The Use of Bioinformatic Tools in Symbiosis and Co-Evolution Studies

Through millions of years, the multicellular organisms have coexisted and coevolved with the surrounding microorganisms, in an almost symbiotic relationship forming a complex entity known as holobiont. The composition and functions of these microbial communities were limited during many years to only a mere fraction, due to the use of culture-based techniques. The advent of molecular-based techniques allowed the identification of uncultured organisms in a culture-free manner. In recent years, the development of next generation sequencing techniques have allowed the high-throughput study of microbial communities allowing the identification and classification of otherwise uncultured microorganisms in a given environment, tissue or host through metagenomics. The next generation sequencing techniques have been used in the functional study of microbial assemblages and were able to identify the role of the microorganisms in biogeochemical cycles, pathogenic processes, metabolism and development, through metatranscriptomics. Taken together, the next generation sequencing based-studies have shown the existence of a complex metabolic network in different hosts and environments, with the microbial communities. This chapter will focus in different available bioinformatic tools that are suitable to study symbiosis and coevolution processes in a given sample

Primer reporte de Pectobacterium spp. asociada a Opuntia ficus en Baja California, México

During the 2013-2014 production cycle, the presence of soft rot in Opuntia ficus cv Chicomostoc plants in the Mexicali Valley and West Coast of Baja California. The aim of this study was to determine the etiological agent of those symptoms, so infected pads were collected and proceeded to run morphological, physiological, and pathogenicity tests as well. Based on the results of the tests, the etiological agent of the soft rot observed in Opuntia was Pectobacterium spp. This is the first report of this bacteria in the Baja California area.Durante el ciclo de producción 2013-2014, se detectó la presencia de pudriciones blandas en plantas de nopal (Opuntia ficus cv Chicomostoc) en el Valle de Mexicali y Zona Costa de Baja California. El objetivo del presente trabajo fue determinar el agente causal de dichos síntomas, por lo que cladodios infectados fueron colectados y analizados con pruebas bioquímicas y fisiológicas, así como de patogenicidad. Basado en los resultados de las pruebas, el agente causal de las pudriciones blandas observadas en nopal fue Pectobacterium spp. Este es el primer reporte de dicha bacteria en la zona de Baja Californi

Red de mercadeo y rentabilidad de flor de corte en el Valle de Mexicali, Baja California, México

Cut flower commercialization for Baja California contributed during 2004 with more than 122 million pesos, considering flower seed and cut flower production. Most of cut flowers produced in state of Baja California Norte is for export market, by this reason local market means an opportunity for introducing quality products at market prices from national companies. Mexicali city, by being near USA and together with its population economic wealth thanks to profitability of cotton and orchards production in Mexicali Valley, is one or the main producer region in the country. By this reason and thanks to great amount of flower shops located in the region the aim of describing marketing network and profitability for cut flower in Mexicali Valley is proposed. Market study and diagnose to make FODA analysis were developed, defining strategies in order to seize economic potential. Actual distribution networks and marketing system consist in moving cut flowers from production centers, Córdoba, Veracruz and Coatepec de Harinas district, state of Mexico, up to Mexicali Valley, Baja California, keeping quality and optimum vase life for final customer, also proper planning for production chain due not covered demand along year it is required, the population has economical potential and tradition to give flowers guaranteeing good profitability. Roses (Rosa gigantea and R. chinensis L.), asian lilies (Lilium spp.), chrysanthemum [Dendranthema x grandiflorum (Ramat) Kitamura c. v. Polaris White], carnation (Dianthus caryophyllus), gerbera (Gerbera jamesonii H. Bolux ex Hook F.) and oriental lilies (Lilium spp.) are species with more consumers' interestLa comercialización de flor de corte para Baja California aportó durante 2004 poco más de 122 millones de pesos, considerando semilla para flor y producción de flor de corte. Debido a la exportación de casi la totalidad de la producción estatal de flor cortada, el mercado local representa una oportunidad para la introducción de productos de calidad a precios competitivos de empresas nacionales, siendo Mexicali una ciudad cercana Estados Unidos de América, y aunado al poder adquisitivo de la población es la rentabilidad de las producciones de algodón y hortalizas del Valle de Mexicali, una de las principales zonas productoras del país. Por lo anterior y aunado al importante número de florerías localizadas en la zona se planteó como objetivo describir la red de mercadeo y rentabilidad de la flor de corte en el Valle de Mexicali. Se realizó un estudio de mercado y el diagnóstico para elaborar el análisis FODA, se determinaron las estrategias para el aprovechamiento del potencial económico. El sistema de redes de distribución y mercadeo actual consiste en trasladar las flores de corte desde los centros de producción, Córdoba, Veracruz y distrito de Coatepec Harinas, Estado de México, hasta el Valle de Mexicali, Baja California conservando la calidad y óptima vida de florero hasta su consumo final, asimismo, se requiere de una adecuada planeación de la cadena productiva debido a la presencia de una demanda insatisfecha a lo largo del año, la población cuenta con el potencial económico y la tradición de obsequiar flores lo cual garantiza una buena rentabilidad. Las especies de mayor interés de los consumidores son rosas (Rosa gigantea y R. chinensis L.), lilis asiáticas (Lilium spp.), polar [Dendranthemaxgrandiflorum (Ramat) Kitamura c. v. Polaris White], clavel (Dianthus caryophyllus), gerbera (Gerbera jamesonii H. Boluxex Hook F.) y lilis orientales (Lilium spp.

RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (Litopenaeus vannamei) in Different Stages of Development

White leg shrimp (Litopenaeus vannamei) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of L. vannamei has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of L. vannamei. In this study the metatranscriptome in different developmental stages of L. vannamei (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the Proteobacteria, Firmicutes and Actinobacteria, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in L. vannamei and the microbiome were shown. This study provides evidence of the interaction of the microbiome with L. vannamei, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of L. vannamei

RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (<i>Litopenaeus vannamei</i>) in Different Stages of Development

White leg shrimp (Litopenaeus vannamei) is a widely cultured species along the Pacific coast and is one of the most important crustaceans in world aquaculture. The microbiome composition of L. vannamei has been previously studied in different developmental stages, but there is limited information regarding the functional role of the microbiome during the development of L. vannamei. In this study the metatranscriptome in different developmental stages of L. vannamei (larvae, juvenile and adult) were generated using next generation sequencing techniques. The bacterial phyla found throughout all the stages of development belonged to the Proteobacteria, Firmicutes and Actinobacteria, these bacterial phyla are present in the digestive tract and are capable of producing several hydrolytic enzymes, which agrees with high representation of the primary metabolism and energy production, in both host and the microbiome. In this sense, functional changes were observed as the development progressed, in both host and the microbiome, in stages of larvae the most represented metabolic functions were associated with biomass production; while in juvenile and adult stages a higher proportion of metabolic functions associated to biotic and abiotic stress in L. vannamei and the microbiome were shown. This study provides evidence of the interaction of the microbiome with L. vannamei, and how the stage of development and the culture conditions of this species influences the gene expression and the microbiome composition, which suggests a complex metabolic network present throughout the life cycle of L. vannamei

Compound Identification from Bromelia karatas Fruit Juice Using Gas Chromatography&ndash;Mass Spectrometry and Evaluation of the Bactericidal Activity of the Extract

Fruits of species of the genus Bromelia contain compounds with health benefits and potential biotechnological applications. For example, Bromelia karatas fruits contain antioxidants and proteins with bactericidal activity, but studies regarding the activity of these metabolites and potential benefits are required. We evaluated the bactericidal activity of the methanolic extract (treated and not treated with activated charcoal) and its fractions (hexane, ethyl acetate, and methanol) from ripe B. karatas fruit (8 &deg;Brix) against Escherichia coli, Enterococcus faecalis, Salmonella enteritidis, and Shigella flexneri. The methanolic extract (ME) minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined at eight concentrations. The methanolic extract MIC was 5 mg/mL for E. faecalis and 10 mg/mL for the other bacteria; the MBC was 20 mg/mL for E. coli and E. faecalis, and 40 mg/mL for S. enteritidis and S. flexneri. Through gas chromatography&ndash;mass spectrometry, 131 compounds were identified, some of which had previously been reported to have biological activities, such as bactericidal, fungicide, anticancer, anti-inflammatory, enzyme inhibiting, and anti-allergic properties. The most abundant compounds found in the ME of B. karatas fruits were maleic anhydride, 5-hydroxymethylfurfural, and itaconic anhydride. This study shows that B. karatas fruits contain metabolites that are potentially beneficial for health