Adopting a spatially explicit perspective to study the mysterious fairy circles of Namibia

The mysterious ‘fairy circles’ are vegetation‐free discs that cover vast areas along the pro‐Namib Desert. Despite 30 yr of research their origin remains unknown. Here we adopt a novel approach that focuses on analysis of the spatial patterns of fairy circles obtained from representative 25‐ha aerial images of north‐west Namibia. We use spatial point pattern analysis to quantify different features of their spatial structures and then critically inspect existing hypotheses with respect to their ability to generate the observed circle patterns. Our working hypothesis is that fairy circles are a self‐organized vegetation pattern. Finally, we test if an existing partial‐differential‐equation model, that was designed to describe vegetation pattern formation, is able to reproduce the characteristic features of the observed fairy circle patterns. The model is based on key‐processes in arid areas such as plant competition for water and local resource‐biomass feedbacks. The fairy circles showed at all three study areas the same regular spatial distribution patterns, characterized by Voronoi cells with mostly six corners, negative correlations in their size up to a distance of 13 m, and remarkable homogeneity over large spatial scales. These results cast doubts on abiotic gas‐leakage along geological lines or social insects as causal agents of their origin. However, our mathematical model was able to generate spatial patterns that agreed quantitatively in all of these features with the observed patterns. This supports the hypothesis that fairy circles are self‐organized vegetation patterns that emerge from positive biomass‐water feedbacks involving water transport by extended root systems and soil‐water diffusion. Future research should search for mechanisms that explain how the different hypotheses can generate the patterns observed here and test the ability of self‐organization to match the birth‐ and death dynamics of fairy circles and their regional patterns in the density and size with respect to environmental gradients.     

Experiments Testing the Causes of Namibian Fairy Circles

The grasslands on the sandy soils of the eastern edge of the Namib Desert of Namibia are strikingly punctuated by millions of mostly regularly-spaced circular bare spots 2 to 10 m or more in diameter, generally with a margin of taller grasses. The causes of these so called fairy circles are unknown, but several hypotheses have been advanced. In October 2009, we set up experiments that specifically tested four hypothesized causes, and monitored these 5 times between 2009 and 2015. Grass exclusion in circles due to seepage of subterranean vapors or gases was tested by burying an impermeable barrier beneath fairy circles, but seedling density and growth did not differ from barrier-less controls. Plant germination and growth inhibition by allelochemicals or nutrient deficiencies in fairy circle soils were tested by transferring fairy circle soil to artificially cleared circles in the grassy matrix, and matrix soil to fairy circles (along with circle to circle and matrix to matrix controls). None of the transfers changed the seedling density and growth from the control reference conditions. Limitation of plant growth due to micronutrient depletion within fairy circles was tested by supplementing circles with a micronutrient mixture, but did not result in differences in plant seedling density and growth. Short-range vegetation competitive feedbacks were tested by creating artificially-cleared circles of 2 or 4 m diameter located 2 or 6 m from a natural fairy circle. The natural circles remained bare and the artificial circles revegetated. These four experiments provided evidence that fairy circles were not caused by subterranean vapors, that fairy circle soil per se did not inhibit plant growth, and that the circles were not caused by micronutrient deficiency. There was also no evidence that vegetative feedbacks affected fairy circles on a 2 to 10 m scale. Landscape-scale vegetative self-organization is discussed as a more likely cause of fairy circles.     

Edaphic properties enable facilitative and competitive interactions resulting in fairy circle formation

Millions of generally regularly spaced, roughly circular barren patches called fairy circles occur in a narrow band ca 100 km inland of the south‐west African coast. These generally have conspicuously taller peripheral grasses in a shorter grass matrix. The origins of these fairy circles are controversial, but one possibility is that they are self‐organizing emergent vegetation patterns that are the consequence of interplay between positive (facilitative) and negative (competitive) interactions between grasses. We hypothesized that the coarse textured sand on which fairy circles occur creates a hydraulically and nutritionally connected landscape, in which neighbouring fairy circles competitively influence each other over several metres, while providing opportunity for focusing of resources around the peripheral grasses. To test our hypotheses we conducted three main groups of analyses: 1) we measured grass biomass to assess facilitative and competitive effects of the component grasses; 2) across a region with fairy circles we measured the size and density of fairy circles and correlated that with water infiltration rates into soil; 3) we measured the capacity of soil to conduct water pulses and ¹⁵N tracers. We found evidence of facilitative interactions in the periphery of the fairy circles and competitive suppression of the matrix grass proximal to the periphery. Across the region, fairy circle size was positively correlated with soil infiltration rates and negatively with precipitation. This suggests that fairy circles emerge in soils with high capacity for water flux that enables landscape hydraulic connectivity. Water‐ and ¹⁵N‐pulse experiments showed that edaphic resources were highly mobile, moving up to 7.5 m over a period of 1–3 weeks. We concluded that the evidence is consistent with an emergent vegetation pattern explanation for the origins of fairy circles and that the circles are more closely associated with a highly connective edaphic environment, rather than with particular biota.     

Are Namibian “Fairy Circles” the Consequence of Self-Organizing Spatial Vegetation Patterning?

Causes of over-dispersed barren “fairy circles” that are often surrounded by ca. 0.5 m tall peripheral grasses in a matrix of shorter (ca. 0.2 m tall) grasses in Namibian grasslands remain mysterious. It was hypothesized that the fairy circles are the consequence of self-organizing spatial vegetation patterning arising from resource competition and facilitation. We examined the edaphic properties of fairy circles and variation in fairy circle size, density and landscape occupancy (% land surface) with edaphic properties and water availability at a local scale (<50 km) and with climate and vegetation characteristics at a regional scale. Soil moisture in the barren fairy circles declines from the center towards the periphery and is inversely correlated with soil organic carbon, possibly indicating that the peripheral grass roots access soil moisture that persists into the dry season within fairy circles. Fairy circle landscape occupancy is negatively correlated with precipitation and soil [N], consistent with fairy circles being the product of resource-competition. Regional fairy circle presence/absence is highly predictable using an empirical model that includes narrow ranges of vegetation biomass, precipitation and temperature seasonality as predictor variables, indicating that fairy circles are likely a climate-dependent emergent phenomenon. This dependence of fairy circle occurrence on climate explains why fairy circles in some locations may appear and disappear over time. Fairy circles are only over-dispersed at high landscape occupancies, indicating that inter-circle competition may determine their spacing. We conclude that fairy circles are likely to be an emergent arid-grassland phenomenon that forms as a consequence of peripheral grass resource-competition and that the consequent barren circle may provide a resource-reservoir essential for the survival of the larger peripheral grasses and provides a habitat for fossicking fauna.     

Niche-Partitioning of Edaphic Microbial Communities in the Namib Desert Gravel Plain Fairy Circles

Endemic to the Namib Desert, Fairy Circles (FCs) are vegetation-free circular patterns surrounded and delineated by grass species. Since first reported the 1970''s, many theories have been proposed to explain their appearance, but none provide a fully satisfactory explanation of their origin(s) and/or causative agent(s). In this study, we have evaluated an early hypothesis stating that edaphic microorganisms could be involved in their formation and/or maintenance. Surface soils (0–5cm) from three different zones (FC center, FC margin and external, grass-covered soils) of five independent FCs were collected in April 2013 in the Namib Desert gravel plains. T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil and that each FC was also characterized by significantly different communities. Intra-FC communities (margin and centre) presented higher variability than the controls. Together, these results provide clear evidence that edaphic microorganisms are involved in the Namib Desert FC phenomenon. However, we are, as yet, unable to confirm whether bacteria and/or fungi communities are responsible for the appearance and development of FCs or are a general consequence of the presence of the grass-free circles.     

Ants and the enigmatic Namibian fairy circles – cause and effect?

1. Parts of the Namibian landscape show extensive surface perturbation in the form of long‐lived, yet dynamic ‘fairy circles'. While exerting profound ecological effects on 7.3% of the land surface, the origin and nature of these large bare discs embedded in an arid grassland matrix remains unresolved. 2. We found no evidence to support the current hypothesis of a termite origin for fairy circles but instead observed a strong spatial association between fairy circles and large nests of the ant Black pugnacious ant Anoplolepis steingroeveri Forel, with much higher ant abundances on the circles compared with the matrix. 3. Aggression trials showed that different colonies of A. steingroeveri were located on different circles, and that the species was polydomous. 4. Fairy circles and Pogonomyrmex ant nests both have a bare disc surrounding the nest, are overdispersed (evenly spaced), and are associated with elevated soil moisture. Fairy circle soils exhibited a five‐fold increase in soil moisture when compared with the matrix. 5. Senescent Stipagrostis obtusa (Delile) Nees seedlings were only observed on the circles and not in the matrix, and were found to have a reduction in both root length and number of roots. 6. Anoplolepis steingroeveri excavated the root system of both S. obtusa seedlings on the disc and Stipagrostis ciliata (Desf.) de Winter grasses on the perimeter of the circles, where they tended honeydew‐secreting Meenoplidae bugs that fed on grass roots and culms. The bugs occurred almost exclusively on grasses associated with the circles. This ant–bug interaction is a possible mechanism for the observed reduction in root length and number of senescent grass seedlings on the circles.     

Micromechanics of fibroblast contraction of a collagen-GAG matrix

The contractile force developed by fibroblasts has been studied by measuring the macroscopic contraction of porous collagen-GAG matrices over time. We have identified the microscopic deformations developed by individual fibroblasts which lead to the observed macroscopic matrix contraction. Observation of live cells attached to the matrix revealed that matrix deformation occurred as a result of cell elongation. The time dependence of the increase in average fibroblast aspect ratio over time corresponded with macroscopic matrix contraction, further linking cell elongation and matrix contraction. The time dependence of average fibroblast aspect ratio and macroscopic matrix contraction was found to be the result of the stochastic nature of cell elongation initiation and of the time required for cells to reach a final morphology (2-4 h). The proposed micromechanics associated with observed buckling or bending of individual struts of the matrix by cells may, in part, explain the observation of a force plateau during macroscopic contraction. These findings indicate that the macroscopic matrix contraction measured immediately following cell attachment is related to the extracellular force necessary to support cell elongation, and that macroscopic time dependence is not directly related to microscopic deformation events.     

Social dominance and feeding patterns of spotted hyaenas

In some parts of East Africa, spotted hyaenas (Crocuta crocuta) live in large groups and at high population densities, and scramble competition among clan members during feeding at large carcasses is reported. By contrast, spotted hyaenas in the Namib Desert of southwestern Africa live in small groups and at low densities. When assembled at carcasses, Namib Desert spotted hyaenas show linear dominance hierarchies. Adult females outrank adult males and usually feed one at a time or with their dependent offspring. Feeding rates at small carcasses in the Namib Desert are approximately equal to those reported in East Africa, but at large carcasses Namib Desert spotted hyaenas show linear dominance hierarchies. Adult females outrank adult males and usually feed one at a time or with their dependent offspring. Feeding rates at small carcasses in the Namib Desert are approximately equal to those reported in East Africa, but at large carcasses Namib Desert spotted hyaenas feed significantly more slowly. Thus lower-ranking individuals eventually gain access to large carcasses but are excluded from smaller ones. We relate these patterns of food consumption to possible evolutionary pathways to social hunting by spotted hyaenas.     

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus

Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. Sialic acids present on the epithelial surface have long been considered to be determinants of influenza virus tropism. However, mucus which is also rich in sialic acids may serve as the first barrier of selection. It was investigated how influenza virus interacts with the mucus to infect epithelial cells. Two techniques were applied to track SIV H1N1 in porcine mucus. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. Furthermore, the effects of neuraminidase on SIV getting through or binding to the mucus were studied by using zanamivir, a neuraminidase inhibitor (NAI), and Arthrobacter ureafaciens neuraminidase. The distribution of the diffusion coefficient shows that 70% of SIV particles were entrapped, while the rest diffused freely in the mucus. Additionally, SIV penetrated the porcine mucus with time, reaching a depth of 65 µm at 30 min post virus addition, 2 fold of that at 2 min. Both the microscopic diffusion and macroscopic penetration were largely diminished by NAI, while were clearly increased by the effect of exogenous neuraminidase. Moreover, the exogenous neuraminidase sufficiently prevented the binding of SIV to mucus which was reversely enhanced by effect of NAI. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract.     

Definitions of state variables and state space for brain–computer interface

The hypothesis is proposed that the central dynamics of the action–perception cycle has five steps: emergence from an existing macroscopic brain state of a pattern that predicts a future goal state; selection of a mesoscopic frame for action control; execution of a limb trajectory by microscopic spike activity; modification of microscopic cortical spike activity by sensory inputs; construction of mesoscopic perceptual patterns; and integration of a new macroscopic brain state. The basis is the circular causality between microscopic entities (neurons) and the mesoscopic and macroscopic entities (populations) self-organized by axosynaptic interactions. Self-organization of neural activity is bidirectional in all cortices. Upwardly the organization of mesoscopic percepts from microscopic spike input predominates in primary sensory areas. Downwardly the organization of spike outputs that direct specific limb movements is by mesoscopic fields constituting plans to achieve predicted goals. The mesoscopic fields in sensory and motor cortices emerge as frames within macroscopic activity. Part 1 describes the action–perception cycle and its derivative reflex arc qualitatively. Part 2 describes the perceptual limb of the arc from microscopic MSA to mesoscopic wave packets, and from these to macroscopic EEG and global ECoG fields that express experience-dependent knowledge in successive states. These macroscopic states are conceived to embed and control mesoscopic frames in premotor and motor cortices that are observed in local ECoG and LFP of frontoparietal areas. The fields sampled by ECoG and LFP are conceived as local patterns of neural activity in which trajectories of multiple spike activities (MSA) emerge that control limb movements. Mesoscopic frames are located by use of the analytic signal from the Hilbert transform after band pass filtering. The state variables in frames are measured to construct feature vectors by which to describe and classify frame patterns. Evidence is cited to justify use of linear analysis. The aim of the review is to enable researchers to conceive and identify goal-oriented states in brain activity for use as commands, in order to relegate the details of execution to adaptive control devices outside the brain. http://sulcus.berkeley.edu     

Harderian gland ultrastructure of the black sea bottlenose dolphin (Tursiops truncatus ponticus)

Examination of the Harderian gland structure of the Black Sea bottlenose dolphin, Tursiops truncatus ponticus, at macroscopic, microscopic, and electron microscopic levels shows significant sexual dimorphism. The epithelial cells of male and female glands are different cell types, capable of producing chemically different products. Secretory cells in both sexes contain secretion granules that produce a secretion consisting mainly of proteins and carbohydrates, but thought to be sex-specific in composition. The female glands also contain lipid secretion granules. It is suggested that in the bottlenose dolphin the Harderian gland functions to produce sexually distinct pheromones and may have other physiological activities, e.g., participating in local immunological or endocrine-related reactions. © 1994 Wiley-Liss, Inc.     

Spiral vegetation patterns in high-altitude wetlands

When plant communities suffer the stress of limited resources, for instance adverse environmental conditions such as extreme aridity, the spatial homogeneity of the biomass is lost and self-organized patterns may arise. Here, we report the observation of spiral-shaped patterns in the biomass of grass (genus deyeuxia), under highland arid conditions in the north of Chile. The spiral arms are a few meters long and a few centimeters wide. These dynamic structures are observed in the grazing area of an herbivore member of the South American camelids, the vicuna, on the border of highland wetlands. These spirals cannot be explained by the well-established mathematical models which describe other vegetation patterns (that emerge from a Turing-type of instability) such as stripes, rings, or fairy circles. We attribute the formation of spirals to the coupling between the growth of vegetation in semiarid regions and the grazing of vicunas. The mathematical analysis of this coupling reveals an excitable behavior, i.e. small perturbations of the equilibrium generate large trajectories before coming back, that is the origin of the spirals.     

Long-Term Evolution of Email Networks: Statistical Regularities,Predictability and Stability of Social Behaviors

In social networks, individuals constantly drop ties and replace them by new ones in a highly unpredictable fashion. This highly dynamical nature of social ties has important implications for processes such as the spread of information or of epidemics. Several studies have demonstrated the influence of a number of factors on the intricate microscopic process of tie replacement, but the macroscopic long-term effects of such changes remain largely unexplored. Here we investigate whether, despite the inherent randomness at the microscopic level, there are macroscopic statistical regularities in the long-term evolution of social networks. In particular, we analyze the email network of a large organization with over 1,000 individuals throughout four consecutive years. We find that, although the evolution of individual ties is highly unpredictable, the macro-evolution of social communication networks follows well-defined statistical patterns, characterized by exponentially decaying log-variations of the weight of social ties and of individuals’ social strength. At the same time, we find that individuals have social signatures and communication strategies that are remarkably stable over the scale of several years.     

Quasi-elastic light scattering from migrating chemotactic bands of Escherichia coli. III. Studies of band formation propagation and motility in oxygen and serine substrates.

A series of light scattering experiments have been performed to study both macroscopic aspects of band formation and propagation and microscopic motility parameters of Escherichia coli in the combined substrate gradients of oxygen and serine. From the band formation experiment the conclusion is drawn that a minimum threshold gradient of the substrate is required for bacteria to form a band. From the band propagation experiment in the serine substrate the motility coefficient mu and chemotactic coefficient delta are determined. A separate quasi-elastic scattering experiment has been made with a propagating band to obtain three microscopic motility parameters: mean twiddle time tau 1, mean run time tau 2, and mean run speed V2. Finally, a scaling argument is made to connect the macroscopic parameters mu and delta with the microscopic parameters tau 1, tau 2, and V2, thus achieving a unified understanding of macroscopic and microscopic aspect of chemotaxis.     

Evidence for distinct populations of human Merkel cells

Merkel cells (MCs) are neuroendocrine cells of unknown origin located in the skin. They are identified at electron microscopic level by electron dense granules, at light microscopic level by the presence of cytokeratins 8, 18, 19 and 20. Contradictory reports concerning the presence of other molecules of epithelial as well as neural origin prompted us to investigate whether there are distinct populations of human MCs. Here, we show the heterogeneous expression of villin, N-CAM, NGF-R, and neurofilaments in MCs. Synaptophysin is found in all MCs but with different intensity, nestin is absent. Expression patterns vary between interfollicular epidermis, hair follicles and glabrous epidermis. We conclude that there are distinct populations of MCs, but all populations contain markers for epithelial as well as neural cells. Putative functions of the distinct populations are discussed. A.-C. Eispert and F. Fuchs have contributed equally to the paper.     

Definitions of state variables and state space for brain-computer interface

Neocortical state variables are defined and evaluated at three levels: microscopic using multiple spike activity (MSA), mesoscopic using local field potentials (LFP) and electrocorticograms (ECoG), and macroscopic using electroencephalograms (EEG) and brain imaging. Transactions between levels occur in all areas of cortex, upwardly by integration (abstraction, generalization) and downwardly by differentiation (speciation). The levels are joined by circular causality: microscopic activity upwardly creates mesoscopic order parameters, which downwardly constrain the microscopic activity that creates them. Integration dominates in sensory cortices. Microscopic activity evoked by receptor input in sensation induces emergence of mesoscopic activity in perception, followed by integration of perceptual activity into macroscopic activity in concept formation. The reverse process dominates in motor cortices, where the macroscopic activity embodying the concepts supports predictions of future states as goals. These macroscopic states are conceived to order mesoscopic activity in patterns that constitute plans for actions to achieve the goals. These planning patterns are conceived to provide frames in which the microscopic activity evolves in trajectories that adapted to the immediate environmental conditions detected by new stimuli. This circular sequence forms the action-perception cycle. Its upward limb is understood through correlation of sensory cortical activity with behavior. Now brain-machine interfaces (BMI) offer a means to understand the downward sequence through correlation of behavior with motor cortical activity, beginning with macroscopic goal states and concluding with recording of microscopic MSA trajectories that operate neuroprostheses. Part 1 develops a hypothesis that describes qualitatively the neurodynamics that supports the action-perception cycle and derivative reflex arc. Part 2 describes episodic, “cinematographic” spatial pattern formation and predicts some properties of the macroscopic and mesoscopic frames by which the embedded trajectories of the microscopic activity of cortical sensorimotor neurons might be organized and controlled. URL: http://sulcus.berkeley.edu     

Spiral and Rotor Patterns Produced by Fairy Ring Fungi

A broad class of soil fungi form the annular patterns known as ‘fairy rings’ and provide one of the only means to observe spatio-temporal dynamics of otherwise cryptic fungal growth processes in natural environments. We present observations of novel spiral and rotor patterns produced by fairy ring fungi and explain these behaviors mathematically by first showing that a well known model of fairy ring fungal growth and the Gray-Scott reaction-diffusion model are mathematically equivalent. We then use bifurcation analysis and numerical simulations to identify the conditions under which spiral waves and rotors can arise. We demonstrate that the region of dimensionless parameter space supporting these more complex dynamics is adjacent to that which produces the more familiar fairy rings, and identify experimental manipulations to test the transitions between these spatial modes. These same manipulations could also feasibly induce fungal colonies to transition from rotor/spiral formation to a set of richer, as yet unobserved, spatial patterns.     

Hormonal control of enzyme activity during the plasma membrane transformation of uterine epithelial cells

Ultrastructural and light microscopic catalytic histochemical methods were used to study the distribution and changes in distribution of four phosphatase enzymes; alkaline phosphatase, 5'-nucleotidase, thiamine pyrophosphatase and adenosine triphosphatase in uterine epithelial cells in response to the ovarian hormones, oestrogen, progesterone or a combination of both used in different regimes on ovariectomised rats. Reaction product for all four enzymes was clearly localised in the epithelial cells, especially with oestrogen priming. However, the four enzymes showed markedly different patterns of organisation of reaction product in response to other hormonal treatments.Our findings clearly show that the expression of these enzymes is under ovarian hormonal control. However, while all of the enzymes are upregulated by oestrogen, the response to progesterone is variable, which can upregulate or downregulate different enzymes. The findings are particularly obvious at the electron microscopic level on the apical plasma membrane of the uterine epithelial cells, which was the main focus of our study.     

Quantitative measurement of cell migration using time-lapse videomicroscopy and non-linear system analysis

Epithelial cells of the mammary gland possess the inherent capacity to form epithelial monolayers in vitro. This requires coordination of cell migration, cell-cell contact formation, and cell proliferation. Using time-lapse phase contrast videomicroscopy we have observed mammary gland epithelial cells over different time scales. We show the generation of a complete polarized epithelial monolayer in real-time, starting from a few cells. We subsequently concentrated on the early stages of this process by tracking epithelial cells during phases of polarized migration. We performed migration analysis using fractal measures. With this technology the structure of seemingly random processes not accessible to the usual methods of linear analysis can be measured. As a control and proof of principle approach we applied infection of cells with an adenoviral vector, which is used as a gene targeting vector for many applications. Infection markedly influenced the patterns of migratory behavior. We, therefore, believe that time-lapse videomicroscopy in combination with fractal analysis can contribute to differential characterization of distinct cellular migration patterns. This will be useful in situations of long-term alterations in cell culture systems.