High Prevalence,Coinfection Rate,and Genetic Diversity of Retroviruses in Wild Red Colobus Monkeys (Piliocolobus badius badius) in Ta? National Park,C?te d'Ivoire

Simian retroviruses are precursors of all human retroviral pathogens. However, little is known about the prevalence and coinfection rates or the genetic diversity of major retroviruses—simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus type 1 (STLV-1), and simian foamy virus (SFV)—in wild populations of nonhuman primates. Such information would contribute to the understanding of the natural history of retroviruses in various host species. Here, we estimate these parameters for wild West African red colobus monkeys (Piliocolobus badius badius) in the Taï National Park, Côte d''Ivoire. We collected samples from a total of 54 red colobus monkeys; samples consisted of blood and/or internal organs from 22 monkeys and additionally muscle and other tissue samples from another 32 monkeys. PCR analyses revealed a high prevalence of SIV, STLV-1, and SFV in this population, with rates of 82%, 50%, and 86%, respectively. Forty-five percent of the monkeys were coinfected with all three viruses while another 32% were coinfected with SIV in combination with either STLV or SFV. As expected, phylogenetic analyses showed a host-specific pattern for SIV and SFV strains. In contrast, STLV-1 strains appeared to be distributed in genetically distinct and distant clades, which are unique to the Taï forest and include strains previously described from wild chimpanzees in the same area. The high prevalence of all three retroviral infections in P. b. badius represents a source of infection to chimpanzees and possibly to humans, who hunt them.Lentiviruses and deltaretroviruses that infect African nonhuman primates have received considerable attention as they are the precursors of all pathogenic human retroviruses: human immunodeficiency virus types 1 and 2 (HIV-1/HIV-2) and human T-cell lymphotropic virus type 1 (HTLV-1). These human infections are the results of past zoonotic transfers of simian immunodeficiency virus (SIV) and simian T-cell lymphotropic viruses type 1 (STLV-1) from wild monkeys and apes into local human populations, presumably through primate hunting and handling of primate bushmeat (13, 19, 43, 46, 55, 58, 59). Via the same route, zoonotic transmission of simian foamy virus (SFV), a spumaretrovirus whose exact pathogenicity in human hosts is still unknown, has also been shown (64). The increasing contact between humans and wild primates implies that further zoonotic transmission of retroviruses is likely to happen (42, 63). Studying the occurrence and circulation of simian retroviruses such as SIV, STLV-1, and SFV in wild primate populations enables us to better understand retrovirus evolution in primates and also provides tools for monitoring possible future retroviral zoonotic events.Systematic studies of SIV, STLV-1, and SFV in wild primates are relatively rare. Many use bushmeat samples, which can vary in their quality and are prone to cross-contamination from butchering and storage with other carcasses. Confiscated primates are also not representative of the situation in the wild since the animals are caught at a young age when the occurrence of different retroviruses may be extremely low (24). The technical possibilities for the detection of various pathogens in noninvasive samples such as urine and feces have greatly improved and are frequently used; however, in general, the sensitivity of detection methods is higher when blood and tissue samples are used (25, 32, 47). Such samples can be collected if fresh carcasses are found, or they can be collected by anesthetizing live primates for sampling purpose, animal translocation, or medical intervention, such as snare removal. The practical and ethical issues of each of the sampling methods have been discussed elsewhere (12, 14).Red colobus monkeys [Procolobus (Piliocolobus)] are interesting subjects for retroviral infection studies for a number of reasons. First, they are widely distributed (yet in a fragmented manner) from East to West Africa, which suggests that red colobus species and subspecies, or more likely ancestor(s) of these, could have been key hosts in transmitting retroviruses across tropical Africa (4, 54). Second, as they are herbivore primates, the hunting of other primates can be excluded as a route of infection. Finally, these monkeys are frequently hunted by humans and chimpanzees and represent a possibly large reservoir for retroviruses and other pathogens that ought to be investigated further (2, 45).Very little information is available about the prevalence and coinfection of SIV, STLV-1, and SFV in wild red colobus monkeys across Africa. In other colobine monkeys only SIV has been documented: in olive colobus (Procolobus verus) in Côte d''Ivoire and in black and white colobus (Colobus guereza) in Cameroon (7, 8). Based on fecal samples from habituated adult individuals, the prevalence of SIV in West African red colobus monkeys (SIVwrc; local subspecies, Piliocolobus badius badius) has been estimated to a minimum of 26% in the Taï National Park, Côte d''Ivoire, but the authors recognized the low sensitivity of viral RNA detection in fecal samples (34). Another study conducted on the same population revealed that 5 out of 10 blood samples were SIV positive (7). These results highlight that the most reliable prevalence data are based on analyses of blood/tissue samples although such sampling is not always feasible for reasons discussed above. Published prevalence information concerning STLV-1 and SFV in wild red colobus monkeys (STLV-1wrc and SFVwrc) in the same area is restricted to results obtained from analyses of a limited number of blood and necropsy samples collected as a part of studies whose focus was on cross-species transmission of these two viruses to chimpanzees (27, 28). However, these samples indicated a high prevalence of STLV-1wrc and SFVwrc in the red colobus monkey population (56% and 90%, respectively). A recent study from Uganda, East Africa, estimated the prevalence of SIV, STLV-1, and SFV in another red colobus species (Piliocolobus rufomitratus tephrosceles) to be 22.6%, 6.4%, and 97%, respectively (15). The study was performed using blood samples collected from anesthetized wild red colobus monkeys living in their natural habitat, which allowed reliable assessment of the prevalence and genetic diversity of these three retroviruses.The preliminary data from the Taï National Park indicate that there might be great variation in the prevalence of retroviruses across the African continent, even in closely related species of wild primates. Here, we aimed at generating reliable prevalence and coinfection data for SIVwrc, STLV-1wrc, and SFVwrc based on the analysis of blood and tissue samples from wild Western red colobus monkeys. We expected that this would allow for proper comparison of retroviral prevalence in the allied species P. b. badius and P. r. tephrosceles.     

RPA Accumulation during Class Switch Recombination Represents 5′–3′ DNA-End Resection during the S–G2/M Phase of the Cell Cycle

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Highlights? RPA and Rad51 bind asymmetrically to recombining immunoglobulin genes ? Ig gene DNA breaks are resected as B cells enter the S–G2/M cell-cycle stages ? ATM regulates localized DNA-end resection in G1 ? DNA-end resection in S–G2/M is extensive and ATM independent     

Bayes factor between Student t and Gaussian mixed models within an animal breeding context

The implementation of Student t mixed models in animal breeding has been suggested as a useful statistical tool to effectively mute the impact of preferential treatment or other sources of outliers in field data. Nevertheless, these additional sources of variation are undeclared and we do not know whether a Student t mixed model is required or if a standard, and less parameterized, Gaussian mixed model would be sufficient to serve the intended purpose. Within this context, our aim was to develop the Bayes factor between two nested models that only differed in a bounded variable in order to easily compare a Student t and a Gaussian mixed model. It is important to highlight that the Student t density converges to a Gaussian process when degrees of freedom tend to infinity. The twomodels can then be viewed as nested models that differ in terms of degrees of freedom. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling of the complex model (Student t mixed model). The performance of this Bayes factor was tested under simulation and on a real dataset, using the deviation information criterion (DIC) as the standard reference criterion. The two statistical tools showed similar trends along the parameter space, although the Bayes factor appeared to be the more conservative. There was considerable evidence favoring the Student t mixed model for data sets simulated under Student t processes with limited degrees of freedom, and moderate advantages associated with using the Gaussian mixed model when working with datasets simulated with 50 or more degrees of freedom. For the analysis of real data (weight of Pietrain pigs at six months), both the Bayes factor and DIC slightly favored the Student t mixed model, with there being a reduced incidence of outlier individuals in this population.     

Structure of ground-foraging ant assemblages in relation to land-use change in the northwestern Mediterranean region

The abandonment by humans of marginal and less productive zones signifies an important change in land use in North Mediterranean agroecosystems. Human perturbations have led to a highly diversified landscape, with a mosaic made up of patches of land at different stages of succession, from cultivated fields to closed forest. Our aim here is to characterize ant assemblages and their functional groups in response to these land-use changes. This progressive abandonment results in an initial increase in ant richness and abundance, which can reach high levels if the succession proceeds as far as woodland. In terms of the ant functional groups, this land-use change implies: (1) the appearance of Subordinate Camponotini; (2) an increase in Generalized Myrmicinae, Cryptics and Cold-climate specialists in terms of ant species richness, overall abundance and, for Generalized Myrmicinae and Cryptics, an increase in abundance percentage; (3) a decrease in percentage abundance of Opportunists; (4) a progressive decrease in species richness as well as overall and percentage abundance of Hot-climate Specialists throughout the transformation from crops to woodlands; and (5) an initial increase of Dominant Dolichoderinae followed by a decrease in ant species richness, overall abundance and percentage abundance. Using the ant functional group approach for the clearly separate stages of the regeneration process is a promising method for comparing responses of ant communities to human land use.     

High prevalence of vancomycin-resistant enterococci in Swedish sewage

In Europe the use of the growth promoter avoparcin is considered to have selected for vancomycin-resistant enterococci (VRE). Sweden ceased using avoparcin in 1986, and only occasional cases of VRE from hospitals have been reported since 1995. Within the framework of a European study, samples from urban raw sewage, treated sewage, surface water, and hospital sewage in Sweden (n = 118) were screened for VRE. Surprisingly, VRE were isolated from 21 of 35 untreated sewage samples (60%), from 5 of 14 hospital sewage samples (36%), from 6 of 32 treated sewage samples (19%), and from 1 of 37 surface water samples. Thirty-five isolates from 33 samples were further characterized by geno- and phenotyping, MIC determination, and PCR analysis. Most isolates (30 of 35) carried the vanA gene, and the majority (24 of 35) of the isolates were Enterococcus faecium. Most of the VRE were multiresistant. The typing revealed high diversity of the isolates. However, one major cluster with seven identical or similar isolates was found. These isolates came from three different sewage treatment plants and were collected at different occasions during 1 year. All VRE from hospital sewage originated from one of the two hospitals studied. That hospital also had vancomycin consumption that was 10-fold that of the other. We conclude that VRE were commonly found in sewage samples in Sweden. The origin might be both healthy individuals and individuals in hospitals. Possibly, antimicrobial drugs or chemicals released into the sewage system may sustain VRE in the system.     

The formation of collective silk balls in the spider mite Tetranychus urticae Koch

Tetranychus urticae is a phytophagous mite that forms colonies of several thousand individuals. These mites construct a common web to protect the colony. When plants become overcrowded and food resources become scarce, individuals gather at the plant apex to form a ball composed of mites and their silk threads. This ball is a structure facilitating group dispersal by wind or animal transport. Until now, no quantitative study had been done on this collective form of migration. This is the first attempt to understand the mechanisms that underlie the emergence and growth of the ball. We studied this collective behaviour under laboratory conditions on standardized infested plants. Our results show that the collective displacement and the formation of balls result from a recruitment process: by depositing silk threads on their way up to the plant apex, mites favour and amplify the recruitment toward the balls. A critical threshold (quorum response) in the cumulative flow of mites must be reached to observe the emergence of a ball. At the beginning of the balls formation, mites form an aggregate. After 24 hours, the aggregated mites are trapped inside the silk balls by the complex network of silk threads and finally die, except for recently arrived individuals. The balls are mainly composed of immature stages. Our study reconstructs the key events that lead to the formation of silk balls. They suggest that the interplay between mites' density, plant morphology and plant density lead to different modes of dispersions (individual or collective) and under what conditions populations might adopt a collective strategy rather than one that is individually oriented. Moreover, our results lead to discuss two aspects of the cooperation and altruism: the importance of Allee effects during colonization of new plants and the importance of the size of a founding group.     

High throughput screening with chlorophyll fluorescence imaging and its use in crop improvement

Marker assisted plant breeding is a powerful technique for targeted crop improvement in horticulture and agriculture. It depends upon the correlation of desirable phenotypic characteristics with specific genetic markers. This can be determined by statistical models that relate the variation in the value of genetic markers to variation in phenotypic traits. It therefore depends upon the convergence of three technologies; the creation of genetically characterised (and thus marked) populations, high throughput screening procedures, and statistical procedures. While a large number of high throughput screening technologies are available, real-time screening techniques are usually based on some kind of imaging technologies, such as chlorophyll fluorescence imaging, that offers physiological data that are eminently suitable as a quantitative trait for genetic mapping.     

Interplay between Allee effects and collective movement in metapopulations

Population growth can be positively or negatively dependent on density. Therefore, the distribution pattern of individuals in a patchy environment can greatly affect the growth of each subpopulation and thereby of the metapopulation. When population growth presents positive density‐dependence (Allee effect), the distribution pattern becomes crucial, as small populations have an increased extinction risk. The way in which individuals move between patches largely determines the distribution pattern and thereby the population dynamics. Collective movement, in particular, should be expected to increase the potential number of colonisers and therefore the probability of colonising success. Here, we use mathematical modelling (differential equations and stochastic simulations) to study how collective movement can influence metapopulation dynamics when Allee effects are at stake. The models are inspired by the two‐spotted spider mite, a phytophagous pest of recognised agricultural importance. This sub‐social mite displays trail laying/following behaviour that can provoke collective movement. Moreover, experimental evidence suggests that it is subject to Allee effects. In the first part of this study we present a single‐species population growth model incorporating Allee effects, and study its properties. In the second part, this growth model is integrated into a larger simulation model consisting of a set of interconnected patches, in which the individuals move from one patch to the other either independently or collectively. Our results show that collective movement is more advantageous than independent dispersal only when Allee effects are present and strong enough. Furthermore they provide a theoretical framework that allows the quantification of the interplay between Allee effects and collective movement.     

Testing for collective choices in the two-spotted spider mite

Silk is a vector for collective behaviour in many spinning arthropods, including social spiders, social caterpillars, and some spider mites. In this study, the potential for silk-mediated collective choices is evaluated for the two-spotted spider mite Tetranychus urticae. This subsocial mite lives in large colonies on plants, sheltered under a collectively spun silk web. The silk has an attractive and arresting effect. We test whether the silk trails left by the spider mites can give rise to the collective choice of a path. The experiment consists in offering two identical paths to a group of migrating mites. Our results show that the presence of a silk trail influences the mites, but not sufficiently to systematically provoke a collective choice. In order to determine the trail following potential of T. urticae, we parameterise a theoretical trail following model to fit our experiments and those found in the literature. Our prediction is that even after a large number of mites have passed (200), a systematic collective choice of path should not be expected under the tested conditions. Our results, combined with what is known from the literature, allow us to propose a general scenario for the dispersal behaviour of T. urticae.