Genetic control of root architectural plasticity in maize

© 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology. Root phenotypes regulate soil resource acquisition; however, their genetic control and phenotypic plasticity are poorly understood. We hypothesized that the responses of root architectural phenes to water deficit (stress plasticity) and different environments (environmental plasticity) are under genetic control and that these loci are distinct. Root architectural phenes were phenotyped in the field using a large maize association panel with and without water deficit stress for three seasons in Arizona and without water deficit stress for four seasons in South Africa. All root phenes were plastic and varied in their plastic response. We identified candidate genes associated with stress and environmental plasticity and candidate genes associated with phenes in well-watered conditions in South Africa and in well-watered and water-stress conditions in Arizona. Few candidate genes for plasticity overlapped with those for phenes expressed under each condition. Our results suggest that phenotypic plasticity is highly quantitative, and plasticity loci are distinct from loci that control phene expression in stress and non-stress, which poses a challenge for breeding programs. To make these loci more accessible to the wider research community, we developed a public online resource that will allow for further experimental validation towards understanding the genetic control underlying phenotypic plasticity

Mapping B-cell responses to Salmonella enterica serovars Typhimurium and Enteritidis in chickens for the discrimination of infected from vaccinated animals

Serological surveillance and vaccination are important strategies for controlling infectious diseases of food production animals. However, the compatibility of these strategies is limited by a lack of assays capable of di erentiating infected from vaccinated animals (DIVA tests) for established killed or attenuated vaccines. Here, we used next generation phage-display (NGPD) and a 2-proportion Z score analysis to identify peptides that were preferentially bound by IgY from chickens infected with Salmonella Typhimurium or S. Enteritidis compared to IgY from vaccinates, for both an attenuated and an inactivated commercial vaccine. Peptides that were highly enriched against IgY from at least 4 out of 10 infected chickens were selected: 18 and 12 peptides for the killed and attenuated vaccines, respectively. The ten most discriminatory peptides for each vaccine were identi ed in an ELISA using a training set of IgY samples. These peptides were then used in multi-peptide assays that, when analysing a wider set of samples from infected and vaccinated animals, diagnosed infection with 100% sensitivity and speci city. The data describes a method for the development of DIVA assays for conventional attenuated and killed vaccines

Resonant nonlinear magneto-optical effects in atoms

In this article, we review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. We begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances, and contrast these effects with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultra-narrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.Comment: 51 pages, 23 figures, to appear in Rev. Mod. Phys. in Oct. 2002, Figure added, typos corrected, text edited for clarit

Postcolonial healing landscapes and mental health in a remote Indigenous community in subarctic Ontario, Canada

The concept of therapeutic landscape is concerned with a holistic, socio-ecological model of health, but most studies have attempted to explore land-health links from a Western perspective. On an Indigenous reserve in Northern Ontario, part of the Canadian subarctic, we explore the importance of spaces and places in creating postcolonial therapeutic landscapes to treat the wounds inflicted by colonialism. The aim of this research is to gain insight from views and experiences of First Nations residents living on reservations that are undergoing a process of regaining traditional spiritual beliefs and teachings to construct therapeutic spaces to face mental health problems caused by legal opioid analgesic abuse. This qualitative study used semi-structured interviews with Cree and Ojibwe participants to understand how they are reconnecting with earth, spirituality and traditional animist beliefs on their way to recovery. We find that practices such as taking part in ceremonies and ritual spaces, and seeking knowledge and advice from Elders assist with personal healing and enable Indigenous people to be physically and mentally healthy. Our research findings provide important insights into the relationship between space, healing and culture as determinants of health and well-being and document some key factors that contribute to substance abuse recovery.This work was supported by the Ministry of Education and Science (Spain) [I + D+i SEJ2005-09344/SOCI]; Social Sciences and Humanities Research Council (Canada) [I + D+i CURA/NORTHERN]

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing

Writing impact case studies: a comparative study of high-scoring and low-scoring case studies from REF2014

This paper reports on two studies that used qualitative thematic and quantitative linguistic analysis, respectively, to assess the content and language of the largest ever sample of graded research impact case studies, from the UK Research Excellence Framework 2014 (REF). The paper provides the first empirical evidence across disciplinary main panels of statistically significant linguistic differences between high- versus low-scoring case studies, suggesting that implicit rules linked to written style may have contributed to scores alongside the published criteria on the significance, reach and attribution of impact. High-scoring case studies were more likely to provide specific and high-magnitude articulations of significance and reach than low-scoring cases. High-scoring case studies contained attributional phrases which were more likely to attribute research and/or pathways to impact, and they were written more coherently (containing more explicit causal connections between ideas and more logical connectives) than low-scoring cases. High-scoring case studies appear to have conformed to a distinctive new genre of writing, which was clear and direct, and often simplified in its representation of causality between research and impact, and less likely to contain expressions of uncertainty than typically associated with academic writing. High-scoring case studies in two Main Panels were significantly easier to read than low-scoring cases on the Flesch Reading Ease measure, although both high-scoring and low-scoring cases tended to be of “graduate” reading difficulty. The findings of our work enable impact case study authors to better understand the genre and make content and language choices that communicate their impact as effectively as possible. While directly relevant to the assessment of impact in the UK’s Research Excellence Framework, the work also provides insights of relevance to institutions internationally who are designing evaluation frameworks for research impact

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead