Development of a Multiplex PCR Assay for Genotyping the Fish Pathogen Piscirickettsia salmonis Through Comparative Genomics

Piscirickettsia salmonis is a bacterial pathogen that severely impact the aquaculture in several countries as Canada, Scotland, Ireland, Norway, and Chile. It provokes Piscirickettsiosis outbreaks in the marine phase of salmonid farming, resulting in economic losses. The monophyletic genogroup LF-89 and a divergent genogroup EM-90 are responsible for the most severe Piscirickettsiosis outbreaks in Chile. Therefore, the development of methods for quick genotyping of P. salmonis genogroups in field samples is vital for veterinary diagnoses and understanding the population structure of this pathogen. The present study reports the development of a multiplex PCR for genotyping LF-89 and EM-90 genogroups based on comparative genomics of 73 fully sequenced P. salmonis genomes. The results revealed 2,322 sequences shared between 35 LF-89 genomes, 2,280 sequences in the core-genome of 38 EM-90 genomes, and 331 and 534 accessory coding sequences each genogroup, respectively. A total of 1,801 clusters of coding sequences were shared among all tested genomes of P. salmonis (LF-89 and EM-90), with 253 and 291 unique sequences for LF-89 and EM-90 genogroups, respectively. The Multiplex-1 prototype was chosen for reliable genotyping because of differences in annealing temperatures and respective reaction efficiencies. This method also identified the pathogen in field samples infected with LF-89 or EM-90 strains, which is not possible with other methods currently available. Finally, the genome-based multiplex PCR protocol presented in this study is a rapid and affordable alternative to classical sequencing of PCR products and analyzing the length of restriction fragment polymorphisms

Role of age and comorbidities in mortality of patients with infective endocarditis

[Purpose]: The aim of this study was to analyse the characteristics of patients with IE in three groups of age and to assess the ability of age and the Charlson Comorbidity Index (CCI) to predict mortality. [Methods]: Prospective cohort study of all patients with IE included in the GAMES Spanish database between 2008 and 2015.Patients were stratified into three age groups:<65 years,65 to 80 years,and ≥ 80 years.The area under the receiver-operating characteristic (AUROC) curve was calculated to quantify the diagnostic accuracy of the CCI to predict mortality risk. [Results]: A total of 3120 patients with IE (1327 < 65 years;1291 65-80 years;502 ≥ 80 years) were enrolled.Fever and heart failure were the most common presentations of IE, with no differences among age groups.Patients ≥80 years who underwent surgery were significantly lower compared with other age groups (14.3%,65 years; 20.5%,65-79 years; 31.3%,≥80 years). In-hospital mortality was lower in the <65-year group (20.3%,<65 years;30.1%,65-79 years;34.7%,≥80 years;p < 0.001) as well as 1-year mortality (3.2%, <65 years; 5.5%, 65-80 years;7.6%,≥80 years; p = 0.003).Independent predictors of mortality were age ≥ 80 years (hazard ratio [HR]:2.78;95% confidence interval [CI]:2.32–3.34), CCI ≥ 3 (HR:1.62; 95% CI:1.39–1.88),and non-performed surgery (HR:1.64;95% CI:11.16–1.58).When the three age groups were compared,the AUROC curve for CCI was significantly larger for patients aged <65 years(p < 0.001) for both in-hospital and 1-year mortality. [Conclusion]: There were no differences in the clinical presentation of IE between the groups. Age ≥ 80 years, high comorbidity (measured by CCI),and non-performance of surgery were independent predictors of mortality in patients with IE.CCI could help to identify those patients with IE and surgical indication who present a lower risk of in-hospital and 1-year mortality after surgery, especially in the <65-year group

Marejadas rurales y luchas por la vida, vol. iv: permanencias, resistencias y luchas por la vida

Volumen 4. Permanencias, resistencias y luchas por la vida, coordinado por: Elisabeth A. Mager Hois, Miguel Ángel Paz Frayre y Carla Zamora Lomelí, integra 15 capítulos y está dividido en tres secciones, la primera denominada Permanencia, contiene 5 capítulos que intentan establecer como eje común la lucha continua en las comunidades campesinas para continuar con la vida rural. La segunda, Identidad y resistencia, está compuesta por 4 capítulos que reflexionan sobre varios procesos de resistencia de la vida rural ante los cambios globales e internos en su propio proceso de vida, otros trabajos intentan encontrar aquellos elementos que generan y mantienen alguna forma de identidad, y la tercera sección, Lucha por la vida, contiene 6 trabajos que demuestran todas aquellas posibilidades que existen en el medio rural para sostenerse y mantenerse, generando diferentes formas y estrategias que los une en la continua lucha por vivir con pocas pretensiones y con difíciles perspectivas pero siempre encontrando alternativas.ASOCIACIÓN MEXICANA DE ESTUDIOS RURALES, INSTITUTO DE CIENCIAS AGROPECUARIAS Y RURALES (ICAR), UNIVERSIDAD DE GUADALAJARA, FACULTAD DE ESTUDIOS SUPERIORES ACATLÁN-UNAM, ECOSUR, CUCOSTA SUR GRANA, EL COLEGIO DE MICHOACÁN A.C., UNIVERSIDAD MICHOACANA DE SAN NICOLAS HIDALG

Anales del III Congreso Internacional de Vivienda y Ciudad "Debate en torno a la nueva agenda urbana"

Acta de congresoEl III Congreso Internacional de Vivienda y Ciudad “Debates en torno a la NUEVa Agenda Urbana”, ha sido una apuesta de alto compromiso por acercar los debates centrales y urgentes que tensionan el pleno ejercicio del derecho a la ciudad. Para ello las instituciones organizadoras (INVIHAB –Instituto de Investigación de Vivienda y Hábitat y MGyDH-Maestría en Gestión y Desarrollo Habitacional-1), hemos convidado un espacio que se concretó con potencia en un debate transdisciplinario. Convocó a intelectuales de prestigio internacional, investigadores, académicos y gestores estatales, y en una metodología de innovación articuló las voces académicas con las de las organizaciones sociales y/o barriales en el Foro de las Organizaciones Sociales que tuvo su espacio propio para dar voz a quienes están trabajando en los desafíos para garantizar los derechos a la vivienda y los bienes urbanos en nuestras ciudades del Siglo XXI

Real time algorithm invariant to natural lighting with LBP techniques through an adaptive thresholding implemented in GPU processors

Video analysis in real time requires fast and efficient algorithms to extract relevant information from a considerable number, commonly 25, of frames per second. Furthermore, robust algorithms for outdoor visual scenes may retrieve correspondent features along the day where a challenge is to deal with lighting changes. Currently, Local Binary Pattern (LBP) techniques are widely used for extracting features due to their robustness to illumination changes and the low requirements for implementation. We propose to compute an automatic threshold based on the distribution of the intensity residuals resulting from the pairwise comparisons when using LBP techniques. The intensity residuals distribution can be modelled by a Generalized Gaussian Distribution (GGD). In this paper we compute the adaptive threshold using the parameters of the GGD. We present a CUDA implementation of our proposed algorithm. We use the LBPSYM technique. Our approach is tested on videos of four different urban scenes with mobilities captured during day and night. The extracted features can be used in a further step to determine patterns, identify objects or detect background. However, further research must be conducted for blurring correction since the scenes at night are commonly blurred due to artificial lighting

Sodium Tungstate (NaW) Decreases Reactive Oxygen Species (ROS) Production in Cells: New Cellular Antioxidant

Diabetic nephropathy (DN) is the leading cause of end-stage renal failure worldwide. Hyperglycemia generates reactive oxygen species (ROS), contributing to diabetic complications, especially in DN. Sodium Tungstate (NaW) is an effective antidiabetic agent for short and long-term treatments of both type 1 and type 2 diabetes models. In this study, we evaluated the effect of NaW on ROS production in bovine neutrophils incubated with platelet-activating factor (PAF) and in HK-2 cells induced by high glucose or H2O2. In addition, we evaluated the effect on iNOS expression in the type 1 diabetic rat model induced with streptozotocin (STZ). NaW inhibited ROS production in PAF-induced bovine neutrophils, and human tubular cells (HK-2) were incubated in high glucose or H2O2. In addition, NaW inhibited iNOS expression in glomeruli and tubular cells in the type 1 diabetic rat. This study demonstrates a new role for NaW as an active antioxidant and its potential use in treating DN

Core non-coding RNAs of <i>Piscirickettsia salmonis</i>

<div><p><i>Piscirickettsia salmonis</i>, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. <i>P</i>. <i>salmonis</i> has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of <i>P</i>. <i>salmonis</i> pathogenesis are relatively unknown, mainly due to its difficult <i>in vitro</i> culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (<i>trans</i>-acting) or antisense strand of open reading frames (<i>cis</i>-acting). The repertoire of ncRNAs present in the genome of <i>P</i>. <i>salmonis</i> and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of <i>P</i>. <i>salmonis</i> base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all <i>P</i>. <i>salmonis</i> genomes, constituting the core ncRNAs of <i>P</i>. <i>salmonis</i>. The ncRNA core of <i>P</i>. <i>salmonis</i> could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.</p></div

Predicted <i>P</i>. <i>salmonis</i> GacS/GacA-CsrA/CsrB/CsrC regulatory system.

<p>Predicted <i>P</i>. <i>salmonis</i> GacS/GacA-CsrA/CsrB/CsrC regulatory system.</p