Detection of Retroviral Super-Infection from Non-Invasive Samples

While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has remained largely neglected. In particular, methods possibly allowing the investigation of super-infection from samples collected non-invasively (such as faeces) have never been properly compared. Here, we fill in this gap by assessing the costs and benefits of end-point dilution PCR (EPD-PCR) and multiple bulk-PCR cloning, as applied to a case study focusing on simian foamy virus super-infection in wild chimpanzees (Pan troglodytes). We show that, although considered to be the gold standard, EPD-PCR can lead to massive consumption of biological material when only low copy numbers of the target are expected. This constitutes a serious drawback in a field in which rarity of biological material is a fundamental constraint. In addition, we demonstrate that EPD-PCR results (single/multiple infection; founder strains) can be well predicted from multiple bulk-PCR clone experiments, by applying simple statistical and network analyses to sequence alignments. We therefore recommend the implementation of the latter method when the focus is put on retroviral super-infection and only low retroviral loads are encountered

PLA scaffolds production from Thermally Induced Phase Separation: effect of process parameters and development of an environmentally improved route assisted by supercritical carbon dioxide

In this work, a relatively large scale of PLA scaffolds was produced using thermally induced phase separation (TIPS) combined with a supercritical carbon dioxide (SC-CO2) drying step as a green alternative. For the TIPS step, the phase separation of PLA and 1,4-dioxane solvent was controlled by adjusting the process conditions such as the polymer concentration and molecular weight, the 1,4-dioxane solvent power and the cooling conditions. The scaffolds morphology was analyzed by scanning electron microscopy. Their structural and mechanical properties were correlated together with the possibility to tune them by controlling the process conditions. An environmental analysis using the Life Cycle Assessment (LCA) methodology confirmed a reduction of at least 50% of the environmental impact of the whole process using the SC-CO2 drying compared to the traditional freeze-drying technology. This work is the first known attempt to conduct the LCA methodology on TIPS process for the PLA scaffolds production

Synthesis of hollow vaterite CaCO(3) microspheres in supercritical carbon dioxide medium

We here describe a rapid method for synthesizing hollow core, porous crystalline calcium carbonate microspheres composed of vaterite using supercritical carbon dioxide in aqueous media, without surfactants. We show that the reaction in alkaline media rapidly conducts to the formation of microspheres with an average diameter of 5 mu m. SEM, TEM and AFM observations reveal that the microspheres have a hollow core of around 0.7 mu m width and are composed of nanograins with an average diameter of 40 nm. These nanograins are responsible for the high specific surface area of 16 m(2) g(-1) deduced from nitrogen absorption/desorption isotherms, which moreover confers an important porosity to the microspheres. We believe this work may pave the way for the elaboration of a biomaterial with a large potential for therapeutic as well as diagnostic applications

Comparison of target enrichment strategies for ancient pathogen DNA

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods ? array-based hybridization capture and in-solution capture using either RNA or DNA baits ? have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits

Novel Mycobacterium tuberculosis Complex Isolate from a Wild Chimpanzee

Tuberculosis (TB) is caused by gram-positive bacteria known as the Mycobacterium tuberculosis complex (MTBC). MTBC include several human-associated lineages and several variants adapted to domestic and, more rarely, wild animal species. We report an M. tuberculosis strain isolated from a wild chimpanzee in Côte d’Ivoire that was shown by comparative genomic and phylogenomic analyses to belong to a new lineage of MTBC, closer to the human-associated lineage 6 (also known as M. africanum West Africa 2) than to the other classical animal-associated MTBC strains. These results show that the general view of the genetic diversity of MTBC is limited and support the possibility that other MTBC variants exist, particularly in wild mammals in Africa. Exploring this diversity is crucial to the understanding of the biology and evolutionary history of this widespread infectious disease

Development of an eco-friendly Thermal Induced Phase Separation (TIPS) process assisted by supercritical CO2 for the production of PLA scaffolds with tunable structural and mechanical properties

Many routes are nowadays utilized for the production of PLA scaffolds. In this study, a relative large scale of scaffolds was produced combining thermal induced phase separation and supercritical CO2 as a green alternative drying. The phase separation between polylactic acid and 1,4-dioxane was monitored by adjusting the process parameters such as the polymer concentration, the molecular weight, the solvent power and the cooling conditions. The morphologic changes occurring during the phase separation were analyzed by scanning electron microscopy. Structural and mechanical properties of scaffolds were correlated and it was possible to tune them depending on the process parameters. Moreover, an environmental analysis of the thermal induced phase separation (TIPS) process and the comparison between supercritical CO2 and the traditional freeze drying technologies were investigated. This work is the first known attempt to conduct the life cycle assessment (LCA) methodology on TIPS process and the polylactic acid scaffolds production. The results of the LCA have demonstrated that using supercritical-CO2 drying technology allows to reduce by at least 50 % the environmental impact of the whole process and to drastically diminish the production time

Novel polyomaviruses of nonhuman primates: genetic and serological predictors for the existence of multiple unknown polyomaviruses within the human population.

Polyomaviruses are a family of small non-enveloped DNA viruses that encode oncogenes and have been associated, to greater or lesser extent, with human disease and cancer. Currently, twelve polyomaviruses are known to circulate within the human population. To further examine the diversity of human polyomaviruses, we have utilized a combinatorial approach comprised of initial degenerate primer-based PCR identification and phylogenetic analysis of nonhuman primate (NHP) polyomavirus species, followed by polyomavirus-specific serological analysis of human sera. Using this approach we identified twenty novel NHP polyomaviruses: nine in great apes (six in chimpanzees, two in gorillas and one in orangutan), five in Old World monkeys and six in New World monkeys. Phylogenetic analysis indicated that only four of the nine chimpanzee polyomaviruses (six novel and three previously identified) had known close human counterparts. To determine whether the remaining chimpanzee polyomaviruses had potential human counterparts, the major viral capsid proteins (VP1) of four chimpanzee polyomaviruses were expressed in E. coli for use as antigens in enzyme-linked immunoassay (ELISA). Human serum/plasma samples from both Côte d'Ivoire and Germany showed frequent seropositivity for the four viruses. Antibody pre-adsorption-based ELISA excluded the possibility that reactivities resulted from binding to known human polyomaviruses. Together, these results support the existence of additional polyomaviruses circulating within the human population that are genetically and serologically related to existing chimpanzee polyomaviruses

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation