Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster

The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history. Surprisingly, despite the availability of effective antibiotic treatment since the mid-twentieth century, this bacterial infection, which is caused by Treponema pallidum subsp. pallidum (TPA), has been re-emerging globally in the last few decades with an estimated 10.6 million cases in 2008. Although resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the secondline antibiotic azithromycin. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the low quantities of treponemal DNA in clinical samples and difficulties in cultivating the pathogen. Here, we used DNA capture and whole-genome sequencing to successfully interrogate genome-wide variation from syphilis patient specimens, combined with laboratory samples of TPA and two other subspecies. Phylogenetic comparisons based on the sequenced genomes indicate that the TPA strains examined share a common ancestor after the fifteenth century, within the early modern era. Moreover, most contemporary strains are azithromycin-resistant and are members of a globally dominant cluster, named here as SS14-Ω. The cluster diversified from a common ancestor in the mid-twentieth century subsequent to the discovery of antibiotics. Its recent phylogenetic divergence and global presence point to the emergence of a pandemic strain cluster

Combining isotopic signatures of n(87Sr)/n(86Sr) and light stable elements (C, N, O, S) with multi-elemental profiling for the authentication of provenance of European cereal samples

The aim of this work (from the FP6 project TRACE) was to develop methods based on the use of geochemical markers for the authentication of the geographical origin of cereal samples in Europe (cf. EC regulations 2081/92 and 1898/06). For the first time, the potential usefulness of combining n(87Sr)/n(86Sr) and δ13C, δ15N, δ18O and δ34S isotopic signatures, alone or with key element concentrations ([Na], [K], [Ca], [Cu] and [Rb], progressively identified out of 31 sets of results), was investigated through multiple step multivariate statistics for more than 500 cereal samples collected over 2 years from 17 sampling sites across Europe representing an extensive range of geographical and environmental characteristics. From the classification categories compared (north/south; proximity to the Atlantic Ocean/to the Mediterranean Sea/to else; bed rock geologies) the first two were the most efficient (particularly with the ten variables selected together). In some instances element concentrations made a greater impact than the isotopic tracers. Validation of models included external prediction tests on 20% of the data randomly selected and, rarely done, a study on the robustness of these multivariate data treatments to uncertainties on measurement results. With the models tested it was possible to individualise 15 of the sampling sites

Advancing the understanding of treponemal disease in the past and present

Syphilis was perceived to be a new disease in Europe in the late 15th century, igniting a debate about its origin that continues today in anthropological, historical, and medical circles. We move beyond this age-old debate using an interdisciplinary approach that tackles broader questions to advance the understanding of treponemal infection (syphilis, yaws, bejel, and pinta). How did the causative organism(s) and humans co-evolve? How did the related diseases caused by Treponema pallidum emerge in different parts of the world and affect people across both time and space? How are T. pallidum subspecies related to the treponeme causing pinta? The current state of scholarship in specific areas is reviewed with recommendations made to stimulate future work. Understanding treponemal biology, genetic relationships, epidemiology, and clinical manifestations is crucial for vaccine development today and for investigating the distribution of infection in both modern and past populations. Paleopathologists must improve diagnostic criteria and use a standard approach for recording skeletal lesions on archaeological human remains. Adequate contextualization of cultural and environmental conditions is necessary, including site dating and justification for any corrections made for marine or freshwater reservoir effects. Biogeochemical analyses may assess aquatic contributions to diet, physiological changes arising from treponemal disease and its treatments (e.g., mercury), or residential mobility of those affected. Shifting the focus from point of origin to investigating who is affected (e.g., by age/sex or socioeconomic status) and disease distribution (e.g., coastal/ inland, rural/urban) will advance our understanding of the treponemal disease and its impact on people through time

Neutron activation cross sections on lead isotopes

The cross sections for the reactions Pb-204(n,n(')gamma)Pb-204(m), Pb-204(n,2n)Pb-203, Pb-204(n,2n)Pb-203(m1), Pb-204(n,3n)Pb-202(m), Pb-206(n,3n)Pb-204(m), Pb-206(n,alpha)Hg-203, and Pb-208(n,p)Tl-208 were determined at the IRMM van de Graaff laboratory in the neutron energy range from 14 to 21 MeV. Both natural and enriched samples were irradiated with neutrons produced via the H-3(d,n)He-4 reaction. The induced activities were determined by gamma-ray spectrometry using a HPGe detector in a low-background shield. Neutron fluences were determined with the well-known cross section of the Al-27(n,alpha)Na-24 reaction. Enriched samples were essential to determine the cross sections for the reactions with Pb-204(m) and Pb-206(m) isomers in the final state. Accurate results for reactions with Pb-204,Pb-206 as target nuclei with natural lead samples were enabled through a precise measurement of the isotopic ratios. For a first investigation of the consequences of the present data for nuclear reaction models they were confronted with calculations based on global parameter systematics in a phenomenological and in a microscopic approach and with parameters selected to reproduce the available data. The TALYS code was used for the former two calculations involving parameter systematics while the STAPRE code was used for the latter calculation

Iles Eparses (SW Indian Ocean) as reference ecosystems for environmental research

International audienceTAAF ensures since 2007 the management of 5 small tropical islands lying in the southwestern Indian Ocean: the Iles Eparses. These islands share an exceptional natural heritage including many marine and terrestrial endemic species. At a regional scale the Iles Eparses are some of the most pristine ecosystems, largely preserved from anthropogenic impacts due to their geographical isolation and a historically very limited human occupation. In this context, TAAF wished that Iles Eparses become unique natural laboratories for earth scientists and environmental process observation – like climate change impacts - but also sustainable biodiversity sanctuaries for which the scientific community should provide baseline ecological data to inform on appropriate conservation tools. An inter-agency research consortium emerged in 2009 to meet this commitment for the Iles Eparses. This program was intended to set a science framework in accordance with France' objectives for Research and Conservation. It enabled between 2009 and 2014 the implementation of 18 cross-disciplinary research projects ranging from geology to ecology and represented by the variety of the proposed articles in this special issue. Altogether research projects have dramatically increased knowledge on the Iles Eparses' ecosystems and have provided the first overview of their diversity, their functions and their dynamics and its determinants. In particular applied research efforts have supplied a significant amount of ecological evidence that is now available to develop optimal conservation strategy to ensure the Iles Eparses' long-term biodiversity value. These findings point out that the continuation of research activity in the Iles Eparses should be considered a priority

High concentrations of complexed metals in the guts of deposit feeders

cited By 32International audienceSediment particles passing through the guts of deposit feeders are subject to an environment unusually rich in dissolved organic material, especially proteinaceous materials, capable of binding metals. Concentrations of many heavy metals are high in gut fluids of various deposit feeders from pristine environments. Concentrations of Cu and Cd show strong correlations with total acid-hydrolyzed amino acids (TAHAA) in gut fluids in a cross-phyletic survey of 35 deposit feeder species. Similar correspondence with TAHAA obtains among individuals, along longitudinal gut sections, and among molecular weight fractions. Multiple incubations of sediments with a commercial protein solution having similar TAHAA concentration as gut fluid solubilized many metals, showing convergence toward similar composition as gut fluid. Adherence of gut-dissolved metal concentrations to the Irving-Williams order suggests that the rich milieu of soft ligands contained in gut fluids provides a mechanism for mobilization of softer metals in sediments