Architecture of Burkholderia cepacia complex σ70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability

<p>Abstract</p> <p>Background</p> <p>The <it>Burkholderia cepacia </it>complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF) or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional σ⁷⁰factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the σ⁷⁰family of these bacteria.</p> <p>Results</p> <p>Twenty σ⁷⁰paralogous genes were detected in the <it>Burkholderia cenocepacia </it>strain J2315 (<it>Bcen</it>-J2315) genome, of which 14 were of the ECF (extracytoplasmic function) group. Non-ECF paralogs were related to primary (<it>rpoD</it>), alternative primary, stationary phase (<it>rpoS</it>), flagellin biosynthesis (<it>fliA</it>), and heat shock (<it>rpoH</it>) factors. The number of σ⁷⁰genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of <it>Pseudomonas aeruginosa</it>, a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different σ⁷⁰family architectures, with only three ECF paralogs in common (<it>fecI</it>-like, <it>pvdS </it>and <it>algU</it>). <it>Bcen</it>-J2315 σ⁷⁰paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone (<it>ecfA2</it>), particular Bcc species (<it>sigI</it>), the <it>Burkholderia </it>genus (<it>ecfJ</it>, <it>ecfF</it>, and <it>sigJ</it>), certain proteobacterial groups (<it>ecfA1</it>, <it>ecfC</it>, <it>ecfD</it>, <it>ecfE</it>, <it>ecfG</it>, <it>ecfL</it>, <it>ecfM </it>and <it>rpoS</it>), or were broadly distributed in the eubacteria (<it>ecfI</it>, <it>ecfK</it>, <it>ecfH</it>, <it>ecfB</it>, and <it>rpoD</it>-, <it>rpoH</it>-, <it>fliA</it>-like genes). Genomic instability of this gene family was driven by chromosomal inversion (<it>ecfA2</it>), recent duplication events (<it>ecfA </it>and <it>RpoD</it>), localized (<it>ecfG</it>) and large scale deletions (<it>sigI</it>, <it>sigJ</it>, <it>ecfC</it>, <it>ecfH</it>, and <it>ecfK</it>), and a phage integration event (<it>ecfE</it>).</p> <p>Conclusion</p> <p>The Bcc σ⁷⁰gene family was found to be under strong selective pressures that could lead to acquisition/deletion, and duplication events modifying its architecture. Comparative analysis of Bcc and <it>Pseudomonas aeruginosa </it>σ⁷⁰gene families revealed distinct evolutionary strategies, with the Bcc having selected several alternative primary factors, something not recorded among <it>P. aeruginosa </it>and only previously reported to occur among the actinobacteria.</p

Online leak diagnosis in pipelines using an EKF-based and steady-state mixed approach

This paper proposes a methodology for leak detection and isolation (LDI) in pipelines based on data fusion from two approaches: a steady-state estimation and an Extended Kalman Filter (EKF). The proposed method considers only pressure head and flow rate measurements at the pipeline ends, which contain intrinsic sensor and process noise. The LDI system is tested in real-time by using an USB data acquisition device that is implemented in MATLAB environment. The effectiveness of the method is analyzed by considering: online detection, location as well as quantification of non-concurrent leaks at different positions. The leak estimation error average is less than 1% of the flow rate and less than 3% in the leakage position. Furthermore, the incorporation of a steady-state estimation shows that the solution of the LDI problem has improved significantly with respect to the one that only considers the EKF estimation. An experimental analysis was also performed on the effectiveness of the proposed approach for different sampling rates and for different leakage positionsPeer ReviewedPostprint (author's final draft

Caracterización de especies de Paraburkholderia como promotoras del crecimiento vegetal

Un desafío en la actualidad para la agricultura es proporcionar suficientes alimentos, debido a esto los agricultores han hecho uso excesivo de fertilizantes o plaguicidas, ocasionando problemas en el ecosistema y en la calidad del suelo. Con el fin de mantener la calidad y fertilidad del mismo, diversas investigaciones han hecho énfasis en la implementación del uso de microorganismos benéficos para el mantenimiento de la calidad del suelo. Este tipo de bacterias son nombrados rizobacterias promotoras del crecimiento de las plantas (PGPR). Los mecanismos por los cuales, pueden mejorar el estado nutricional de las plantas son: fijación de N2, producción de ácido indol acético (AIA), solubilización de fosfatos, producción de sideróforos y control de fitopatógenos, principalmente. Se han publicado investigaciones donde se muestra que el género Paraburkholderia, presenta características de PGPR, ubicando a este género como un potencial bioinsumo para aplicación agrícola. El objetivo general del trabajo es: Determinar el potencial de Paraburkholderia tropica, Paraburkholderia unamae, Paraburkholderia silvatlantica y Paraburkholderia caballeronis para promover el crecimiento en plantas de maíz y realizar su caracterización genómica. A partir de los 23 genomas en estudio, P. tropica (6), P. unamae (3), P. silvatlantica (6), P. caballeronis (8) se realizó la caracterización genómica, primero se hizo una comparación de las 4 con sus cepas tipo, utilizando identidad de nucleótidos promedio (ANI) y calculadora de distancia genoma a genoma (GGDC). Así mismo, se hizo una comparación de los genomas en estudio con los genomas más relacionados usando la plataforma TYGS, finalmente una construcción filogenómica y búsqueda de los genes in silico, usando las plataformas JGI y AntiSMASH, este último para la búsqueda de metabolitos secundarios. Para la caracterización in silico de las cepas como PGPR, se determinó la producción de AIA, utilizando el reactivo de Salkowski, donde se muestra que solo algunas cepas poseen valores significativos, seguido a esto se realizó la fijación de N2 mediante el método de la reducción del acetileno donde se observó esta característica en las 4 especies, posteriormente se realizaron las pruebas para producción de sideróforos (medio MM9) y solubilización de fosfatos (medio NBRIP modificado), las 23 cepas presentaron esta actividad, aunque en diferente medida a excepción de P. silvatlantica TPCrh-89 y SRCL-318, para la solubilización de fosfato. Finalmente, se realizaron las pruebas de inoculación en plantas de maíz y se determinó el peso en seco para cada una de ellas, obteniendo valores significativos en peso en seco de la parte aérea para P. tropica Sir-6529 y P. silvatlantica PSCR-88. Como conclusiones las cepas en estudio, concuerdan con la especie en las que se les había asignado previamente y esto se corrobora con el análisis filogenómico. Todas las cepas presentan la actividad de producción de AIA, aunque su comportamiento fue diferente entre las cepas a los diferentes tiempos, todas presentan la actividad de fijación de N2, producción de sideróforos, a excepción de 2 cepas todos solubilizaron fosfatos. Así mismo, las 4 especies cuentan en su genoma con diferentes genes relacionados a las actividades PGP. Se obtuvieron valores significativos en la parte de peso en seco respecto al control

Efecto de rizobacterias promotoras del crecimiento vegetal en plantas sometidas a estrés hídrico: un enfoque desde la fisiología vegetal

RESUMEN La sequía afecta significativamente el estado fisiológico de las plantas y, en consecuencia, la producción agrícola. El cambio climático supone un reto mayor para la agricultura, ya que las proyecciones indican la disminución del agua disponible para los cultivos en varias regiones del mundo. En este sentido, es necesario buscar estrategias que permitan la viabilidad de la producción sin provocar los daños que la agricultura intensiva convencional trae al equilibrio planetario. En este trabajo se abordan, desde un enfoque fisiológico, los impactos que tiene la sequía sobre las plantas y que afectan negativamente su productividad. Asimismo, se revisan los diferentes mecanismos de resistencia que han desarrollado las plantas para enfrentar la falta de agua para así comprender las características que presentan las rizobacterias promotoras del crecimiento vegetal y que, de diversas maneras, refuerzan o inducen resistencia ante el estrés hídrico en las plantas con las que se asocian, convirtiéndolas en una opción de interés para la adaptación de los cultivos ante condiciones de baja disponibilidad de agua. Asimismo, se plantea la importancia de transitar hacia la concepción de los ecosistemas rizosféricos como un sistema complejo y favorecer prácticas agrícolas basadas en el profundo entendimiento de los procesos ecológicos que se llevan a cabo entre el microbioma y la planta para coadyuvar a generar agroecosistemas productivos y resilientes ante los embates del cambio climático, reduciendo las afectaciones al ambiente y la salud humana. ABSTRACT Drought is a stressor that significantly affects the physiological state of plants and, consequently, agricultural production. Climate change possess a major challenge to agriculture as projections indicate a decrease in water availability for crops in various world regions. Therefore, it is necessary to seek strategies that enable viable production without causing the damage associated with conventional intensified agriculture which disrupts the planetary balance. This review focuses on the physiological impacts of drought on plants which negatively affect productivity. It also examines the different resistance mechanisms that plants have developed to cope with water scarcity, aiming to understand the characteristics of plant growth promoting rhizobacteria. These bacteria, in various ways, reinforce or induce resistance to water stress in the plants they associated with, making them an interesting option for adapting crops to conditions of low water availability. Additionally, we highlight the importance of viewing rhizospheric ecosystems as complex systems that favor agricultural practices based on a deep understanding of the ecological processes occurring between the microbiome and the plant. The creation of productive and resilient agroecosystems in the face of climate change will likely reduce negative effects on the environment and human health

Development of non-invasive monitoring approach to diagnose leaks in liquid pipelines

This paper presents a novel non-invasive monitoring method, based on a Liénard-type model (LTM) to diagnose single and sequential leaks in liquid pipelines. The LTM describes the fluid behavior in a pipeline and is given only in terms of the flow rate. Our method was conceived to be applied in pipelines mono-instrumented with flowmeters or in conjunction with pressure sensors that are temporarily unavailable. The approach conception starts with the discretization of the LTM spatial domain into a prescribed number of sections. Such discretization is performed to obtain a lumped model capable of providing a solution (an internal flow rate) for every section. From this lumped model, a set of algebraic equations (known as residuals) are deduced as the difference between the internal discrete flows and the nominal flow (the mean of the flow rate calculated before the leak). Once the residuals are calculated a principal component analysis (PCA) is carried out to detect a leak occurrence. In the presence of a leak, the residual closest to zero will indicate the section where a leak is occurring. Some simulation-based tests in PipelineStudio® and experimental tests in a lab-pipeline illustrating the suitability of our method are shown at the end of this article

Evaluation of cytotoxic and genotoxic effects with micronucleus test in the oral mucosa of patients with orthodontic appliances. Review of the literature

Las maloclusiones representan un problema de salud bucodental, que se resuelven mediante la colocación de aparatología ortodóncica fija (AOF). Esta aparatología provoca corrosión y liberación de iones metálicos por las aleaciones que la constituyen y por el tiempo prolongado del tratamiento. El objetivo de este trabajo fue analizar las alteraciones citotóxicas y genotóxicas de las células de la mucosa oral provocadas por el uso de AOF, reportadas en la literatura y evaluadas con ensayo de micronúcleos (MN); el cual es uno de los ensayos más utilizados para identificar el daño al ácido desoxirribonucleico (ADN). Se realizó una revisión de la literatura de los últimos 10 años, donde se incluyeron nueve estudios, el 55% de estos mostró evidencia de daño citotóxico y genotóxico posterior a la terapia ortodóncica. El promedio de incremento de MN debido al uso de AOF en estos estudios, fue tres veces mayor con respecto a las células bucales sin tratamiento, este dato es similar a reportes de células orales precancerosas investigadas por otros autores. Además los artículos evaluados, reportaron alteración celular a partir de la primera semana de la colocación de los dispositivos y señalaron que hay una disminución del daño con el tiempo de exposición. En conclusión, el ensayo de MN utilizado en la cavidad bucal demostró ser útil para detectar alteraciones en el ADN debido al uso de AOF. Los datos analizados permiten a los ortodoncistas implementar mejoras en la terapéutica ortodóncica.Malocclusions represent an oral health problem, which is resolved by the placement of fixed orthodontic appliances (FOA). This orthodontic appliance causes corrosion and release of metal ions due to the alloys they constitute and due to the prolonged time of treatment. The objective of this work was to analyze the cytotoxic and genotoxic alterations from oral mucosa cells, caused by the use of FOA, reported in the literature and evaluated with micronucleus (MN) test, which is one of the most widely used tests to identify damage to deoxyribonucleic acid (DNA). A review of the literature of the last 10 years was carried out, where nine studies were included, 55% of these studies showed evidence of cytotoxic and genotoxic damage after orthodontic therapy. The increased average in MN due to the use of FOA in these studies, represent values of approximately three-fold more respect to oral cells without treatment, this data is similar to reports of precancerous oral cells that have been reported by other authors. Besides, the articles analyzed reported cell alterations after the first week of the devices placement and indicated a decrease in damage with exposure time. In conclusion, the MN test used in the oral cavity was useful in detecting DNA alterations due to the use of FOA. The data analyzed allow orthodontists to implement improvements in orthodontic therapy

Analyzing connectivity in collective transportation line networks by means of hypergraphs

In this paper we will show how hypergraphs and some measures related to them can help in extracting information about Collective Transportation Line Networks. We will also prove that these measures satisfy certain properties that validate their use to compare the connectivity of different networks. © 2013 EDP Sciences and Springer.This work was partially supported by Ministerio de Educacion, Ciencia e Innovacion (Spain)/FEDER under project MTM2009-14243 and by Junta de Andalucia (Spain)/FEDER under excellence proyects P09-TEP-5022 and FQM-5849. Special thanks are due to two anonymous referees for their valuable comments and advice.Barrena, E.; De-Los-Santos, A.; Mesa López-Colmenar, JA.; Perea Rojas Marcos, F. (2013). Analyzing connectivity in collective transportation line networks by means of hypergraphs. European Physical Journal - Special Topics. 215(1):93-108. https://doi.org/10.1140/epjst/e2013-01717-3S931082151D.J. Watts, S.H. Strogatz, Nature 393, 440 (1998)V. Latora, M. Marchiori, Phys. Rev. Lett. 87, 198701 (2001)V. Latora, M. Marchiori, Physica A 314, 109 (2002)R. Criado, B. Hernández-Bermejo, M. Romance, Int. J. Bifurcation Chaos 17, 2289 (2007)A. De-Los-Santos, G. Laporte, J.A. Mesa, F. Perea, Transp. Res. Part C: Emerging Technol. 20, 34 (2012)E. Barrena, A. De-Los-Santos, J.A. Mesa, F. Perea, Technical proofs of paper “Analyzing Connectivity in Collective Transportation Line Networks by means of Hypergraphs”, http://grupo.us.es/transfers/ (2012)C. Berge, Graphs and Hypergraphs (Elsevier Science Ltd., 1985)C. Berge, Hypergraphs: combinatorics of finite sets (North Holland)D.J. Watts, Small Worlds: The Dynamics of Networks between Order and Randomness (Princeton University Press, Princeton, 1999), p. 262M.E.J. Newman, Technical report, Santa Fe Institute (2001)M.E.J. Newman, Phys. Rev. E 64, 016131 (2001)M.E.J. Newman, Phys. Rev. E 64, 016132 (2001)E. Estrada, J.A. Rodríguez-Velázquez, Phys. A: Statist. Mech. Appl. 364, 581 (2006)R. Dechter, Constraint Processing (Morgan Kaufmann, 2003), p. 450P. Sen, S. Dasgupta, A. Chatterjee, P.A. Sreeram, G. Mukherjee, S.S. Manna, Phys. Rev. E 67 (2003)P. Crucitti, V. Latora, M. Marchiori, A. Rapisarda, Physica A 320, 642 (2002) [cond-mat/0205601]V. Latora, M. Marchiori, Chaos Solitons Fract. 20, 69 (2004)V. Latora, M. Marchiori, Eur. Phys. J. B 32, 249 (2002

PHÂN TÍCH DI TRUYỀN KHẢ NĂNG DI CHUYỂN THEO PHENANTHRENE CỦA VI KHUẨN PSEUDOMONAS STUTZERI E1

ABSTRACTPseudomonas stutzeri strain E1 shows a two-time accelerated swarming behavior in minimal medium with sprayed phenanthrene in swimming assays and a five-time higher chemotaxis towards dissolved phenanthrene in capillary assays.  A mutant bank of strain E1 was constructed using the pTnMod-OGm plasposon mutagenesis system.  82 out of 2639 electroporants screened showed an altered phenotype of phenanthrene-driven motility and/or phenanthrene degradation. 16 representative mutants were selected for sequencing the genes flanking the plasposon insertion. Mutations in flhA resulted in abolished swimming and swarming phenotype, and in flgK resulted in abolished swimming and diminished swarming phenotype.  A mutation in cheY performed abolished swimming and reduced swarming activity while a gidA mutation resulted in decreased phenanthrene degradation and both decreased swimming and swarming behavior. A mutation in gene encoding a Zn dependent protease and in a gene encoding capsular polysaccharide biosynthesis protein resulted in abolished swarming suggesting that these proteins also play a potential role in the swarming activity of P. stutzeri E1.Keywords: Pseudomonas stutzeri, polycyclic aromatic hydrocarbon, phenanthrene, chemotaxis, plasposon pTnMod-OGm, swimming, swarmingTitle: Genetic analysis of phenanthrene-driven motility by the phenanthrene-degrading soil isolate Pseudomonas stutzeri E1TóM TắTPseudomonas stutzeri dòng E1 có khả năng di chuyển bề mặt tăng gấp đôi khi nuôi trong môi trường tối thiểu được phủ phenanthrene.  Thí nghiệm mao dẫn cũng cho thấy E1 di chuyển nhanh gấp năm lần về hướng có phenanthrene.  Plasposon pTnMod-OGm được dùng để tạo thư viện đột biến dòng E1.  Trong số 2639 đột biến đã khảo sát, 82 đột biến biểu hiện những thay đổi về khả năng di chuyển theo phenanthrene và/hoặc phân hủy phenanthrene.  16 đột biến được chọn để giải trình tự của các gen đột biến tương ứng. Đột biến gen flhA làm E1 mất khả năng bơi và di chuyển bề mặt, đột biến gen flgK làm mất khả năng bơi và giảm khả năng di chuyển bề mặt của E1.  Đột biến gen cheY làm mất khả năng bơi và giảm khả năng di chuyển bề mặt trong khi đột biến gen gidA làm giảm khả năng phân hủy phenanthrene và giảm cả khả năng bơi và di chuyển bề mặt của E1.  Đột biến gen tổng hợp protein Zn-dependent protease và gen tổng hợp vỏ polysaccharide làm cho E1 mất khả năng di chuyển bề mặt chứng tỏ các protein này cũng giữ vai trò tiềm năng trong hoạt động di chuyển bề mặt của P. stutzeri E1.Từ khoá: Pseudomonas stutzeri, hydrocarbon đa vòng thơm, phenanthrene, hóa hướng động, plasposon pTnMod-OGm, bơi, di chuyển bề mặt</p