays. In addition, strain SR1 significantly increased shoot and root length and shoot and root dry weight of soybean plants in M. phaseolina infested soil, as compared to control plants in infested soil. Fragments for the phenazine-1-carboxylic acid, pyrrolnitrin and hydrogen cyanide encoding genes were amplified from the DNA of strain SR1 after polymerase chain reaction (PCR) assays with specific primers. Thus, this study establishes that P. chlororaphis subsp. aurantiaca SR1 provides control of M. phaseolina in vivo and suggests that strain SR1 might be applied as an effective biocontrol agent to protect soybean plants from this phytopathogen.Fil: Rovera, Marisa. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Microbiología e Inmunología; ArgentinaFil: Pastor, Nicolás Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; ArgentinaFil: Niederhauser, Marina Cristina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; ArgentinaFil: Rosas, Susana Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentin

Riego deficitario contolado en granado (Punica granatun L.). Poster

En el sureste español el granado se cultiva fundamentalmente en suelos marginales y de mala calidad agronómica. No obstante, este cultivo ha adquirido en dicha zona una importancia considerable, muestra de ello es que la provincia de Alicante es la primera productora española de granadas (MAPA, 1999). Por ello es conveniente adoptar una serie de medidas para la mejor explotación de este cultivo, encaminadas no solo a obtener mayores producciones, sino también el máximo aprovechamiento de los recursos naturales empleados, y entre ellos el agua. El objetivo de nuestro experimento es evaluar la respuesta del granado frente a diferentes estrategias de Riego Deficitario Controlado (RDC)