Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 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 gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

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

RNAseq of diverse spring wheat cultivars released during last 110 years

awais rasheed Huihui Li (2023, [Artículo])

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA RNA SEQUENCE SPRING WHEAT ROOT ARCHITECTURE GENES

Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India

Anup Das virender kumar Peter Craufurd Andrew Mcdonald Sonam Sherpa (2023, [Artículo])

Introduction: Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied. Methods: Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods. Results and Discussion: Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50–23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2–13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.

Metagenomics Bacterial Diversity Rice-Wheat-Greengram CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CONSERVATION AGRICULTURE DNA SEQUENCES EARTHWORMS METAGENOMICS SOIL QUALITY AGROECOSYSTEMS

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Spurthi Nayak Polavarapu Kavi Kishor Rajeev Varshney (2010, [Artículo])

Simple Sequence Repeats Mapping Population Translational Studies CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ANCHORS CHICKPEAS CICER ARIETINUM GENETIC MAPS GENETIC MARKERS MEDICAGO MEDICAGO TRUNCATULA MICROSATELLITES SINGLE NUCLEOTIDE POLYMORPHISM GENES

The past, the present, the future, and occupational self-efficacy: an attributions and cultural differences perspective

Daniel Arturo Cernas Ortiz (2023, [Artículo, Artículo])

This study´s objective was to examine empirical relationships between three dimensions of time perspective (future, present fatalistic, and past negative) and occupational self-efficacy. By surveying Mexican (n = 286) and U.S. (n = 272) respondents, we also tested the moderating role of culture. Regression analyses revealed that time perspective dimensions have significant associations with occupational self-efficacy, being future time perspective more potent than its past negative and present fatalistic counterparts. Moderation analyses indicated that none of the examined time perspective-self-efficacy relationships varied significantly between the U.S. and Mexico. Overall, this study suggests that relationships between time perspective and occupational self-efficacy vary according to different temporal dimensions, that future TP is key to develop occupational self-efficacy, and that cultural values may not exert a significant influence on the time perspective-occupational self-efficacy connection.

Perspectiva de tiempo autoeficacia diferencias culturales análisis de moderación CIENCIAS SOCIALES CIENCIAS SOCIALES Time perspective self-efficacy cultural differences moderation analysis

Natural disasters and economic growth: a synthesis of empirical evidence

Fernando Antonio Ignacio González (2023, [Artículo, Artículo])

Natural disasters pose a serious threat globally and, in the future, their frequency and severity are expected to increase due to climate change. Empirical evidence has reported conflicting results in terms of the impact of disasters on economic growth. In this context, the present work seeks to synthesize the recent empirical evidence related to this topic. More than 650 estimates, from studies published in the last five years (2015-2020), are used. Meta-analysis and meta-regression techniques are employed. The review includes three sources (Scopus, Science Direct, and Google Scholar). The results identified the existence of a negative and significant combined effect (-0.015). Developing countries are especially vulnerable to disasters. The negative impact is greater for disasters that occurred in the last decade -in relation to previous disasters-. These findings constitute a call for attention in favor of mitigation and adaptation policies.

Disasters GDP meta-analysis meta-regression desastres crecimiento PIB meta-análisis meta-regresión CIENCIAS SOCIALES CIENCIAS SOCIALES

On-farm assessment of yield and quality traits in durum wheat

Facundo Tabbita Iván Ortíz-Monasterios Francisco Javier Pinera-Chavez Maria Itria Ibba Carlos Guzman (2023, [Artículo])

BACKGROUND: Durum wheat is key source of calories and nutrients for many regions of the world. Demand for it is predicted to increase. Further efforts are therefore needed to develop new cultivars adapted to different future scenarios. Developing a novel cultivar takes, on average, 10 years and advanced lines are tested during the process, in general, under standardized conditions. Although evaluating candidate genotypes for commercial release under different on-farm conditions is a strategy that is strongly recommended, its application for durum wheat and particularly for quality traits has been limited. This study evaluated the grain yield and quality performance of eight different genotypes across five contrasting farmers’ fields over two seasons. Combining different analysis strategies, the most outstanding and stable genotypes were identified. RESULTS: The analyses revealed that some traits were mainly explained by the genotype effect (thousand kernel weight, flour sodium dodecyl sulfate sedimentation volume, and flour yellowness), others by the management practices (yield and grain protein content), and others (test weight) by the year effect. In general, yield showed the highest range of variation across genotypes, management practices, and years and test weight the narrowest range. Flour yellowness was the most stable trait across management conditions, while yield-related traits were the most unstable. We also determined the most representative and discriminative field conditions, which is a beneficial strategy when breeders are constrained in their ability to develop multi-environment experiments. CONCLUSIONS: We concluded that assessing genotypes in different farming systems is a valid and complementary strategy for on-station trials for determining the performance of future commercial cultivars in heterogeneous environments to improve the breeding process and resources.

Wheat Quality GGE Analysis Flour Yellowness CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA FLOURS WHEAT QUALITY YIELDS FIELD EXPERIMENTATION

Gender, rainfall endowment, and farmers’ heterogeneity in wheat trait preferences in Ethiopia

Hom Nath Gartaula Moti Jaleta (2024, [Artículo])

Wheat is a vital cereal crop for smallholders in Ethiopia. Despite over fifty years of research on wheat varietal development, consideration of gendered trait preferences in developing target product profiles for wheat breeding is limited. To address this gap, our study used sex-disaggregated survey data and historical rainfall trends from the major wheat-growing regions in Ethiopia. The findings indicated heterogeneity in trait preferences based on gender and rainfall endowment. Men respondents tended to prefer wheat traits with high straw yield and disease-resistance potential, while women showed a greater appreciation for wheat traits related to good taste and cooking quality. Farmers in high rainfall areas seemed to prioritize high straw yield and disease resistance traits, while those in low rainfall areas valued good adaptation traits more highly. Most of the correlation coefficients among the preferred traits were positive, indicating that farmers seek wheat varieties with traits that serve multiple purposes. Understanding men's and women's preferences and incorporating them in breeding and seed systems could contribute to the development of more targeted and effective wheat varieties that meet the diverse needs of men and women farmers in Ethiopia.

Trait Preferences Multivariate Probit Model CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA WHEAT AGRONOMIC CHARACTERS GENDER RAINFALL PROBIT ANALYSIS

Estimation of general and specific combining ability effects for quality protein maize inbred lines

Adefris Teklewold Dagne Wegary Gissa (2022, [Artículo])

General Combining Ability Specific Combining Ability CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA COMBINING ABILITY MAIZE PROTEIN QUALITY INBRED LINES DATA ANALYSIS