Transcriptome mining provides insights into cell wall metabolism and fiber lignification in Agave tequilana Weber

Luis Fernando Maceda Lopez ELSA BEATRIZ GONGORA CASTILLO Enrique Ibarra-Laclette DALIA C. MORAN VELAZQUEZ AMARANTA GIRON RAMIREZ Matthieu Bourdon José Luis Villalpando Aguilar Gabriela Chavez-Calvillo Toomer John Tang Parastoo Azadi Jorge Manuel Santamaría Fernández Itzel López-Rosas Mercedes G Lopez June Simpson FULGENCIO ALATORRE COBOS (2022, [Artículo])

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioen-ergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for un-derstanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

AGAVE CELL WALLS LIGNOCELLULOSE CAD PROTEIN CESA PROTEIN SCLERENCHYMA BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS

A Computational Method for the Binding Mode Prediction of COX-1 and COX-2 Inhibitors: Analyzing the Union of Coxibs, Oxicams, Propionic and Acetic Acids

ESTEFANY BELLO VARGAS JOSE MARIO ORDOÑEZ PALACIOS (2023, [Artículo])

Among the biological targets extensively investigated to improve inflammation and chronic inflammatory conditions, cyclooxygenase enzymes (COXs) occupy a prominent position. The inhibition of these enzymes, essential for mitigating inflammatory processes, is chiefly achieved through Non-Steroidal Anti-Inflammatory Drugs (NSAIDs). In this work, we introduce a novel method—based on computational molecular docking—that could aid in the structure-based design of new compounds or the description of the anti-inflammatory activity of already-tested compounds. For this, we used eight crystal complexes (four COX-1 and COX-2 each), and each pair had a specific NSAID: Celecoxib, Meloxicam, Ibuprofen, and Indomethacin. This selection was based on the ligand selectivity towards COX-1 or COX-2 and their binding mode. An interaction profile of each NSAID was compiled to detect the residues that are key for their binding mode, highlighting the interaction made by the Me group. Furthermore, we rigorously validated our models based on structural accuracy (RMSD < 1) and (R2 > 70) using eight NSAIDs and thirteen compounds with IC50 values for each enzyme. Therefore, this model can be used for the binding mode prediction of small and structurally rigid compounds that work as COX inhibitors or the prediction of new compounds that are designed by means of a structure-based approach.

BIOLOGÍA Y QUÍMICA QUÍMICA anti-inflammatory, cyclooxygenase (COXs), molecular docking, NSAIDs, Celecoxib, Meloxicam, Ibuprofen,

Estudios de genética en poblaciones de abulón y sus aplicaciones en ordenamiento pesquero

RICARDO PEREZ ENRIQUEZ NOE DIAZ VILORIA JOSE LUIS GUTIERREZ GONZALEZ ALEJANDRA ARCINIEGA DE LOS SANTOS ADRIANA MAX AGUILAR Pedro Cruz Hernández Fernando Aranceta Garza (2016, [Artículo])

"Se presenta la integración de más de 10 años de investigación científica en genética de las poblaciones de abulón en México realizada en el CIBNOR. Esta investigación muestra cómo se pueden aplicar los marcadores genéticos tanto en estudios de genética poblacional como en identificación forense con la finalidad de contribuir al conocimiento aplicado para manejo de la pesquería. Se desarrollaron marcadores genéticos tipo microsatélites de ADN enfocados tanto al abulón azul Haliotis fulgens como amarillo Haliotis corrugata para diferenciación de poblaciones y análisis de parentesco. Un análisis de estructura genética de las poblaciones silvestres de ambas especies de abulón mostró homogeneidad genética en la costa del Pacífico en la región centro-sur de la Península de Baja California, México, pero con diferenciación genética en localidades distantes debido a un flujo genético limitado producto del aislamiento reproductivo. Por ello, no existen elementos que den soporte a un manejo pesquero delimitado por bancos en ambas especies. De manera particular, el abulón amarillo mostró una menor de diversidad genética que el azul, posiblemente debido a una mayor explotación pesquera histórica. Los resultados obtenidos en pruebas de parentesco han indicado que la retención larvaria en bancos específicos es reducida, por lo que ni la agregación de reproductores ni la liberación de larvas han mostrado ser estrategias eficientes para favorecer el incremento de reclutas en bancos definidos. Un análisis de perfiles genéticos con el gen de la lisina permitió la identificación de las especies de abulón que se capturan y enlatan en México. El análisis comparativo de perfi les genéticos, basado en el gen nuclear 18S de abulón y otros moluscos, detectó producto enlatado conteniendo especies de moluscos comercializadas falsamente como abulón, lo que puede constituirse como una herramienta forense en futuras disputas legales. Este tipo de aplicación es potencialmente utilizable con otros productos comestibles en los cuales se sospecha de prácticas fraudulentas, ya sea por captura o comercialización ilegal o por sustitución de contenidos en productos procesados."

"This is an integrative work of more than 10 years of research in population genetics of abalone in Mexico performed at CIBNOR. It shows how molecular tools have the potential to support abalone fisheries management through population genetics and forensic analyses. Microsatellite DNA markers were developed on blue (green for its name in English) Haliotis fulgens and yellow abalone (pink for its name in English) H. corrugata to be used for genetic differentiation on populations and for parentage analysis. The analysis of genetic structure on wild populations of both species revealed genetic homogeneity in the Pacific coast of the central region of the Baja California Peninsula, Mexico, with genetic differentiation on distant localities due to a limited gene flow as a result of reproduction isolation. From this result we suggest that no evidences were found supporting the management of the fishery based on individual abalone beds. Pink abalone shows lower genetic diversity than green abalone, possibly due to higher historical fishery exploitation. The parentage analysis suggested that larval retention within beds is reduced, indicating that neither broodstockaggregation nor the release of abalone larvae for stock enhancement are efficient strategies to increase recruitment in specific beds.

An analysis of the genetic profiles with the lysine gene allowed the identification of abalone species captured and processed in Mexico. The comparative analysis, based on the 18S gene, among abalone and other mollusks, detected canned product containing mollusks that are commercialized allegedly as abalone or ‘abalone type’, which could constitute a forensic tool in future legal disputes. This type of application can also be used with other edible products in which fraudulent practices are suspected either because of illegal catch or commercialization or substitution in processed products."

Análisis forense, diversidad genética, gen 18S, genética de poblaciones, marcadores genéticos, retención larvaria Forensic analysis, genetic diversity, 18S gene, genetic markers, population genetics, larval retention BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA DE POBLACIONES GENÉTICA DE POBLACIONES

Interfaces hápticas para identificar marcadores digitales del Trastorno del Espectro Autista

Haptic interfaces to identify digital markers of Autism Spectrum Disorder

GLORIA IVONNE MONARCA PINTLE (2023, [Tesis de doctorado])

El uso de herramientas de cribado durante la infancia es de suma importancia para identificar a niños que pueden Trastorno del Espectro Autista (TEA); sin embargo, las pruebas que existen en la actualidad se basan en cuestionarios y observaciones contestadas por los padres por lo que el resultado puede ser subjetivo. Además, la mayoría de las pruebas de cribado se enfocan en el área social y de comunicación, dejando a un lado las características sensoriales, un área donde los padres notan las primeras señales de un desarrollo atípico. En los últimos años, ha crecido el interés por identificar marcadores digitales del TEA que puedan apoyar el cribado de dicho trastorno, usando tecnología que pueda ser usada en cualquier lugar y momento para agilizar el proceso de cribado. Hasta el momento, la investigación en torno a marcadores digitales del TEA relacionados con el procesamiento táctil, ha sido poco explorada debido a que la investigación se ha centrado en explorar otros comportamientos, como la atención visual, movimientos motores, y voz. El crecimiento de las interfaces hápticas abre la posibilidad de explorar el procesamiento táctil e identificar marcadores digitales del TEA. En esta tesis exploramos si las interfaces hápticas pueden ser usadas para promover y recolectar interacciones táctiles que revelen marcadores digitales del TEA. Para tener un mejor entendimiento de las interfaces hápticas, en este trabajo de tesis exploramos dos interfaces hápticas. Una interfaz háptica pasiva llamada BendableSound, la cual cuenta con una retroalimentación por textura y espacio; y una interfaz háptica activa llamada Feel and Touch, la cual es un juego móvil que utiliza patrones vibrotactiles para retroalimentar las interacciones de los niños. Los resultados muestran que las interfaces hápticas tienen la capacidad recolectar interacciones táctiles y revelar marcadores digitales que pueden estar asociados al TEA. En el caso pasivo, participaron 37 niños neurotípicos (NT) y 22 niños con TEA quienes interactuar con BendableSound; los resultados muestran que existen diferencias entre los niños NT y TEA en cuanto al ancho de las interacciones táctiles, la fuerza que aplican y el tiempo que utilizan para realizar interacciones táctiles. En el caso activo, participaron 36 niños NT y 19 niños con TEA quienes interactuaron con Feel and Touch; los resultados muestran que existen diferencias entre los niños NT y TEA en cuanto a la ...

The use of screening tools during infancy is crucial to identify children who are likely to have Autism Spectrum Disorder (ASD); however, the current screening tests are based on questionnaires and observations that parents answer bases on their observations; however, the results might be subjective. In addition, most screening tests focus on the assessment of social and communication skills, disregard sensory skills, an area where parents often notice the first signals of ASD. In recent years, there has been growing interest in identifying digital markers of ASD that can support screening, particularly those that that can be used at any time and any place to speed up the screening process. So far, research on digital markers of ASD related to tactile processing has been little explored due to the lack of tools to assess it. The growth of haptic interfaces opens the possibility to explore tactile processing and identify digital markers of ASD. In this thesis, we propose to investigate the use of haptic interfaces to promote and collect tactile interactions that can reveal digital markers of ASD. To have a better understanding of haptic interfaces, in this thesis work we explore two types of haptic interface. A passive haptic interface called BendableSound, which features texture and spatial feedback; and an active haptic interface called Feel and Touch, which is a mobile game that uses vibrotactile patterns to provide feedback on children’s interactions. The results show that haptic interfaces have the potential to collect touch interactions and reveal digital markers that may be associated with ASD. In the first case, 37 neurotypical (NT) children and 22 children with ASD participated and interacted with BendableSound; the results show that there are differences between NT and ASD children in the width of tactile interactions, the force they apply, and the time they use to perform tactile interactions. In the second case, 36 NT children and 19 children with ASD participated and interacted with Feel and Touch; the results show that there are differences between NT and ASD children in terms of the tilt they produce on the mobile when performing tactile interactions, the total acceleration they produce, and the closeness to the center of the screen of their tactile interactions. The results of this thesis indicate that haptic interfaces have the ability to gather touch interactions and uncover digital markers associated with ASD. The findings of this ...

autismo, cribado, marcadores digitales, interfaces hápticas, aprendizaje automático autism, screnning, digital markers, haptic interfaces, machine learning INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS TECNOLOGÍA DE LOS ORDENADORES ORDENADORES DIGITALES ORDENADORES DIGITALES

Búsqueda de un conjunto óptimo de descriptores moleculares para la modelación QSAR

Search for an optimal subset of molecular descriptors for QSAR modeling

Luis Antonio García González (2023, [Tesis de doctorado])

En la actualidad, se estima que más de 10 millones de vertebrados son utilizados cada año en estudios toxicológicos. Dadas estas circunstancias, varias agencias regulatorias están impulsando activamente a la comunidad científica para el desarrollo de una alternativa a la experimentación con animales. Entre las alternativas existentes se pueden encontrar los estudios in-silico, especialmente los métodos de Relación Cuantitativa Estructura-Actividad (QSAR por sus siglas en inglés), los cuales se destacan como uno de los más utilizados. Los estudios QSAR se basan en la hipótesis de que compuestos estructuralmente similares presentan una actividad similar, lo que permite predecir la actividad de nuevos compuestos en función de compuestos estructuralmente similares, para los cuales se definió su actividad de forma experimental. Estudios han demostrado que la selección del subconjunto “óptimo” de las variables (descriptores moleculares) que caracterizan estructuralmente los compuestos tiene mayor importancia para la construcción de un modelo QSAR robusto que la estrategia de modelación utilizada. Actualmente, los descriptores moleculares (DMs) utilizados para la modelación QSAR son calculados con herramientas computacionales que no tienen en cuenta si estos caracterizan bien la actividad que se quiere modelar y los compuestos que se están analizando. En este trabajo se describen las limitaciones del enfoque actual, teniendo en cuenta que, si se sigue este enfoque, se puede pasar por alto información relevante al suponer que el conjunto de DMs calculado caracteriza bien las estructuras químicas que se están analizando, cuando en realidad puede que esto no suceda. Estas limitaciones se deben principalmente a que dichas herramientas limitan el número de DMs que calculan, restringiendo el dominio de los parámetros en los que se definen los algoritmos que calculan los DMs, parámetros que definen el Espacio de Configuración de Descriptores (DCS por sus siglas en inglés). En este trabajo se propone relajar estas restricciones en un enfoque DCS abierto, de manera que se pueda considerar inicialmente un universo más amplio de DMs y que estos caractericen de manera adecuada las estructuras a modelar. La generación de DMs se aborda entonces como un problema de optimización multicriterio, y para darle solución, dos algoritmos evolutivos son propuestos. Estos algoritmos incluyen conceptos de coevolución cooperativa para medir la sinergia entre descriptores moleculares ...

Currently, it is estimated that more than 10 million vertebrates are used per year for toxicological studies. Numerous regulatory agencies are actively advocating for the development of alternative methods to avoid unnecessary experimentation on animals. Among the existing alternatives in silico studies, especially Quantitative Structure Activity Relationships (QSAR) methods, stands out as one ofthe most widely used approaches. QSAR Methods are based on the premise that molecules with similar structures presents similar activities, which makes it possible to predict the activity of new compounds based on structurally similar compounds, for which their activity has been defined experimentally. Studies have demonstrated that the selection of the “optimal” set of molecular descriptors (MDs) is more important to build a robust QSAR models than the choice of the learning algorithm. Nowadays, the molecular descriptors (MD) used for QSAR modeling are calculated using computational tools that do not consider whether they accurately characterize the activity to be modeled and the compounds being analyzed. We demonstrate here that this approach may miss relevant information by assuming that the initial universe of MDs codifies, when it does not, all relevant aspects for the respective learning task. We argue that the limitation is mainly because of the constrained intervals of the parameters used in the algorithms that compute the MDs, parameters that define the Descriptor Configuration Space (DCS). We propose to relax these constraints in an open CDS approach, so that a larger universe of MDs can initially be considered, and these descriptors can adequately characterize the structures to be modeled. We model the MD generation as a multicriteria optimization problem, and two genetic algorithms-based approaches are proposed to solve it. These algorithms include cooperative-coevolutionary concepts to consider the synergism between theoretically different MDs during the evolutionary process. As a novel component, the individual fitness function is computed by aggregating four criteria via the Choquet Integral using a fuzzy non-additive measure. Experimental outcomes on benchmarking chemical datasets show that models created from an “optimized” sets of MDs present greater probability to achieve better performances than models created from sets of MDs obtained without optimizing their DCSs. Therefore, it can be concluded that the proposed algorithms are more suitable ..

algoritmos genéticos, descriptores moleculares QuBiLS-MAS, QSAR, DILI, cooperación coevolutiva genetics algorithms, QuBiLS-MAS molecular descriptors, QSAR, DILI, cooperativecoevolutionary algorithms INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS TECNOLOGÍA DE LOS ORDENADORES DISEÑO CON AYUDA DE ORDENADOR DISEÑO CON AYUDA DE ORDENADOR

Expansión poblacional reciente en la historia evolutiva de la anchoveta de California Engraulis mordax

Recent population expansion in the evolutionary history of the Californian anchovy Engraulis mordax

NOE DIAZ VILORIA LAURA SANCHEZ VELASCO RICARDO PEREZ ENRIQUEZ (2012, [Artículo])

"La anchoveta de California Engraulis mordax, es una especie templada que pudo haber pasado por un proceso de disyunción poblacional, debido al proceso postglacial de calentamiento del agua alrededor de la punta de la península de Baja California, hace unos 10,000 años. Se realizó un análisis genético para probar la hipótesis nula de homogeneidad genética entre el Golfo de California, México y el sur de California, EUA y si este era el caso, estimar el tiempo de surgimiento de haplotipos en términos de coalescencia. Se analizaron en total 80 secuencias de la región control hipervariable (ADNmt) de E. mordax, capturadas en la región central del Golfo de California (n = 40) y el sur de California (n = 40). A pesar del gran número de haplotipos únicos, no se observó diferenciación genética significativa entre localidades (FST = –0.0025, p = 0.686). Una distribución unimodal en la frecuencia del número de diferencias entre haplotipos indica un modelo de expansión rápida en el tamaño poblacional, que basado en una tasa mutacional de 3.6% por millón de años para la región control, indicó un tiempo de diferenciación nucleotídica relativamente reciente de aproximadamente 61,000 años. Este periodo de tiempo corresponde al Pleistoceno tardío, después de la formación de la península de Baja California, sugiriendo expansiones poblacionales en cada una de las localidades, seguidas del último episodio de glaciación, el cual quizás contribuyó a la migración de esta especie de afinidad templada entre las dos localidades y a su homogenización genética. Sin embargo este único evento reciente de flujo genético en la historia evolutiva de la especie, no explica por sí solo los patrones de distribución encontrados en las frecuencias de diferencias nucleotídicas."

"The Californian anchovy Engraulis mordax, a temperate species, may have undergone a process of population disjunction from experiencing post-glacial water heating processes around the tip of the Baja California Peninsula, Mexico about 10,000 b.p. A genetic analysis was performed to test the null hypothesis of genetic homogeneity between the Gulf of California and Southern California, U. S. A., and if this is the case, to estimate the time of haplotype emergence in terms of coalescence. A total of 80 sequences of the mtDNA hypervariable control region of E. mordax captured in the central Gulf of California (n = 40) and Southern California (n = 40) were analyzed. In spite of the large number of private haplotypes, no significant genetic differentiation among sites (FST = –0.0025, p = 0.686) was observed. An unimodal distribution of mismatch frequency between haplotypes indicated a model of rapid expansion in population size that, based on a mutation rate of 3.6% per million years in the control region, indicates a relatively recent nucleotide differentiation

time of approximately 61,000 years. This time period corresponds to the late Pleistocene, suggesting population expansions at each locality, followed by the last episode of glaciation, which may have contributed to migration of this temperate-affinity species between two locations and the genetic homogenization. However this unique recent event of gene flow in the evolutionary history of species does not explain by itself the mismatch distribution patterns found."

ADN mitocondrial, expansión poblacional reciente, flujo genético, región control, reloj molecular. Control region, gene flow, mitochondrial DNA, molecular clock, recent population expansion. BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) ZOOLOGÍA MARINA ZOOLOGÍA MARINA

Estructura, dinámica y evaporación de cúmulos atómicos.

Carlos Enrique Román Velázquez (1991, [Tesis de maestría])

Se realizaron dos estudios sobre cúmulos atómicos utilizando el método de simulación de Dinámica Molecular. En el primero se desarrolló un procedimiento para el estudio y caracterización del proceso de evaporación de cúmulos atómicos. Se calcularon la tasa de evaporación y la energía cinética liberada promedio de cúmulos de varios tamaños a distintas energias. Los resultados se compararon con las predicciones de los modelos teóricos de Engelking y RRK, encontrándose una mejor descripción por parte de este último, aunque no suficientemente adecuada. En la segunda parte se realizó un estudio sistemático de la dinámica de cúmulos de átomos que interacionan mediante un potencial que involucra términos de dos y tres cuerpos diseñado para representar la interacción entre átomos de berilio. En el transcurso de este estudio se analizaron las propiedades estructurales y dinámicas de los cúmulos. Se observó un comportamiento más complejo que el manifestado por el potencial de interacción de dos cuerpos de Lennard-Jones, con frecuente aparición de fenómenos de prefusión. También se encontró una evidencia de la limitación que tiene este potencial para reproducir la dinámica de los materiales de berilio.

Dinámica molecular - Simulación por computadora, Microgrupos - Simulación por computadora, Química, física y teórica - Simulación por computadora, Mecánica cuántica CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA FÍSICA OTRAS ESPECIALIDADES FÍSICAS OTRAS ESPECIALIDADES FÍSICAS

Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific

José Antonio Cruz-Barraza (2012, [Artículo])

Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history. © 2012 Cruz et al.

chitin, genomic DNA, mitochondrial DNA, molecular marker, ribosome DNA, allopatry, Aplysina clatharata, Aplysina gerardogreeni, Aplysina revillagigedi, article, DNA barcoding, DNA sequence, genetic polymorphism, genetic variability, infrared spectros CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Freshwater exchanges and surface salinity in the Colombian basin, Caribbean Sea

Emilio Beier (2017, [Artículo])

Despite the heavy regional rainfall and considerable discharge of many rivers into the Colombian Basin, there have been few detailed studies about the dilution of Caribbean Surface Water and the variability of salinity in the southwestern Caribbean. An analysis of the precipitation, evaporation and runoff in relation to the climate variability demonstrates that although the salt balance in the Colombian Basin overall is in equilibrium, the area south of 12N is an important dilution sub-basin. In the southwest of the basin, in the region of the Panama-Colombia Gyre, Caribbean Sea Water is diluted by precipitation and runoff year round, while in the northeast, off La Guajira, its salinity increases from December to May by upwelling. At the interannual scale, continental runoff is related to El Niño Southern Oscillation, and precipitation and evaporation south of 12°N are related to the Caribbean Low Level Jet. During El Niño years the maximum salinification occurs in the dry season (December-February) while in La Niña years the maximum dilution (or freshening), reaching La Guajira Coastal Zone, occurs in the wet season (September-November). © 2017 Beier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

sea water, fresh water, Article, Caribbean, dilution, dry season, El Nino, environmental parameters, evaporation, freshwater exchange, geographic distribution, molecular weight, oscillation, precipitation, river basin, salinity, seasonal variation, s CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO OCEANOGRAFÍA OCEANOGRAFÍA

Genetic analysis of Vibrio parahaemolyticus O3:K6 strains that have been isolated in Mexico since 1998

CARLOS ABRAHAM GUERRERO RUIZ (2017, [Artículo])

Vibrio parahaemolyticus is an important human pathogen that has been isolated worldwide from clinical cases, most of which have been associated with seafood consumption. Environmental and clinical toxigenic strains of V. parahaemolyticus that were isolated in Mexico from 1998 to 2012, including those from the only outbreak that has been reported in this country, were characterized genetically to assess the presence of the O3:K6 pandemic clone, and their genetic relationship to strains that are related to the pandemic clonal complex (CC3). Pathogenic tdh+ and tdh+/trh+ strains were analyzed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Also, the entire genome of a Mexican O3:K6 strain was sequenced. Most of the strains were tdh/ORF8-positive and corresponded to the O3:K6 serotype. By PFGE and MLST, there was very close genetic relationship between ORF8/O3:K6 strains, and very high genetic diversities from non-pandemic strains. The genetic relationship is very close among O3:K6 strains that were isolated in Mexico and sequences that were available for strains in the CC3, based on the PubMLST database. The whole-genome sequence of CICESE-170 strain had high similarity with that of the reference RIMD 2210633 strain, and harbored 7 pathogenicity islands, including the 4 that denote O3:K6 pandemic strains. These results indicate that pandemic strains that have been isolated in Mexico show very close genetic relationship among them and with those isolated worldwide. © 2017 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial strain, biofouling, controlled study, Crassostrea, food intake, gene sequence, genetic analysis, genetic variability, Japan, Mexican, Mexico, molecular phylogeny, nonhuman, pandemic, pathogenicity island, sea food, serotyping, toxi BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA