The critical needs and challenges for genetic architecture studies in Africa

Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.Peer reviewe

Genetic resistance to Mycobacterium Tuberculosis infection and disease

CITATION: Möller, M. et al. 2018. Genetic resistance to Mycobacterium tuberculosis infection and disease. Frontier in Immunology, 9:2219, 1-13. doi:10.3389/fimmu.2018.02219.The original publication is available from https://www.frontiersin.org/journals/immunology#Natural history studies of tuberculosis (TB) have revealed a spectrum of clinical outcomes after exposure to Mycobacterium tuberculosis, the cause of TB. Not all individuals exposed to the bacteriumwill become diseased and depending on the infection pressure, many will remain infection-free. Intriguingly, complete resistance to infection is observed in some individuals (termed resisters) after intense, continuing M. tuberculosis exposure. After successful infection, the majority of individuals will develop latent TB infection (LTBI). This infection state is currently (and perhaps imperfectly) defined by the presence of a positive tuberculin skin test (TST) and/or interferon gamma release assay (IGRA), but no detectable clinical disease symptoms. The majority of healthy individuals with LTBI are resistant to clinical TB, indicating that infection is remarkably well-contained in these non-progressors. The remaining 5–15% of LTBI positive individuals will progress to active TB. Epidemiological investigations have indicated that the host genetic component contributes to these infection and disease phenotypes, influencing both susceptibility and resistance. Elucidating these genetic correlates is therefore a priority as it may translate to new interventions to prevent, diagnose or treat TB. The most successful approaches in resistance/susceptibility investigation have focused on specific infection and disease phenotypes and the resister phenotype may hold the key to the discovery of actionable genetic variants in TB infection and disease. This review will not only discuss lessons from epidemiological studies, but will also focus on the contribution of epidemiology and functional genetics to human genetic resistance to M. tuberculosis infection and disease.https://www.frontiersin.org/articles/10.3389/fimmu.2018.02219/fullhttps://doi.org/10.3389/fimmu.2018.02219Published review articlePublishers versio

A practical guide for assessing respiratory burst and phagocytic cell activity in the fathead minnow, an emerging model for immunotoxicity

Article is a study with the goal of optimizing and validating the use of a colorimetric plate-based respiratory burst and fluorometric plate-based phagocytic cell activity assays for use with kidney cells from the fathead minnow (Pimephales promelas), an emerging immunotoxicity model

Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method

Admixed populations can make an important contribution to the discovery of disease susceptibility genes if the parental populations exhibit substantial variation in susceptibility. Admixture mapping has been used successfully, but is not designed to cope with populations that have more than two or three ancestral populations. The inference of admixture proportions and local ancestry and the imputation of missing genotypes in admixed populations are crucial in both understanding variation in disease and identifying novel disease loci. These inferences make use of reference populations, and accuracy depends on the choice of ancestral populations. Using an insufficient or inaccurate ancestral panel can result in erroneously inferred ancestry and affect the detection power of GWAS and meta-analysis when using imputation. Current algorithms are inadequate for multi-way admixed populations. To address these challenges we developed PROXYANC, an approach to select the best proxy ancestral populations. From the simulation of a multi-way admixed population we demonstrate the capability and accuracy of PROXYANC and illustrate the importance of the choice of ancestry in both estimating admixture proportions and imputing missing genotypes

Browsing Space Weather Data and Models with the Integrated Space Weather Analysis (iSWA) System

The Integrated Space Weather Analysis (iSWA) System is a comprehensive web-based platform for space weather information that combines data from solar, heliospheric and geospace observatories with forecasts based on the most advanced space weather models. The iSWA system collects, generates, and presents a wide array of space weather resources in an intuitive, user-configurable, and adaptable format - thus enabling users to respond to current and future space weather impacts as well as enabling post-impact analysis. iSWA currently provides over 200 data and modeling products, and features a variety of tools that allow the user to browse, combine, and examine data and models from various sources. This presentation will consist of a summary of the iSWA products and an overview of the customizable user interfaces, and will feature several tutorial demonstrations highlighting the interactive tools and advanced capabilities

Variational Monte Carlo for Interacting Electrons in Quantum Dots

We use a variational Monte Carlo algorithm to solve the electronic structure of two-dimensional semiconductor quantum dots in external magnetic field. We present accurate many-body wave functions for the system in various magnetic field regimes. We show the importance of symmetry, and demonstrate how it can be used to simplify the variational wave functions. We present in detail the algorithm for efficient wave function optimization. We also present a Monte Carlo -based diagonalization technique to solve the quantum dot problem in the strong magnetic field limit where the system is of a multiconfiguration nature.Comment: 34 pages, proceedings of the 1st International Meeting on Advances in Computational Many-Body Physics, to appear in Journal of Low Temperature Physics (vol. 140, nos. 3/4

Assisting Vietnamese Mango Farmers to Capture Greater Benefi ts through Improved Supply Chain Management

In the developing countries, traditional supply chains for fresh produce are giving way to new supermarket-led supply chains. The rapid transformation in the fruit and vegetable sector is due to the meteoric rise of supermarkets, hypermarkets, superstores, neighbourhood stores, convenience stores, and discount stores, which are impacting on smallholder farmers. This change is also impacting on both upstream and downstream market intermediaries through the demand for safe, high-quality produce that has been produced in a sustainable manner. Problems with procurement in traditional supply chains include few product standards, inconsistent supply, highly variable transaction costs, and limited market information. Supermarkets are now setting new procurement practices and supply systems which focus on reducing costs and improving quality to enable them to sell at lower prices. This will allow them to win over consumers and to obtain a larger market share. However, the ability of smallholder farmers, collector agents, and wholesalers in the Mekong Delta to meet safe food levels and the quality demands of domestic and overseas supermarkets can only be obtained through improving their production and supply chain practices. The implementation of new production and postharvest practices and the modernization of these supply chains may preclude many smallholder farmers from participating. Smallholder farmers must develop risk minimization strategies, such as forming collaborative marketing groups, implementing new crop management and production systems, improving the packaging, and creating more efficient transport methods and handling practices to provide a safe, competitively priced, high-quality product. Understanding the supply chain and where to intervene are essential if farmers and all supply chain participants are to benefit. In this paper, we describe mango supply chains in the Mekong Delta, provide empirical data collected from surveys, and highlight improvements smallholder farmers have been making to achieve greater benefits