The effects of vaccination and immunity on bacterial infection dynamics in vivo.

Salmonella enterica infections are a significant global health issue, and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host. We have combined in vivo tracking of molecularly tagged bacterial subpopulations with mathematical modelling to gain a novel insight into how different classes of vaccines and branches of the immune response protect against secondary Salmonella enterica infections of the mouse. We have found that a live Salmonella vaccine significantly reduced bacteraemia during a secondary challenge and restrained inter-organ spread of the bacteria in the systemic organs. Further, fitting mechanistic models to the data indicated that live vaccine immunisation enhanced both the bacterial killing in the very early stages of the infection and bacteriostatic control over the first day post-challenge. T-cell immunity induced by this vaccine is not necessary for the enhanced bacteriostasis but is required for subsequent bactericidal clearance of Salmonella in the blood and tissues. Conversely, a non-living vaccine while able to enhance initial blood clearance and killing of virulent secondary challenge bacteria, was unable to alter the subsequent bacterial growth rate in the systemic organs, did not prevent the resurgence of extensive bacteraemia and failed to control the spread of the bacteria in the body.This work was supported by the Biotechnology and Biological Sciences Research Council [grant number BB/I002189/1].This is the published manuscript. It was originally published by PLOS One here: http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004359

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled duplications contain protein-coding genes that are mostly involved in reproductive function

Stroke genetics informs drug discovery and risk prediction across ancestries

Previous genome-wide association studies (GWASs) of stroke — the second leading cause of death worldwide — were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries

A database of experimentally measured lithium solid electrolyte conductivities evaluated with machine learning

AbstractThe application of machine learning models to predict material properties is determined by the availability of high-quality data. We present an expert-curated dataset of lithium ion conductors and associated lithium ion conductivities measured by a.c. impedance spectroscopy. This dataset has 820 entries collected from 214 sources; entries contain a chemical composition, an expert-assigned structural label, and ionic conductivity at a specific temperature (from 5 to 873 °C). There are 403 unique chemical compositions with an associated ionic conductivity near room temperature (15–35 °C). The materials contained in this dataset are placed in the context of compounds reported in the Inorganic Crystal Structure Database with unsupervised machine learning and the Element Movers Distance. This dataset is used to train a CrabNet-based classifier to estimate whether a chemical composition has high or low ionic conductivity. This classifier is a practical tool to aid experimentalists in prioritizing candidates for further investigation as lithium ion conductors.</jats:p

Unravelling the complexities in high-grade rocks using multiple techniques : the Achankovil Zone of southern India

The Achankovil Zone of southern India forms a distinct isotopic and structural boundary separating the Madurai Block to the north from the Trivandrum Block to the south. We combine isotopic and trace element geochemistry of major and accessory phases with phase equilibria modelling to provide quantitative constraints on the timing and conditions of peak metamorphism and the nature of the protoliths within the Achankovil Zone. The results suggest a clockwise pressure–temperature path with peak metamorphic temperatures of up to 950 °C at pressures of around 0.7 GPa followed by high temperature decompression. The metamorphic peak occurred at 545–512 Ma. U–Pb and Hf isotopic analysis of detrital zircon shows the rocks have a strong affinity with the southern part of the Madurai Block. The Achankovil Zone is interpreted as the reworked southern margin of the Madurai Block, which was metamorphosed during the final stages of the assembly of Gondwana