Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium’s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic. © 2019 National Academy of Sciences. All rights reserved

Surface gas measurements and related studies for the characterization and monitoring of geological CO2 storage sites; experiences at Weyburn and in Salah.

Preliminary baseline soil gas data collected in the summer and autumn of 2001 above the Phase 1A injection area of the EnCana Enhanced Oil Recovery project at the Weyburn oilfield in south Saskatchewan was presented at GHGT-6 in Kyoto. Data can now be presented for all three years of the study with conclusions, the predominant one being that the major controls on soil gas levels are seasonal and meteorological with no indications of leakage from depth. In the autumns of 2002 and 2003 further in situ monitoring of CO2, CO2 flux, O2, CH4, radon (222Rn) and thoron (220Rn) was carried out. Soil gas samples were also collected for laboratory analysis of helium, permanent gases, sulphur species and light hydrocarbons. All sampling was repeated over the same 360 point sampling grid and more detailed profiles for both follow-up years. Marked changes in CO2 levels (especially flux) for each of the three-year datasets indicate changes in surface conditions, rather than CO2 from a deeper source. The radon and thoron data was found to be similar for the three years but appears to vary in response to drift composition, and seasonal effects, rather than migration from a deep source. In 2003 further work was agreed in addition to the main grid and profile data. A control area was sampled for the same suite of gases, 10km to the northwest of the oil field. It included similar topography, land use and drift composition to the main sampling grid. There were 35 sample locations on a 7 x 5 point grid with 100m spacing and two additional sites. Early conclusions indicate that the soil gas results in the control area are very similar to those from the main grid, vindicating control site selection and further supporting a lack of deeply sourced CO2 over the injection area. Along with the control site, five zones of possible CO2 leakage were also surveyed and sampled. Two cross a river lineament that may be associated with deep faulting, two were abandoned oil well sites and one site overlays a deep salt dissolution feature. (Unfortunately CO2 flux and gamma measurements were not carried out at these sites.) A northeast/southwest trending lineament, just north of the main grid, was sampled along two profiles perpendicular to the feature, with an increased density of sampling over the feature. The feature generally followed an incised river valley and anomalous CO2 was only detected on the valley floor, where it would be expected as there was lush vegetation in this zone. There were no coincident anomalies for other gases. Soils around two abandoned wells were also sampled. A 16-site grid was surveyed around each well. One well had been completely abandoned and the other was suspended due to failed casing. Such boreholes represent possible points of weakness that may be routes for CO2 migration. The well with failed casing had weakly anomalous CO2 locally to the south, again unmatched for other gases. The fully abandoned well had background CO2 values. Two perpendicular profiles of 10 sites at 25m spacing were sampled for soil gas over the mapped centre of the dissolution feature. Background values were obtained. In 2003 two vertical profiles were performed both indicating an increase in CO2 to a depth maximum of 1.80m; this increase is matched by a corresponding decrease only in O2, indicating biological respiration. Radon concentration indicated no anomalies. Portable gamma spectrometric data was collected in 2003 over the west-centre area of the grid, the profiles and over the control grid. The composition of soils from both areas was found to be very similar.PublishedBerkeley, California4.5. Degassamento naturaleope

The toxicological intersection between allergen and toxin: A structural comparison of the cat dander allergenic protein Fel d1 and the slow loris brachial gland secretion protein

Slow lorises are enigmatic animal that represent the only venomous primate lineage. Their defensive secretions have received little attention. In this study we determined the full length sequence of the protein secreted by their unique brachial glands. The full length sequences displayed homology to the main allergenic protein present in cat dander. We thus compared the molecular features of the slow loris brachial gland protein and the cat dander allergen protein, showing remarkable similarities between them. Thus we postulate that allergenic proteins play a role in the slow loris defensive arsenal. These results shed light on these neglected, novel animals

"I am your mother and your father!": In vitro derived gametes and the ethics of solo reproduction

In this paper, we will discuss the prospect of human reproduction achieved with gametes originating from only one person. According to statements by a minority of scientists working on the generation of gametes in vitro, it may become possible to create eggs from men’s non-reproductive cells and sperm from women’s. This would enable, at least in principle, the creation of an embryo from cells obtained from only one individual: ‘solo reproduction’. We will consider what might motivate people to reproduce in this way, and the implications that solo reproduction might have for ethics and policy. We suggest that such an innovation is unlikely to revolutionise reproduction and parenting. Indeed, in some respects it is less revolutionary than in vitro fertilisation as a whole. Furthermore, we show that solo reproduction with in vitro created gametes is not necessarily any more ethically problematic than gamete donation—and probably less so. Where appropriate, we draw parallels with the debate surrounding reproductive cloning. We note that solo reproduction may serve to perpetuate reductive geneticised accounts of reproduction, and that this may indeed be ethically questionable. However, in this it is not unique among other technologies of assisted reproduction, many of which focus on genetic transmission. It is for this reason that a ban on solo reproduction might be inconsistent with continuing to permit other kinds of reproduction that also bear the potential to strengthen attachment to a geneticised account of reproduction. Our claim is that there are at least as good reasons to pursue research towards enabling solo reproduction, and eventually to introduce solo reproduction as an option for fertility treatment, as there are to do so for other infertility related purposes

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally1, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups2, 3 has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa4, although a much younger origin has also been proposed5. The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1’s evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 × 10-7Introduction Results - Retrieved genomes are likely from typical infections - Demographic history of HSV-1 in a global context Discussion Material and Methods - Ethics statement - Sampling - Generation of aDNA libraries - Sequencing - aDNA authentication - Metagenomic screening - Targeted capture of HSV-1 - Alignment of viral data to the reference sequence - Genotyping - HSV-1 linkage disequilibrium and population genetic analysis - Compilation of comparative HSV data - Preparation of genome sequences - HSV-1 phylogenetic analysis and recombination filtering - Phylogenetic dating - Alignment of human data to the reference sequence and quality control - Genetic sex estimation, mtDNA, and Y haplotyping - Human variant calling and imputation of genotype

Genetic history of Cambridgeshire before and after the Black Death.

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death

The Λp\bf{\Lambda p} interaction studied via femtoscopy in p + Nb reactions at sNN=3.18 GeV\mathbf{\sqrt{s_{NN}}=3.18} ~\mathrm{\bf{GeV}}

We report on the first measurement of $p\Lambda$ and $pp$ correlations via the femtoscopy method in p+Nb reactions at $\mathrm{\sqrt{s_{NN}}=3.18} ~\mathrm{GeV}$, studied with the High Acceptance Di-Electron Spectrometer (HADES). By comparing the experimental correlation function to model calculations, a source size for $pp$ pairs of $r_{0,pp}=2.02 \pm 0.01(\mathrm{stat})^{+0.11}_{-0.12} (\mathrm{sys}) ~\mathrm{fm}$ and a slightly smaller value for $p\Lambda$ of $r_{0,\Lambda p}=1.62 \pm 0.02(\mathrm{stat})^{+0.19}_{-0.08}(\mathrm{sys}) ~\mathrm{fm}$ is extracted. Using the geometrical extent of the particle emitting region, determined experimentally with $pp$ correlations as reference together with a source function from a transport model, it is possible to study different sets of scattering parameters. The $p\Lambda$ correlation is proven sensitive to predicted scattering length values from chiral effective field theory. We demonstrate that the femtoscopy technique can be used as valid alternative to the analysis of scattering data to study the hyperon-nucleon interaction.Comment: 12 pages, 11 figure

Searching a Dark Photon with HADES

We present a search for the e+e- decay of a hypothetical dark photon, also names U vector boson, in inclusive dielectron spectra measured by HADES in the p (3.5 GeV) + p, Nb reactions, as well as the Ar (1.756 GeV/u) + KCl reaction. An upper limit on the kinetic mixing parameter squared epsilon^{2} at 90% CL has been obtained for the mass range M(U) = 0.02 - 0.55 GeV/c2 and is compared with the present world data set. For masses 0.03 - 0.1 GeV/c^2, the limit has been lowered with respect to previous results, allowing now to exclude a large part of the parameter region favoured by the muon g-2 anomaly. Furthermore, an improved upper limit on the branching ratio of 2.3 * 10^{-6} has been set on the helicity-suppressed direct decay of the eta meson, eta-> e+e-, at 90% CL