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"Garcia, Antonio"
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Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant–microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (
Phaseolus vulgaris
) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification. Diversity Array Technology-based genotyping and phenotyping of local common bean accessions showed significant genetic and root architectural differences between wild and modern accessions, with a higher specific root length for the wild accessions. Canonical Correspondence Analysis indicated that the divergence in rhizobacterial community composition between wild and modern bean accessions is associated with differences in specific root length. Along the bean genotypic trajectory, going from wild to modern, we observed a gradual decrease in relative abundance of Bacteroidetes, mainly
Chitinophagaceae
and
Cytophagaceae
, and an increase in relative abundance of Actinobacteria and Proteobacteria, in particular
Nocardioidaceae
and
Rhizobiaceae
, respectively. Collectively, these results establish a link between common bean domestication, specific root morphological traits and rhizobacterial community assembly.
Journal Article
Social Entrepreneurship in Non-Profit and Profit Sectors : Theoretical and Empirical Perspectives
This volume examines the theoretical and empirical landscape of social entrepreneurship in both non-profit and profit sectors. It extends the traditional view of social entrepreneurship to include the environmental and institutional factors that affect the emergence of social entrepreneurship activities, such as formal laws, regulations, procedures and informal institutions. The editors aim to provide evidence and increased understanding of this growing phenomenon. Social Entrepreneurship is gaining recognition as a key element of economic and social development. It embraces a wide set of situations with a broad scope of activities in for-profit and non-profit organizations interested in social performance and/or in economically profitable performance, with an emphasis on achieving social aim. In the strict sense, social entrepreneurship corresponds to entrepreneurs whose main concern is to achieve social objectives rather than to obtain personal financial profits. However, there is still much to be learned about the dynamics and processes of social entrepreneurship. The current literature in the field has tended to focus on psychological experiences and personal characteristics, or on organizational perspectives such as resources, capabilities and leadership. This book intends to provide theoretical frameworks and empirical studies to this very new and broad field. Specifically, this book provides a collection of contemporary research in the following topics: How to create opportunity through social innovation How to detect entrepreneurial opportunity to meet social needs How to develop social entrepreneurship, while still seeking profits How to discover opportunities for different forms of social entrepreneurship Featuring contributions from around the world, this book is a valuable source for students, academics, researchers, policy makers, and professionals in the area of social entrepreneurship.
Book
The genetic architecture of resistance to flubendiamide insecticide in Helicoverpa armigera (Hübner)
Insecticide resistance is a major problem in food production, environmental sustainability, and human health. The cotton bollworm Helicoverpa armigera is a globally distributed crop pest affecting over 300 crop species. H. armigera has rapidly evolved insecticide resistance, making it one of the most damaging pests worldwide. Understanding the genetic basis of insecticide resistance provides insights to develop tools, such as molecular markers, that can be used to slow or prevent the evolution of resistance. We explore the genetic architecture of H. armigera resistance to a widely used insecticide, flubendiamide, using two complementary approaches: genome-wide association studies (GWAS) in wild-caught samples and quantitative trait locus (QTL) mapping in a controlled cross of susceptible and resistant laboratory strains. Both approaches identified one locus on chromosome 2, revealing two SNPs within 976 bp that can be used to monitor field resistance to flubendiamide. This was the only region identified using linkage mapping, though GWAS revealed additional sites associated with resistance. Other loci identified by GWAS in field populations contained known insecticide detoxification genes from the ATP-binding cassette family, ABCA1, ABCA3, ABCF2 and MDR1. Our findings revealed an oligogenic genetic architecture, contrasting previous reports of monogenic resistance associated with the ryanodine receptor . This work elucidates the genetic basis of rapidly evolving insecticide resistance and will contribute to developing effective insecticide resistance management strategies.
Journal Article
Defect Formation beyond Kibble-Zurek Mechanism and Holography
We study the dynamic after a smooth quench across a continuous transition from the disordered phase to the ordered phase. Based on scaling ideas, linear response, and the spectrum of unstable modes, we develop a theoretical framework, valid for any second-order phase transition, for the early-time evolution of the condensate in the broken phase. Our analysis unveils a novel period of nonadiabatic evolution after the system passes through the phase transition, where a parametrically large amount of coarsening occurs before a well-defined condensate forms. Our formalism predicts a rate of defect formation parametrically smaller than the Kibble-Zurek prediction and yields a criterion for the breakdown of Kibble-Zurek scaling for sufficiently fast quenches. We numerically test our formalism for a thermal quench in a (2+1 )-dimensional holographic superfluid. These findings, of direct relevance in a broad range of fields including cold atom, condensed matter, statistical mechanics, and cosmology, are an important step toward a more quantitative understanding of dynamical phase transitions.
Journal Article
Genotyping Polyploids from Messy Sequencing Data
Gerard et al. highlight several issues encountered when genotyping polyploid organisms from next-generation sequencing data, including allelic bias, overdispersion, and outlying observations. They present modeling solutions and software to account for these issues... Detecting and quantifying the differences in individual genomes (i.e., genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use reduced representation next-generation sequencing (NGS) approaches for genotyping. Genotyping diploid individuals using NGS is a well-studied field, and similar methods for polyploid individuals are just emerging. However, there are many aspects of NGS data, particularly in polyploids, that remain unexplored by most methods. Our contributions in this paper are fourfold: (i) We draw attention to, and then model, common aspects of NGS data: sequencing error, allelic bias, overdispersion, and outlying observations. (ii) Many datasets feature related individuals, and so we use the structure of Mendelian segregation to build an empirical Bayes approach for genotyping polyploid individuals. (iii) We develop novel models to account for preferential pairing of chromosomes, and harness these for genotyping. (iv) We derive oracle genotyping error rates that may be used for read depth suggestions. We assess the accuracy of our method in simulations, and apply it to a dataset of hexaploid sweet potato (Ipomoea batatas). An R package implementing our method is available at https://cran.r-project.org/package=updog.
Journal Article
Geochemical Background and Baseline Values Determination and Spatial Distribution of Heavy Metal Pollution in Soils of the Andes Mountain Range (Cajamarca-Huancavelica, Peru)
[EN]Concentrations of seven heavy metals (Cd, Cr, Cu, Hg, Ni, Pb, and Zn) and one metalloid (As) as well as various parameters (pH, organic carbon, granulometric analysis and cation exchange capacity) were analyzed in 77 soil samples collected in the mining areas of La Zanja and Colquirrumi (Department of Cajamarca) and Julcani (Department of Huancavelica). Our study proposed geochemical baseline values for heavy metals in a natural region (La Zanja) from samples collected during the period of the environmental impact study (2006), that is, from an earlier period which occurred at the beginning of the exploitation of the current gold mine. The baseline values obtained were as follows: 8.26 mg kg−1 for Cr; 56.97 mg kg−1 for Ni; 22, 20 mg kg−1 for the Cu; 47.42 mg kg−1 for Zn; 27.50 mg kg−1 for As; 4.36 mg kg−1 for Cd; 4.89 mg kg−1 for Hg, and 44.87 mg kg−1 for Pb. Through the use of different indices of heavy metal contamination (geo-accumulation index (Igeo), improved Nemerow index (IIN) and potential ecological risk index (RI)), the degree of pollution caused by mining activities in two areas, Colquirrumi and Julcani, which have a high density of mining sites in operation, was determined.
Journal Article
Leveraging probability concepts for cultivar recommendation in multi-environment trials
Key messageWe propose using probability concepts from Bayesian models to leverage a more informed decision-making process toward cultivar recommendation in multi-environment trials.Statistical models that capture the phenotypic plasticity of a genotype across environments are crucial in plant breeding programs to potentially identify parents, generate offspring, and obtain highly productive genotypes for target environments. In this study, our aim is to leverage concepts of Bayesian models and probability methods of stability analysis to untangle genotype-by-environment interaction (GEI). The proposed method employs the posterior distribution obtained with the No-U-Turn sampler algorithm to get Hamiltonian Monte Carlo estimates of adaptation and stability probabilities. We applied the proposed models in two empirical tropical datasets. Our findings provide a basis to enhance our ability to consider the uncertainty of cultivar recommendation for global or specific adaptation. We further demonstrate that probability methods of stability analysis in a Bayesian framework are a powerful tool for unraveling GEI given a defined intensity of selection that results in a more informed decision-making process toward cultivar recommendation in multi-environment trials.
Journal Article
Adolescent Mental Health and Family Economic Hardships: The Roles of Adverse Childhood Experiences and Family Conflict
Rising and economically disproportionate rates of adverse mental health outcomes among children and youth warrant research investigating the complex pathways stemming from socioeconomic status. While adverse childhood experiences (ACEs) have been considered a possible mechanism linking socioeconomic status (SES) and child and youth psychopathology in previous studies, less is understood about how family environments might condition these pathways. Using data from a longitudinal, multiple-wave study, the present study addresses this gap by examining the direct relationships between family economic status and youth internalizing and externalizing symptoms, if ACEs mediate these relationships, and if conflictual family environments moderate these direct and indirect relationships. The data were obtained from 5510 youth participants [mean age at baseline = 9.52 (SD = 0.50), 47.7% female, 2.1% Asian, 10.3% Black, 17.6% Hispanic, 9.8% Multiracial/Multiethnic, 60.2% White] and their caretakers from the baseline, 1-year, and 2-year follow up waves. Conditional process analysis assessed the direct, indirect, and moderated relationships in separate, equivalent models based on youth- versus caregiver-raters of ACEs and youth psychopathology to capture potential differences based on the rater. The results of both the youth- and caregiver-rated models indicated that lower family economic status directly predicted higher levels of externalizing symptoms, and ACEs indirectly accounted for higher levels of internalizing and externalizing symptoms. Additionally, family conflict moderated some, but not all, of these relationships. The study’s findings highlight that lower family economic status and ACEs, directly and indirectly, contribute to early adolescent psychopathology, and conflictual family environments can further intensify these relationships. Implementing empirically supported policies and interventions that target ACEs and family environments may disrupt deleterious pathways between SES and youth psychopathology.
Journal Article
Snake Venoms in Drug Discovery: Valuable Therapeutic Tools for Life Saving
Animal venoms are used as defense mechanisms or to immobilize and digest prey. In fact, venoms are complex mixtures of enzymatic and non-enzymatic components with specific pathophysiological functions. Peptide toxins isolated from animal venoms target mainly ion channels, membrane receptors and components of the hemostatic system with high selectivity and affinity. The present review shows an up-to-date survey on the pharmacology of snake-venom bioactive components and evaluates their therapeutic perspectives against a wide range of pathophysiological conditions. Snake venoms have also been used as medical tools for thousands of years especially in tradition Chinese medicine. Consequently, snake venoms can be considered as mini-drug libraries in which each drug is pharmacologically active. However, less than 0.01% of these toxins have been identified and characterized. For instance, Captopril® (Enalapril), Integrilin® (Eptifibatide) and Aggrastat® (Tirofiban) are drugs based on snake venoms, which have been approved by the FDA. In addition to these approved drugs, many other snake venom components are now involved in preclinical or clinical trials for a variety of therapeutic applications. These examples show that snake venoms can be a valuable source of new principle components in drug discovery.
Journal Article