Plasticity demonstrated in the proteome of a parasitic nematode within the intestine of different host strains

The soluble global proteome of adult nematode Heligmosomoides polygyrus (H. p.) bakeri, a hookworm laboratory model was compared for the first time in the intestines of a slow-responder mouse host strain (C57/BL10) that is known to support a primary parasite infection for many months, and rapid-responder mouse host (SWR) that is known to eliminate the nematode infection by week 6 postinfection. At week 4 postinfection, major adult nematode proteins selectively produced following establishment of infection in C57/BL10 hosts include several globin forms, calreticulin and a phosphatidylethanolamine-binding protein. The increased synthesis of forms of myosin, actin and troponin in the nematode living in the rapid-responder SWR host may relate to the attempted reorganisation or repair of the cytoskeleton and/or muscle layer in the host immune initiated, increased mucus production and smooth muscle activity within intestinal environment. Initial evidence suggests weakly antigenic forms of globins dominant in the cytosol of H. p. bakeri adults in the intestinal environment compared to their low production in a related free-living nematode. The demonstration of considerable plasticity within a parasitic nematode proteome provides a molecular basis for the previously observed phenotypic plasticity within different host environments. Proteome plasticity has relevance to the efficiency of future vaccine and drug therapy, and the continued failure of defined antigen vaccines in mammalian populations.     

Forest progression modes in littoral Congo, Central Atlantic Africa

Aim To understand the persistence of a forest–savanna mosaic in places where rainfall data suggest that forest take‐over should take place. To study the various modes of forest encroachment, and the role of human activities to hamper it. Location Data were collected on several forest–savanna ecotones in the coastal region of the Republic of Congo. The sites were chosen to illustrate the differing principal modes of forest expansion, corresponding to different levels of anthropic pressure. Methods The study sites were situated on five transects perpendicular to the ecotone (total sampled area: 1.7 ha) and 10 forest clumps in savanna (with diameters from 3 to 20 m). Along the transects botanical identification, diameter measurement and cartography were performed, while leaf area index was measured at a high resolution (every metre) along two of them. Collected data were analysed using a continuous quantification approach, which is much more useful than classical quadrat analysis. Time calibration of progression rates was performed using a simple model of the growth of the characteristic pioneer species, Aucoumea klaineana. Results The two main different modes are reflected in different successional patterns. The edge diffusion is slow (its rate is evaluated to c. 1 m year^?1) and is characterized by a progressive increase in large‐diameter tree density and shade‐tolerant tree density away from the ecotone. Conversely, savanna to forest phase transition by coalescence of clumps exhibits high tree density remnants distributed in established forest. The composition of these remnants is compatible with that of the forest clumps in savannas. Main conclusions Three functional groups of pioneer trees are distinguished: some occupy the edge (edge pioneer), others establish clumps of forest in savanna (clump pioneers) and the longer‐living A. klaineana ensures the transition to ‘mature’ forest. The two different observed patterns (linear edge progression and clump coalescence) can be understood with the use of a model of forest–savanna dynamics, ‘FORSAT’. The two control parameters are the annual rainfall and the frequency of man‐made fires in each savanna. In particular, an increase in the fire frequency can lead to a shift from the coalescence regime to the edge progression one.     

Game On,Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.     

Climatic and cultural changes in the west Congo Basin forests over the past 5000 years

Central Africa includes the world''s second largest rainforest block. The ecology of the region remains poorly understood, as does its vegetation and archaeological history. However, over the past 20 years, multidisciplinary scientific programmes have enhanced knowledge of old human presence and palaeoenvironments in the forestry block of Central Africa. This first regional synthesis documents significant cultural changes over the past five millennia and describes how they are linked to climate. It is now well documented that climatic conditions in the African tropics underwent significant changes throughout this period and here we demonstrate that corresponding shifts in human demography have had a strong influence on the forests. The most influential event was the decline of the strong African monsoon in the Late Holocene, resulting in serious disturbance of the forest block around 3500 BP. During the same period, populations from the north settled in the forest zone; they mastered new technologies such as pottery and fabrication of polished stone tools, and seem to have practised agriculture. The opening up of forests from 2500 BP favoured the arrival of metallurgist populations that impacted the forest. During this long period (2500–1400 BP), a remarkable increase of archaeological sites is an indication of a demographic explosion of metallurgist populations. Paradoxically, we have found evidence of pearl millet (Pennisetum glaucum) cultivation in the forest around 2200 BP, implying a more arid context. While Early Iron Age sites (prior to 1400 BP) and recent pre-colonial sites (two to eight centuries BP) are abundant, the period between 1600 and 1000 BP is characterized by a sharp decrease in human settlements, with a population crash between 1300 and 1000 BP over a large part of Central Africa. It is only in the eleventh century that new populations of metallurgists settled into the forest block. In this paper, we analyse the spatial and temporal distribution of 328 archaeological sites that have been reliably radiocarbon dated. The results allow us to piece together changes in the relationships between human populations and the environments in which they lived. On this basis, we discuss interactions between humans, climate and vegetation during the past five millennia and the implications of the absence of people from the landscape over three centuries. We go on to discuss modern vegetation patterns and African forest conservation in the light of these events.     

A point-process model for variance-occupancy-abundance relationships

The relationship between species abundance, the variance of the number of individuals, and species occupancy is a fundamental ecological characteristic of a community. Moreover, this relationship varies across scales, and any model for the variance-occupancy-abundance (VOA) relationship has to address its scale dependency in a consistent way. In this study, point-process theory was used to define a multiscale model that jointly predicts the VOA relationship across scales in a consistent way. This provides a tool to jointly analyze data sets collected at different scales and to give insights into the biological processes underlying the VOA relationship. This model can also account for different types of individual spatial pattern (clustered, random, or regular). Three stand-mapping data sets of tree species in tropical rain forests were used to assess the relevance of this model. When compared with four existing models, the model based on point-process theory provided the best fit to the data and was the most often ranked as the model with the best predictive performance.     

Abrupt shifts in African savanna tree cover along a climatic gradient

Aim To describe patterns of tree cover in savannas over a climatic gradient and a range of spatial scales and test if there are identifiable climate‐related mean structures, if tree cover always increases with water availability and if there is a continuous trend or a stepwise trend in tree cover. Location Central Tropical Africa. Methods We compared a new analysis of satellite tree cover data with botanical, phytogeographical and environmental data. Results Along the climatic transect, six vegetation structures were distinguished according to their average tree cover, which can co‐occur as mosaics. The resulting abrupt shifts in tree cover were not correlated to any shifts in either environmental variables or in tree species distributions. Main conclusions A strong contrast appears between fine‐scale variability in tree cover and coarse‐scale structural states that are stable over several degrees of latitude. While climate parameters and species pools display a continuous evolution along the climatic gradient, these stable structural states have discontinuous transitions, resulting in regions containing mosaics of alternative stable states. Soils appear to have little effect inside the climatic stable state domains but a strong action on the location of the transitions. This indicates that savannas are patch dynamics systems, prone to feedbacks stabilizing their coarse‐scale structure over wide ranges of environmental conditions.     

Neotropical C3/C4 grass distributions – present,past and future

Changes in C₄ grass distribution and abundance are frequently observed in Quaternary, Holocene and future environmental‐change scenarios. However, the factors driving these dynamics are not fully understood, and conflicting theories have been reported. In this paper, we present a very large dataset of modern altitudinal distribution profiles of C₃ and C₄ grasses covering the entire Neotropical Andes, which was compared with actual climate data. The results of multivariate analysis demonstrate that, in the Neotropical Andes, mean annual temperature is the main factor governing the modern altitudinal distribution of C₃ and C₄ grass species. The C₃ and C₄ grass distributions were compared with simulations based on the Lund‐Potsdam‐Jena dynamic global vegetation model (LPJ‐DGVM), which allowed the present grass distribution to be estimated. Finally, the DGVM was employed to simulate past and future scenarios, using the IPCC's climate projections for 2100 and PMIP2 models for the Holocene Optimum (HO, 6000 years bp ) and the Last Glacial Maximum (LGM, 21 000 years bp ). The results were found to be significantly different from those obtained using a simple photosynthetic model. According to LPJ forced with the PMIP2 models for the LGM, during the LGM, the C₄ grasses would not have reached higher altitudes than found in the present day.     

High-frequency organization and synchrony of activity in the purkinje cell layer of the cerebellum

The cerebellum controls complex, coordinated, and rapid movements, a function requiring precise timing abilities. However, the network mechanisms that underlie the temporal organization of activity in the cerebellum are largely unexplored, because in vivo recordings have usually targeted single units. Here, we use tetrode and multisite recordings to demonstrate that Purkinje cell activity is synchronized by a high-frequency (approximately 200 Hz) population oscillation. We combine pharmacological experiments and modeling to show how the recurrent inhibitory connections between Purkinje cells are sufficient to generate these oscillations. A key feature of these oscillations is a fixed population frequency that is independent of the firing rates of the individual cells. Convergence in the deep cerebellar nuclei of Purkinje cell activity, synchronized by these oscillations, likely organizes temporally the cerebellar output.     

Macrophages in the Small Intestinal Muscularis Externa of Embryos, Newborn and Adult Germ-Free Mice

Previously, we demonstrated the presence of a constant and regularly distributed macrophage population of ramified cells in the intestinal muscle layers of smaller rodents. The function of these resident macrophages under normal conditions remains unknown. Histochemistry, immunohistochemistry and electron microscopy were applied to the muscularis externa of 15- and 17-day-old embryos, 2-day-old mice, adult germ-free and conventional mice. Since lipopolysaccharides (LPS) activates macrophages and inflammation affects gut motility, LPS-treated mice were also included in the study. Two macrophage antibodies, F4/80 and 2F8 were used to demonstrate the presence of macrophages in the muscle layers. The localization was confirmed by electron microscopy. In contrast to conventional adult mice, the muscle layers in embryos, newborn and germ-free adult mice were devoid of class II MHC antigen reactive cells. The acid phosphatase reaction and antibodies directed towards a lysosomal protein (Lamp-2) were used in order to verify other activation markers. None of these showed specific staining of the muscularis macrophages. Only LPS-treated adult mice showed iNOS-positive cells in whole mounts. We conclude that the characteristic organization and distribution of muscularis macrophages in adult mice are also present in embryos, newborn and germ-free mice and thus develop independently of foreign antigens. Further, these macrophages are truly resident and appear to have differential responses to exogene stimuli.