Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine

Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation

Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom’s childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin-–antitoxin systems, were also observed

A new framework for evaluating dust emission model development using dichotomous satellite observations of dust emission

Dust models are essential for understanding the impact of mineral dust on Earth's systems, human health, and global economies, but dust emission modelling has large uncertainties. Satellite observations of dust emission point sources (DPS) provide a valuable dichotomous inventory of regional dust emissions. We develop a framework for evaluating dust emission model performance using existing DPS data before routine calibration of dust models. To illustrate this framework's utility and arising insights, we evaluated the albedo-based dust emission model (AEM) with its areal (MODIS 500 m) estimates of soil surface wind friction velocity (u(s*)) and common, poorly constrained grain-scale entrainment threshold (u(*ts)) adjusted by a function of soil moisture (H). The AEM simulations are reduced to its frequency of occurrence, P(u(s*) > u(*ts)H). The spatio-temporal variability in observed dust emission frequency is described by the collation of nine existing DPS datasets. Observed dust emission occurs rarely, even in North Africa and the Middle East, where DPS frequency averages 1.8 %, (similar to 7 days y(-1)), indicating extreme, large wind speed events. The AEM coincided with observed dust emission similar to 71.4 %, but simulated dust emission similar to 27.4 % when no dust emission was observed, while dust emission occurrence was over-estimated by up to 2 orders of magnitude. For estimates to match observations, results showed that grain- scale u(*ts) needed restricted sediment supply and compatibility with areal u(s*). Failure to predict dust emission during observed events, was due to u(s*) being too small because reanalysis winds (ERA5-Land) were averaged across 11 km pixels, and inconsistent with u(s*)across 0.5 km pixels representing local maxima. Assumed infinite sediment supply caused the AEM to simulate dust emission whenever P(u(s*)>u(*ts)H), producing false positives when wind speeds were large. The dust emission model scales of existing parameterisations need harmonising and a new parameterisation for u(*ts) is required to restrict sediment supply over space and time

Nanocapillary sampling coupled to liquid chromatography mass spectrometry delivers single cell drug measurement and lipid fingerprints

This work describes the development of a new approach to measure drug levels and lipid fingerprints in single living mammalian cells. Nanocapillary sampling is an approach that enables the selection and isolation of single living cells under microscope observation. Here, live single cell nanocapillary sampling is coupled to liquid chromatography for the first time. This allows molecular species to be separated prior to ionisation and improves measurement precision of drug analytes. The efficiency of transferring analytes from the sampling capillary into a vial was optimised in this work. The analysis was carried out using standard flow liquid chromatography coupled to widely available mass spectrometry instrumentation, highlighting opportunities for widespread adoption. The method was applied to 30 living cells, revealing cell-to-cell heterogeneity in the uptake of different antibiotics. Using this system, we detected 14-158 lipid features per single cell, revealing the association between bedaquiline uptake and lipid fingerprints

Parallel evolution in streptococcus pneumoniae biofilms

Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development

Pneumococcal conjugate vaccine implementation in middle-income countries

Since 2000, the widespread adoption of pneumococcal conjugate vaccines (PCVs) has had a major impact in the prevention of pneumonia. Limited access to international financial support means some middle-income countries (MICs) are trailing in the widespread use of PCVs. We review the status of PCV implementation, and discuss any needs and gaps related to low levels of PCV implementation in MICs, with analysis of possible solutions to strengthen the PCV implementation process in MICs

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Satellites reveal Earth's seasonally shifting dust emission sources

Establishing mineral dust impacts on Earth's systems requires numerical models of the dust cycle. Differences between dust optical depth (DOD) measurements and modelling the cycle of dust emission, atmospheric transport, and deposition of dust indicate large model uncertainty due partially to unrealistic model assumptions about dust emission frequency. Calibrating dust cycle models to DOD measurements typically in North Africa, are routinely used to reduce dust model magnitude. This calibration forces modelled dust emissions to match atmospheric DOD but may hide the correct magnitude and frequency of dust emission events at source, compensating biases in other modelled processes of the dust cycle. Therefore, it is essential to improve physically based dust emission modules. Here we use a global collation of satellite observations from previous studies of dust emission point source (DPS) dichotomous frequency data. We show that these DPS data have little-to-no relation with MODIS DOD frequency. We calibrate the albedo-based dust emission model using the frequency distribution of those DPS data. The global dust emission uncertainty constrained by DPS data (±3.8 kg m−2 y−1) provides a benchmark for dust emission model development. Our calibrated model results reveal much less global dust emission (29.1 ± 14.9 Tg y−1) than previous estimates, and show seasonally shifting dust emission predominance within and between hemispheres, as opposed to a persistent North African dust emission primacy widely interpreted from DOD measurements. Earth's largest dust emissions, proceed seasonally from East Asian deserts in boreal spring, to Middle Eastern and North African deserts in boreal summer and then Australian shrublands in boreal autumn-winter. This new analysis of dust emissions, from global sources of varying geochemical properties, have far-reaching implications for current and future dust-climate effects. For more reliable coupled representation of dust-climate projections, our findings suggest the need to re-evaluate dust cycle modelling and benefit from the albedo-based parameterisation