Editorial: Functional genomic approaches in molecular breeding for crop improvement

Philomin Juliana (2023, [Artículo])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA DNA MARKER-ASSISTED SELECTION QUANTITATIVE TRAIT LOCI CROP IMPROVEMENT

Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan

Abdelfattah DABABAT Yong Suk Chung (2023, [Artículo])

Biological Indexing Sequencing Analysis Citrus Orchards CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA PHYLOGENETIC ANALYSIS CITRUS RNA DNA

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

Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis

ELIANA VALENCIA LOZANO LISSET HERRERA ISIDRON Osiel Salvador Recoder-Meléndez Aarón Barraza Celis JOSE LUIS CABRERA PONCE (2022, [Artículo])

"Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs–MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9–may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging."

transcriptome-wide analysis, microtubers, potato, Solanum tuberosum, darkness, cell cycle, ribosomal proteins, PEBP family genes, cytokinin BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS

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

Regional analysis of the wage discrimination in the indigenous workers in Mexico

Christian De la Luz-Tovar SIBYL ITALIA PINEDA SALAZAR (2023, [Artículo, Artículo])

The objective of this research is to estimate and decompose the wage gap between indigenous and non-indigenous workers by region in Mexico, to examine whether there are regional differences in the existing wage inequality that a priori affects the indigenous population and whether these differences can be attributed to the job profile of this group or by systematic labor discrimination against them. Using the data from the 2018 National Household Expenditure Revenue Survey (ENIGH-N) and the Oaxaca-Blinder decomposition, it was found that indigenous workers face a wage gap in all regions of the county. But, this gap is more pronounced in the center and south regions, where, on average, the associated component with labor discrimination has a percentage greater than 56. In contrast, in the north-central and northern regions of Mexico, the residual component is on average less than 33%, which suggests that the wage gap is explained by differences in productivity between groups.                         

Labor economics Ethnicity wage gap Indigenous population Regions Oaxaca-Blinder decomposition Economía laboral Brecha salarial étnica Población indígena Regiones Descomposición de Oaxaca-Blinder CIENCIAS SOCIALES CIENCIAS SOCIALES

Molecular markers help with breeding for agronomic traits of spring wheat in Kazakhstan and Siberia

Alexey Morgounov Cecile Ben Susanne Dreisigacker Laurent Gentzbittel awais rasheed Timur Savin Sergey Shepelev Vladimir Shamanin (2024, [Artículo])

DNA Markers Grain Yield CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CEREALS DNA GENOTYPE ENVIRONMENT INTERACTION GRAIN YIELDS SPRING WHEAT

Regional analysis of the wage discrimination in the indigenous workers in Mexico

Christian De la Luz-Tovar SIBYL ITALIA PINEDA SALAZAR (2023, [Artículo, Artículo])

The objective of this research is to estimate and decompose the wage gap between indigenous and non-indigenous workers by region in Mexico, to examine whether there are regional differences in the existing wage inequality that a priori affects the indigenous population and whether these differences can be attributed to the job profile of this group or by systematic labor discrimination against them. Using the data from the 2018 National Household Expenditure Revenue Survey (ENIGH-N) and the Oaxaca-Blinder decomposition, it was found that indigenous workers face a wage gap in all regions of the county. But, this gap is more pronounced in the center and south regions, where, on average, the associated component with labor discrimination has a percentage greater than 56. In contrast, in the north-central and northern regions of Mexico, the residual component is on average less than 33%, which suggests that the wage gap is explained by differences in productivity between groups.                         

Labor economics Ethnicity wage gap Indigenous population Regions Oaxaca-Blinder decomposition Economía laboral Brecha salarial étnica Población indígena Regiones Descomposición de Oaxaca-Blinder CIENCIAS SOCIALES CIENCIAS SOCIALES

The spatial control of migrants on the Chihuahua border

EDGAR ABEL CASTRO (2023, [Artículo, Artículo])

This article tries to link the immigration policies of the United States and Mexico with the narrative developed by Michel Foucault. It shows how racism is the axis on which the State of biopower exercises its claims and its effects of power on bodies and on life. Thus, the current political rationality goes through the management of the living body of people, their health, and their spatiality. This principle extends to the homicidal function of the State. Two events that occurred on the Chihuahua border demonstrate this.

migrant control Foucault border racism migrante frontera racismo HUMANIDADES Y CIENCIAS DE LA CONDUCTA HUMANIDADES Y CIENCIAS DE LA CONDUCTA

La identificación de agrupamientos industriales como estrategia de análisis de la economía regional.

JOSE MANUEL SANCHEZ GAMBOA (2005, [Tesis de maestría])

CIENCIAS SOCIALES Planificación regional Localización industrial Política económica