Host-parasite local adaptation after experimental coevolution of Caenorhabditis elegans and its microparasite Bacillus thuringiensis

Coevolving hosts and parasites can adapt to their local antagonist. In studies on natural populations, the observation of local adaptation patterns is thus often taken as indirect evidence for coevolution. Based on this approach, coevolution was previously inferred from an overall pattern of either parasite or host local adaptation. Many studies, however, failed to detect such a pattern. One explanation is that the studied system was not subject to coevolution. Alternatively, coevolution occurred, but remained undetected because it took different routes in different populations. In some populations, it is the host that is locally adapted, whereas in others it is the parasite, leading to the absence of an overall local adaptation pattern. Here, we test for overall as well as population-specific patterns of local adaptation using experimentally coevolved populations of the nematode Caenorhabditis elegans and its bacterial microparasite Bacillus thuringiensis. Furthermore, we assessed the importance of random interaction effects using control populations that evolved in the absence of the respective antagonist. Our results demonstrate that experimental coevolution produces distinct local adaptation patterns in different replicate populations, including host, parasite or absence of local adaptation. Our study thus provides experimental evidence of the predictions of the geographical mosaic theory of coevolution, i.e. that the interaction between parasite and host varies across populations.     

Decoding successive computational stages of saliency processing

An important requirement for vision is to identify interesting and relevant regions of the environment for further processing. Some models assume that salient locations from a visual scene are encoded in a dedicated spatial saliency map [1, 2]. Then, a winner-take-all (WTA) mechanism [1, 2] is often believed to threshold the graded saliency representation and identify the most salient position in the visual field. Here we aimed to assess whether neural representations of graded saliency and the subsequent WTA mechanism can be dissociated. We presented images of natural scenes while subjects were in a scanner performing a demanding fixation task, and thus their attention was directed away. Signals in early visual cortex and posterior intraparietal sulcus (IPS) correlated with graded saliency as defined by a computational saliency model. Multivariate pattern classification [3, 4] revealed that the most salient position in the visual field was encoded in anterior IPS and frontal eye fields (FEF), thus reflecting a potential WTA stage. Our results thus confirm that graded saliency and WTA-thresholded saliency are encoded in distinct neural structures. This could provide the neural representation required for rapid and automatic orientation toward salient events in natural environments.     

Expansion of mass-flowering crops leads to transient pollinator dilution and reduced wild plant pollination

Agricultural land use results in direct biodiversity decline through loss of natural habitat, but may also cause indirect cross-habitat effects on conservation areas. We conducted three landscape-scale field studies on 67 sites to test the hypothesis that mass flowering of oilseed rape (Brassica napus) results in a transient dilution of bees in crop fields, and in increased competition between crop plants and grassland plants for pollinators. Abundances of bumble-bees, which are the main pollinators of the grassland plant Primula veris, but also pollinate oilseed rape (OSR), decreased with increasing amount of OSR. This landscape-scale dilution affected bumble-bee abundances strongly in OSR fields and marginally in grasslands, where bumble-bee abundances were generally low at the time of Primula flowering. Seed set of Primula veris, which flowers during OSR bloom, was reduced by 20 per cent when the amount of OSR within 1 km radius increased from 0 to 15 per cent. Hence, the current expansion of bee-attractive biofuel crops results in transient dilution of crop pollinators, which means an increased competition for pollinators between crops and wild plants. In conclusion, mass-flowering crops potentially threaten fitness of concurrently flowering wild plants in conservation areas, despite the fact that, in the long run, mass-flowering crops can enhance abundances of generalist pollinators and their pollination service.     

Interplay between RAGE, CD44, and focal adhesion molecules in epithelial-mesenchymal transition of alveolar epithelial cells

Fibrosis of the lung is characterized by the accumulation of myofibroblasts, a key mediator in the fibrogenic reaction. Cumulative evidence indicates that epithelial-mesenchymal transition (EMT), a process whereby epithelial cells become mesenchyme-like, is an important contributing source for the myofibroblast population. Underlying this phenotypical change is a dramatic alteration in cellular structure. The receptor for advanced glycation end-products (RAGE) has been suggested to maintain lung homeostasis by mediating cell adhesion, while the family of ezrin/radixin/moesin (ERM) proteins, on the other hand, serve as an important cross-linker between the plasma membrane and cytoskeleton. In the present investigation, we tested the hypothesis that RAGE and ERM interact and play a key role in regulating EMT-associated structural changes in alveolar epithelial cells. Exposure of A549 cells to inflammatory cytokines resulted in phosphorylation and redistribution of ERM to the cell periphery and localization with EMT-related actin stress fibers. Simultaneously, blockade of Rho kinase (ROCK) signaling attenuated these cytokine-induced structural changes. Additionally, RAGE expression was diminished after cytokine stimulation, with release of its soluble isoform via a matrix metalloproteinase (MMP)-9-dependent mechanism. Immunofluorescence microscopy and coimmunoprecipitation revealed association between ERM and RAGE under basal conditions, which was disrupted when challenged with inflammatory cytokines, as ERM in its activated state complexed with membrane-linked CD44. Dual-fluorescence immunohistochemistry of patient idiopathic pulmonary fibrosis (IPF) tissues highlighted marked diminution of RAGE in fibrotic samples, together with enhanced levels of CD44 and double-positive cells for CD44 and phospho (p)ERM. These data suggest that dysregulation of the ERM-RAGE complex might be an important step in rearrangement of the actin cytoskeleton during proinflammatory cytokine-induced EMT of human alveolar epithelial cells.     

Identification of the dynein light chains required for human papillomavirus infection

Human papillomaviruses (HPVs) are a family of small non-enveloped DNA viruses. Some genital HPV types, including HPV type 16 (HPV16), are the causative agent for the development of cancer at the site of infection. HPVs encode two capsid proteins, L1 and L2. After endocytic cell entry and egress from endosomes, L2 accompanies the viral DNA to the nucleus where replication is initiated. For cytoplasmic transport, L2 interacts with the microtubule network via the motor protein complex dynein. We have performed yeast two-hybrid screening and identified the dynein light chain DYNLT1 (previously called Tctex1) as interaction partner of HPV16 L2. Using co-immunoprecipitation and immunofluorescence colocalization studies we confirmed the L2-DYNLT1 interaction in mammalian cells. Further studies revealed that DYNLT3, the second member of the Tctex-light chain family, also interacts with L2 in vitro and in vivo, whereas other constituents of the dynein complex were not found to associate with L2. Depletion of DYNLT1 and DYNLT3 by specific siRNAs or cytosolic delivery of light chain-specific antibodies inhibited infection of HPV16. Therefore, this work identified two host cell proteins involved in HPV16 infection that are most likely required for transport purposes towards the nucleus.     

Simulating the mammalian blastocyst--molecular and mechanical interactions pattern the embryo

Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment.     

First set of microsatellite markers for genetic characterization of the Eurasian beaver (Castor fiber) based on tissue and hair samples

Noninvasive genetic techniques have become indispensible tools in wildlife conservation and management. Here, we report the development of the first set of microsatellite markers for the Eurasian beaver (Castor fiber). All 15 loci show considerable variation within the sampled region in southwestern Germany, with number of alleles ranging from two to six alleles per locus. A comparison between tissue and hair samples revealed that amplification success was only slightly lower for hair samples, making their use in noninvasive monitoring feasible. Despite some evidence for false alleles and allelic dropout, 77% of all loci were genotyped successfully among all hair samples and loci tested. The developed markers will be used for subspecies differentiation and reconstruction of dispersal routes, following reintroductions in Central Europe.     

Rseg--an R package to optimize segmentation of SNP array data

The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples. RESULTS: We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts. AVAILABILITY: The R package, Rseg, is available at: http://www.cs.au.dk/~plamy/Rseg/ and runs on Linux and MS-Windows.     

Mixed effects of landscape complexity and farming practice on weed seed removal

Agricultural intensification negatively affects farmland biodiversity, and thereby, ecosystem services such as predation of weed seeds. Landscape complexity (large and diverse areas of semi-natural habitats) and organic farming (without pesticides and mineral fertilizers) can counteract this negative trend, but little is known about their relative importance. We experimentally studied seed removal of four economically relevant weed species by excluding (i) vertebrates, (ii) vertebrates plus large invertebrates and (iii) neither vertebrates nor invertebrates (control) at the field edge and in the interior of 22 organically or conventionally managed winter wheat fields, located across a gradient of landscape complexity (41–94% arable land). Arable land (%) was used as a simple predictor of landscape complexity, as it is closely related to landscape parameters such as habitat type diversity. Seed predation and removal were mainly influenced by large invertebrates, seed species identity, with Cirsium arvense being more affected than Poa trivialis, Apera spica-venti and Galium aparine and landscape complexity in interaction with farming practice, as it increased in conventional fields, but decreased in organic fields as landscape complexity decreased. Seed predation and removal did not consistently correspond to seed predator densities, as small mammal abundances decreased in conventional fields, but increased in organic fields as landscape complexity decreased and carabid activity densities were higher in organic compared to conventional fields. Slug activity density showed same response to landscape complexity and farming practice like seed removal and appeared to additionally influence the movement of seeds. In conclusion, our assessment of interacting local and landscape effect adds to the current knowledge of seed predation and removal. Farming practice and landscape complexity affect seed predator species differentially, thereby resulting in complex pattern of seed predation and removal. The service of weed seed predation is provided by small mammals and invertebrates and the disservice of seed dispersal and movement is provided by slugs.