Accounting for variability in the detection and use of markers for simple and complex traits

There are many sources of variability in gene–phenotype associations. During the measurement of genotype and phenotype and during selection, researchers must deal with experimental error in trials; gene-gene interaction (epistasis) for sub-traits and observed traits; trait-trait interaction (pleiotropy) and gene- or genotype-by-environment interaction. These effects can be structured in a framework that allows simulation of the entire gene-environment ‘landscape’. Studies of these landscapes have been published by others. Here we aim to explain with simple examples some of the types of insights that can be made. A current challenge for breeders working with simple marker–phenotype associations is to design selection strategies that can rapidly create new combinations of multiple marker-based traits. For a real-world example in wheat, we have used simulation to show how gene enrichment during early generations (selection of homozygotes and heterozygotes with desirable alleles) can greatly reduce resource requirements when combining 9 genes into one genotype through marker-assisted selection. Another wheat example compares phenotypic and QTL-based selection for coleoptile length where the QTL also had a pleiotropic association with plant height. These simulations show the relative negative effects of either low heritability, or less than complete detection of QTL associated with traits. Finally, we revisit a marker-assisted selection (MAS) example whereby a QTL study is undertaken on a population for a complex trait, and then those QTL are used in selection. This process is subject to all sources of error described above. If the trait is complex, then interactions among sub-traits; between sub-traits and the environment; or between the chromosomal locations of controlling genes, create an extremely ‘rugged’ selection landscape that slows breeding progress. In this situation, a detailed understanding of some of these interactions is required if MAS is to be able to exceed the progress of conventional breedin

Aggregation of Staphylococcus aureus following treatment with the antibacterial flavonol galangin.

Aim: The flavonol galangin, an antimicrobial constituent of the traditional medicines propolis and Helichrysum aureonitens, is being assessed as part of an ongoing investigation into the antibacterial activity of flavonoids. The present study sought to establish whether galangin has any aggregatory effect on bacterial cells. Methods and Results: In preparatory time-kill assays, 50 μg ml-1 of galangin was found to reduce colony counts of c. 5 × 107 CFU ml-1Staphylococcus aureus NCTC 6571 by approximately 15 000-fold during 60 min of incubation. Subsequent light microscopy studies demonstrated significant increases in the number of large clusters of bacterial cells in populations treated with the flavonol. Conclusion: Data presented here show that galangin causes aggregation of bacterial cells. Significance and Impact of the Study: The finding that galangin causes bacterial cells to clump together may implicate the cytoplasmic membrane as a target site for this compound's activity. More importantly, this observation indicates that decreases in CFU numbers detected in time-kill and minimum bactericidal concentration (MBC) assays in previous investigations were at least partially attributable to this aggregatory effect. This raises the possibility that galangin is not genuinely bactericidal in action, and calls into question the suitability of time-kill and MBC assays for determining the nature of activity of naturally occurring flavonoids

Food web structure and mercury transfer in two contrasting Ugandan highland crater lakes (East Africa)

Abstract in English and FrenchVolcanic crater lakes scattered throughout western Uganda are important local sources of water and fish. Two representative but contrasting crater lakes near the Kibale National Park were sampled in 2000; the hyper-eutrophic Lake Saka, which is highly affected by agricultural practices, and the mesotrophic Lake Nkuruba that is still surrounded by intact forest. The food web structures in these two lakes were assessed using stable nitrogen (d15N) and carbon (d13C) isotope analyses, and the mercury (THg) transfer patterns were quantified. The d15N results indicate that food webs in both lakes are abbreviated, with only one to two trophic levels from primary consumers. The Lake Saka biota had distinctively enriched d13C values compared with those in Lake Nkuruba, which may be due to 12C-limited phytoplankton blooms in this lake. In Lake Nkuruba, two introduced tilapiine species and the introduced guppy Poecilia reticulata fed predominantly upon invertebrates and decomposed terrestrial plant material. In Lake Saka, the introduced Nile perch Lates niloticus appeared to occupy the top trophic position, but stable isotope values of the endemic haplochromine cichlids exclude those as Nile perch prey items. THg was found to biomagnify through the food web, reaching highest concentrations in P. reticulata in Nkuruba, which tended to be higher than for L. niloticus in Saka, suggesting increased bioavailability of THg in Nkuruba. Maximum THg concentrations in fish never approached WHO recommended guidelines (200 ng g-1) designed to protect at-risk groups

Eimeria species occurrence varies between geographic regions and poultry production systems and may influence parasite genetic diversity

Coccidiosis is one of the biggest challenges faced by the global poultry industry. Recent studies have highlighted the ubiquitous distribution of all Eimeria species which can cause this disease in chickens, but intriguingly revealed a regional divide in genetic diversity and population structure for at least one species, Eimeria tenella. The drivers associated with such distinct geographic variation are unclear, but may impact on the occurrence and extent of resistance to anticoccidial drugs and future subunit vaccines. India is one of the largest poultry producers in the world and includes a transition between E. tenella populations defined by high and low genetic diversity. The aim of this study was to identify risk factors associated with the prevalence of Eimeria species defined by high and low pathogenicity in northern and southern states of India, and seek to understand factors which vary between the regions as possible drivers for differential genetic variation. Faecal samples and data relating to farm characteristics and management were collected from 107 farms from northern India and 133 farms from southern India. Faecal samples were analysed using microscopy and PCR to identify Eimeria occurrence. Multiple correspondence analysis was applied to transform correlated putative risk factors into a smaller number of synthetic uncorrelated factors. Hierarchical cluster analysis was used to identify poultry farm typologies, revealing three distinct clusters in the studied regions. The association between clusters and presence of Eimeria species was assessed by logistic regression. The study found that large-scale broiler farms in the north were at greatest risk of harbouring any Eimeria species and a larger proportion of such farms were positive for E. necatrix, the most pathogenic species. Comparison revealed a more even distribution for E. tenella across production systems in south India, but with a lower overall occurrence. Such a polarised region- and system-specific distribution may contribute to the different levels of genetic diversity observed previously in India and may influence parasite population structure across much of Asia and Africa. The findings of the study can be used to prioritise target farms to launch and optimise appropriate anticoccidial strategies for long-term control

Electronic cigarettes: A position statement from the Thoracic Society of Australia and New Zealand*

The TSANZ develops position statements where insufficient data exist to write formal clinical guidelines. In 2018, the TSANZ addressed the question of potential benefits and health impacts of electronic cigarettes (EC). The working party included groups focused on health impacts, smoking cessation, youth issues and priority populations. The 2018 report on the Public Health Consequences of E-Cigarettes from the United States NASEM was accepted as reflective of evidence to mid-2017. A search for papers subsequently published in peer-reviewed journals was conducted in August 2018. A small number of robust and important papers published until March 2019 were also identified and included. Groups identified studies that extended, modified or contradicted the NASEM report. A total of 3793 papers were identified and reviewed, with summaries and draft position statements developed and presented to TSANZ membership in April 2019. After feedback from members and external reviewers, a collection of position statements was finalized in December 2019. EC have adverse lung effects and harmful effects of long-term use are unknown. EC are unsuitable consumer products for recreational use, part-substitution for smoking or long-term exclusive use by former smokers. Smokers who require support to quit smoking should be directed towards approved medication in conjunction with behavioural support as having the strongest evidence for efficacy and safety. No specific EC product can be recommended as effective and safe for smoking cessation. Smoking cessation claims in relation to EC should be assessed by established regulators

Nature and decay of a JπJ\pi=36+36^{+} resonance in the 24^{24}Mg + 24^{24}Mg reaction

It has been proposed to associate the narrow (\Gamma=170 keV) and high spin ($J\pi$=36^+) resonance in the 24Mg + 24Mg reaction at E_c.m= 45.7 MeV with a hyperdeformed molecular state in 48Cr. Such a description has important consequences for the resonance decay into the favoured inelastic channels. Through fragment- coincidence measurements performed ON and OFF resonance using the PRISMA-CLARA array, we have established that the 24Mg states selectively populated are the 2^+ and 4^+ members of the ground state band

Multimessenger astronomy with the Einstein Telescope

Gravitational waves (GWs) are expected to play a crucial role in the development of multimessenger astrophysics. The combination of GW observations with other astrophysical triggers, such as from gamma-ray and X-ray satellites, optical/radio telescopes, and neutrino detectors allows us to decipher science that would otherwise be inaccessible. In this paper, we provide a broad review from the multimessenger perspective of the science reach offered by the third generation interferometric GW detectors and by the Einstein Telescope (ET) in particular. We focus on cosmic transients, and base our estimates on the results obtained by ET's predecessors GEO, LIGO, and Virgo.Comment: 26 pages. 3 figures. Special issue of GRG on the Einstein Telescope. Minor corrections include