Comparisons between Geographically Diverse Samples of Carried Staphylococcus aureus

Approximately one-third of the human population is asymptomatically colonized by Staphylococcus aureus. However, much of the global diversity within the carriage populations remains uncharacterized, and it is unclear to what degree the variation is geographically partitioned. We isolated 300 carriage isolates from 1,531 adults contemporaneously in four countries: France, Algeria, Moldova, and Cambodia. All strains were characterized by multilocus sequence typing. Six clonal complexes (CCs) were present in all four samples (CC30, -45, -121, -15, -5, and -8). Analyses based on the genotype frequencies revealed the French and Algerian samples to be most similar and the Cambodian sample to be most distinct. While this pattern is consistent with likely rates of human migration and geographic distance, stochastic clonal expansion also contributes to regional differences. Phylogenetic analysis revealed a highly divergent and uncharacterized genotype (ST1223) within Cambodia. This lineage is related to CC75, which has previously been observed only in remote aboriginal populations in northern Australia.Although better known as an important human pathogen, Staphylococcus aureus is typically a commensal species and asymptomatically colonizes approximately one-third of the human population globally (18, 20, 29). This high carriage rate potentially represents a vast reservoir of as-yet-uncharacterized S. aureus diversity, an appreciation of which should shed light on the forces underpinning the diversification and dissemination of S. aureus. There are comparatively few studies examining spatial or temporal genotype distributions within carriage populations, and the extent of biogeographical structure is currently unclear, as is the level of discrimination which might be required to detect such structure.Multilocus sequence typing (MLST) has proved to be very successful as an epidemiological tool in that it delimits S. aureus in to a small number of widespread and discrete clonal complexes (CCs) (6, 8). These can be readily identified as clusters of related genotypes which have diversified radially from “founder” genotypes (9), and because this organism is largely clonal (8), assignments of isolates to these groups is broadly robust to the many different typing methods employed (4, 10, 27). The high level of divergence between these lineages suggests that they are relatively ancient and temporally stable (7), and it is possible that isolated host populations may have been colonized by different S. aureus lineages in the past. However, any footprints of geographical partitioning are likely to have been compromised by high rates of migration in recent times, due largely to the advent of air travel.Previous studies addressing the characterization of carried populations have tended to focus on samples from Western Europe or North America, and these have generally not provided strong evidence for geographical structuring. In a recent study using amplified fragment length polymorphism to compare the carried populations in Holland and North America, the authors noted considerable overlap between the samples, suggesting that they effectively constituted a single unstructured population (17). Similarly, independent MLST studies have revealed regional consistencies in Europe, such as the predominance of CC30 in the United Kingdom (8), Ireland (3), and Switzerland (25). Given the high rates of admixture within Europe and North America, the absence of obvious geographical structuring in the carried S. aureus population in these regions is perhaps not very surprising.Although they are currently scarce, current data from carriage populations outside of Europe or North America point to greater geographical structuring. For example, a sample of carried S. aureus recovered from Bamako, Mali, has recently been characterized, constituting the first such study of an African population (23). Although many of the previously characterized CCs were also present in this sample, the authors noted a high frequency (∼25%) of a single genotype, ST152, which is phylogenetically divergent and noted very rarely in Europe. The high frequency of ST152 in this population raises the possibility that this genotype is endemic to the Malian population and possibly elsewhere in sub-Saharan Africa. This in turn hints at greater geographical partitioning on a global scale, although more representative samples are clearly required. To address this, we generated MLST data from contemporaneous carriage samples recovered from four countries representing three continents: France (Western Europe), Moldova (Eastern Europe), Algeria (North Africa), and Cambodia (Southeast Asia). To our knowledge, this is the first time such a study has been carried out on samples from Eastern Europe, North Africa, or Southeast Asia. These data were therefore generated to uncover diversity within the global carriage population but also to understand further the extent to which geographical distance and host migration can explain regional differences.     

Genetic Architecture of Tameness in a Rat Model of Animal Domestication

A common feature of domestic animals is tameness—i.e., they tolerate and are unafraid of human presence and handling. To gain insight into the genetic basis of tameness and aggression, we studied an intercross between two lines of rats (Rattus norvegicus) selected over >60 generations for increased tameness and increased aggression against humans, respectively. We measured 45 traits, including tameness and aggression, anxiety-related traits, organ weights, and levels of serum components in >700 rats from an intercross population. Using 201 genetic markers, we identified two significant quantitative trait loci (QTL) for tameness. These loci overlap with QTL for adrenal gland weight and for anxiety-related traits and are part of a five-locus epistatic network influencing tameness. An additional QTL influences the occurrence of white coat spots, but shows no significant effect on tameness. The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general.ANIMAL domestication marked a turning point in human prehistory (Diamond 2002), and domestic animals have been the subject of research for many years (Darwin 1868). Recently, genetic studies have shed light on when, where, and how often a range of animal species were domesticated (Troy et al. 2001; Vila et al. 2001; Savolainen et al. 2002; Larson et al. 2005; Driscoll et al. 2007; Eriksson et al. 2008; Naderi et al. 2008). With the exception of coat color (e.g., Pielberg et al. 2008) and skin pigmentation (Eriksson et al. 2008), little is known about what occurred genetically during animal domestication. At what genes were allelic variants selected for by would-be practitioners of animal husbandry? Although domestic animals differ from each other in many ways, they all share the trait of tameness—i.e., they tolerate and sometimes even seek human presence and handling. Almost nothing is currently known about the genetic basis of tameness.In a series of studies initiated by D. K. Belyaev, researchers at the Institute for Cytology and Genetics in Novosibirsk (Russia) have subjected several mammalian species to a process of experimental domestication (Trut 1999). These studies, some of them ongoing for several decades, involve selection for tame and aggressive behavior in lines of animals derived from wild populations. They include a fox population that has been “domesticated” to such an extent that the tame foxes are now similar to dogs in some respects (Hare et al. 2005). They also include a population of wild-caught rats (Rattus norvegicus) that was selected for either reduced or enhanced aggression toward humans over >60 generations (Belyaev and Borodin 1982). To select the animals, their response to an approaching human hand was observed, and the rats showing the least and the most aggressive behavior were allowed to mate within the two lines, respectively. The initial response to selection was rapid and then slowed, so that little change in behavior from generation to generation has been observed in the last 10–15 generations, although the selection regime has been continued to the present. Today, the “tame” rats are completely unafraid of humans, they tolerate handling and being picked up, and they sometimes approach a human in a nonaggressive manner. By contrast, the “aggressive” rats ferociously attack or flee from an approaching human hand.To study the genetic basis of tameness we have established populations of both rat lines in Leipzig. In their new environment, the rats maintained their behavioral differences in response to humans, and these differences were not influenced by postnatal maternal factors (Albert et al. 2008). In addition, the rat lines differ in a number of other behavioral, anatomical, and physiological traits, raising the question whether these traits are influenced by the same loci as tameness and aggression toward humans.Many domestic animals display conspicuous coat color variations not found in their wild relatives. Prominent examples include the white color variants in dogs, pigs, cows, horses, and chickens. In laboratory rats, it has been proposed that “coat color genes” may account for many of the differences associated with domestication (Keeler and King 1942). It is thus interesting that individuals with white spots appeared in both the tame foxes (Trut 1999) and the tame rats (Trut et al. 2000) at higher frequency than in the corresponding aggressive lines, although they were absent or rare in the founding fox and rat populations, and although they were not selected for. The rat populations studied here provide an excellent opportunity to examine whether tameness is influenced by the same loci as white coat spotting.In this study, we crossed the two rat lines and bred >700 intercross animals. A broad set of behavioral, anatomical, and physiological traits was measured, and a genomewide set of genetic markers was used to identify genomic regions (quantitative trait loci, QTL) that influence tameness as well as other traits that differ between the lines, including white spots.     

Using a proxy of plant productivity (NDVI) to find key periods for animal performance: the case of roe deer

Animals in seasonal environments are affected by climate in very different ways depending on season and part of the climatic effects operates indirectly through the plants. Vegetation conditions in spring and summer are regarded as decisive for the reproductive success and the offspring's condition of large herbivores, but objective ways to determine key periods during the growing season have not been done often due to limitations in plant data. Using satellite data (NDVI), we determined how plant productivity from birth to fall influences the following winter body mass of roe deer fawns. We do this in two populations, the first inhabiting the low productive Chizé reserve in south western France with an oceanic climate and the second from Trois Fontaines, a highly productive forest with continental climate in east France. The effect of plant productivity was similar for male and female fawn mass, as expected from the weak intensity of sexual selection in roe deer life history traits. We found contrasting results between sites, with a strong effect of plant productivity in spring (April-May) in the Chizé population, but no effect in the Trois Fontaines population. The relatively low variability in winter fawn body mass could account for the absence of NDVI effects at Trois Fontaines. However, such results might also point to a limitation in the use of the NDVI, since the relationship between the canopy and the plant productivity at the ground level might be weak in the highly productive forest of Trois Fontaines.     

Comparison of impedance-based sensors for cell adhesion monitoring and in vitro methods for detecting cytotoxicity induced by chemicals

The recent European Commission REACH (Registration, Evaluation and Authorisation of Chemicals) policy outlines a plan for toxicological testing by using alternative non-animal in vitro methods. In this context, there is a need to develop and standardise high-throughput screening (HTS) methods for studying the cytotoxicity induced by chemicals. Electrochemical impedance spectroscopy (EIS) can be considered as a complementary technique to alternative in vitro testing for studying cell adhesion to the substrate, and can give real-time and kinetic information on cell responses to a toxicant. This paper describes the development of a home-made chip based on impedance spectroscopy, and its application in studying the kinetics of BALB/3T3 cell adhesion and the cellular responses to a toxic product as a function of time. Concentrations of sodium arsenite, ranging from 10 microM up to 1000 microM, were tested in the system, and the results were compared with those obtained with standard protocols used to study basal cytotoxicity induced by chemicals in the BALB/3T3 cell line. The results show that the sensitivity of the developed chip was better than that with the MTT test, with the additional advantages of online monitoring.     

Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between Grainyhead and Pleiohomeotic

Specific targeting of the protein complexes formed by the Polycomb group of proteins is critically required to maintain the inactive state of a group of developmentally regulated genes. Although the role of DNA binding proteins in this process has been well established, it is still not understood how these proteins target the Polycomb complexes specifically to their response elements. Here we show that the grainyhead gene, which encodes a DNA binding protein, interacts with one such Polycomb response element of the bithorax complex. Grainyhead binds to this element in vitro. Moreover, grainyhead interacts genetically with pleiohomeotic in a transgene-based, pairing-dependent silencing assay. Grainyhead also interacts with Pleiohomeotic in vitro, which facilitates the binding of both proteins to their respective target DNAs. Such interactions between two DNA binding proteins could provide the basis for the cooperative assembly of a nucleoprotein complex formed in vitro. Based on these results and the available data, we propose that the role of DNA binding proteins in Polycomb group-dependent silencing could be described by a model very similar to that of an enhanceosome, wherein the unique arrangement of protein-protein interaction modules exposed by the cooperatively interacting DNA binding proteins provides targeting specificity.     

Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland

In a survey of Phytophthora associated with alder decline in Poland, several isolates of a homothallic Phytophthora sp., which could not be assigned to other taxa including Phytophthora alni subspecies, were consistently recovered from rhizosphere soil samples. Their morphology and pathogenicity, as well as sequence data for three nuclear regions (internal transcribed spacer rDNA, elongation factor-1alpha and beta-tubulin) and a coding mitochondrial DNA region (nadh1), were examined. The new Phytophthora species is characterized by the moderate to slow growth rate of its colony in carrot agar at 20 degrees C, high optimal (c. 30 degrees C) and maximum (c. 38 degrees C) growth temperatures, formation of catenulate, often lateral, hyphal swellings, large chlamydospores in agar media and in soil extract, persistent, ovoid to ellipsoid nonpapillate sporangia and large oogonia with paragynous and sometimes amphigynous antheridia. Phytophthora polonica was slightly pathogenic to alder twigs and not pathogenic to trunks of several tree species. In a phylogenetic analysis using either Bayesian inference or maximum likelihood methods, P. polonica falls in clade 8 'sensu Kroon et al. (2004)' of Phytophthora.     

A new dendritic cell vaccine generated with interleukin-3 and interferon-β induces CD8+ T cell responses against NA17-A2 tumor peptide in melanoma patients

Dendritic cells derived from monocytes cultured in the presence of type I interferon were found to induce efficient T cell responses against tumor antigens in vitro. We vaccinated eight stage III or IV melanoma patients with dendritic cells generated with interferon-β and interleukin-3, activated by poly I: C, and pulsed with the tumor-specific antigen NA17.A2. This dendritic cell vaccine was well-tolerated with only minor and transient flu-like symptoms and inflammatory reactions at the injection sites. In most patients, isotopic imaging documented dendritic cells (DC) migration from the intradermal injection site to the draining lymph nodes. Finally, mixed lymphocyte-peptide culture under limiting dilution conditions followed by tetramer labeling indicated that three out of eight patients mounted a CD8 T cell response against the NA17.A2 antigenic peptide. We conclude that DC generated in type I-IFN represent an interesting alternative to DC generated in IL-4 and GM-CSF for cancer immunotherapy.