Linkage Group Selection: Towards Identifying Genes Controlling Strain Specific Protective Immunity in Malaria

Protective immunity against blood infections of malaria is partly specific to the genotype, or strain, of the parasites. The target antigens of Strain Specific Protective Immunity are expected, therefore, to be antigenically and genetically distinct in different lines of parasite. Here we describe the use of a genetic approach, Linkage Group Selection, to locate the target(s) of Strain Specific Protective Immunity in the rodent malaria parasite Plasmodium chabaudi chabaudi. In a previous such analysis using the progeny of a genetic cross between P. c. chabaudi lines AS-pyr1 and CB, a location on P. c. chabaudi chromosome 8 containing the gene for merozoite surface protein-1, a known candidate antigen for Strain Specific Protective Immunity, was strongly selected. P. c. chabaudi apical membrane antigen-1, another candidate for Strain Specific Protective Immunity, could not have been evaluated in this cross as AS-pyr1 and CB are identical within the cell surface domain of this protein. Here we use Linkage Group Selection analysis of Strain Specific Protective Immunity in a cross between P. c. chabaudi lines CB-pyr10 and AJ, in which merozoite surface protein-1 and apical membrane antigen-1 are both genetically distinct. In this analysis strain specific immune selection acted strongly on the region of P. c. chabaudi chromosome 8 encoding merozoite surface protein-1 and, less strongly, on the P. c. chabaudi chromosome 9 region encoding apical membrane antigen-1. The evidence from these two independent studies indicates that Strain Specific Protective Immunity in P. c. chabaudi in mice is mainly determined by a narrow region of the P. c. chabaudi genome containing the gene for the P. c. chabaudi merozoite surface protein-1 protein. Other regions, including that containing the gene for P. c. chabaudi apical membrane antigen-1, may be more weakly associated with Strain Specific Protective Immunity in these parasites

Impacts of ground-level ozone on sugarcane production

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: Data will be made available on request.Sugarcane is a vital commodity crop often grown in (sub)tropical regions which have been experiencing a recent deterioration in air quality. Unlike for other commodity crops, the risk of air pollution, specifically ozone (O3), to this C4 crop has not yet been quantified. Yet, recent work has highlighted both the potential risks of O3 to C4 bioenergy crops, and the emergence of O3 exposure across the tropics as a vital factor determining global food security. Given the large extent, and planned expansion of sugarcane production in places like Brazil to meet global demand for biofuels, there is a pressing need to characterize the risk of O3 to the industry. In this study, we sought to a) derive sugarcane O3 dose-response functions across a range of realistic O3 exposure and b) model the implications of this across a globally important production area. We found a significant impact of O3 on biomass allocation (especially to leaves) and production across a range of sugarcane genotypes, including two commercially relevant varieties (e.g. CTC4, Q240). Using these data, we calculated dose-response functions for sugarcane and combined them with hourly O3 exposure across south-central Brazil derived from the UK Earth System Model (UKESM1) to simulate the current regional impact of O3 on sugarcane production using a dynamic global vegetation model (JULES vn 5.6). We found that between 5.6 % and 18.3 % of total crop productivity is likely lost across the region due to the direct impacts of current O3 exposure. However, impacts depended critically on the substantial differences in O3 susceptibility observed among sugarcane genotypes and how these were implemented in the model. Our work highlights not only the urgent need to fully elucidate the impacts of O3 in this important bioenergetic crop, but the potential implications air quality may have upon tropical food production more generally.Natural Environment Research Council (NERC)FAPESPCNRMet Office Hadley Centre Climate ProgrammeMet Offic

Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1

The Mycobacterium tuberculosis H37Rv genome encodes 20 cytochromes P450, including P450s crucial to infection and bacterial viability. Many M. tuberculosis P450s remain uncharacterized, suggesting that their further analysis may provide new insights into M. tuberculosis metabolic processes and new targets for drug discovery. CYP126A1 is representative of a P450 family widely distributed in mycobacteria and other bacteria. Here we explore the biochemical and structural properties of CYP126A1, including its interactions with new chemical ligands. A survey of azole antifungal drugs showed that CYP126A1 is inhibited strongly by azoles containing an imidazole ring but not by those tested containing a triazole ring. To further explore the molecular preferences of CYP126A1 and search for probes of enzyme function, we conducted a high throughput screen. Compounds containing three or more ring structures dominated the screening hits, including nitroaromatic compounds that induce substrate-like shifts in the heme spectrum of CYP126A1. Spectroelectrochemical measurements revealed a 155-mV increase in heme iron potential when bound to one of the newly identified nitroaromatic drugs. CYP126A1 dimers were observed in crystal structures of ligand-free CYP126A1 and for CYP126A1 bound to compounds discovered in the screen. However, ketoconazole binds in an orientation that disrupts the BC-loop regions at the P450 dimer interface and results in a CYP126A1 monomeric crystal form. Structural data also reveal that nitroaromatic ligands "moonlight" as substrates by displacing the CYP126A1 distal water but inhibit enzyme activity. The relatively polar active site of CYP126A1 distinguishes it from its most closely related sterol-binding P450s in M. tuberculosis, suggesting that further investigations will reveal its diverse substrate selectivity.This work was supported by Biotechnology and Biological Research Council (BBSRC) Grants BB/I019227/1 (to A. W. M.) and BB/I019669/1 (to C. A.) underpinning this research program and supporting the research of A. J. C. and K. J. M

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes

AusTraits, a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge

Increased Litterfall Changes Fine Root Distribution In a Moist Tropical Forest

Root proliferation into the Oa and Oe soil horizons in tropical forests is often substantial and allows direct cycling of nutrients from the organic matter; this was thought to be an adaptation to the low nutrient supply in infertile soils. In this study, we show that experimentally increased litter inputs promote root proliferation into the Oi and Oe horizons in a relatively fertile soil, suggesting that it is a response to a more readily available nutrient source rather than an adaptation to nutrient shortage, and the absence of root mats on fertile tropical soils is simply a consequence of the lack of persistent organic horizons due to high decomposition rates

Determination of neo- and d-chiro-inositol hexakisphosphate in soils by solution 31P NMR spectroscopy

The inositol phosphates are an abundant but poorly understood group of organic phosphorus compounds found widely in the environment. Four stereoisomers of inositol hexakisphosphate (IP6) occur, although for three of these (scyllo, neo, and d-chiro) the origins, dynamics, and biological function remain unknown, due in large part to analytical limitations in their measurement in environmental samples. We synthesized authentic neo- and d-chiro-IP 6 and used them to identify signals from these compounds in three soils from the Falkland Islands. Both compounds resisted hypobromite oxidation and gave quantifiable 31P NMR signals at δ = 6.67 ppm (equatorial phosphate groups of the 4-equatorial/2-axial conformer of neo-IP6) and δ = 6.48 ppm (equatorial phosphate groups of the 2-equatorial/4-axial conformer of d-chiro-IP6) in soil extracts. Inositol hexakisphosphate accounted for 46-54% of the soil organic phosphorus, of which the four stereoisomers constituted, on average, 55.9% (myo), 32.8% (scyllo), 6.1% (neo), and 5.2% (d-chiro). Reappraisal of the literature based on the new signal assignments revealed that neo- and d-chiro-IP6 occur widely in both terrestrial and aquatic ecosystems. These results confirm that the inositol phosphates can constitute a considerable fraction of the organic phosphorus in soils and reveal the prevalence of neo- and d-chiro-IP6 in the environment. The hypobromite oxidation and solution 31P NMR spectroscopy procedure allows the simultaneous quantification of all four IP6 stereoisomers in environmental samples and provides a platform for research into the origins and ecological significance of these enigmatic compounds