Visualizing global properties of large complex networks

For complex biological networks, graphical representations are highly desired for understanding some design principles, but few drawing methods are available that capture topological features of a large and highly heterogeneous network, such as a protein interaction network. Here we propose the circular perspective drawing (CPD) method to visualize global structures of large complex networks. The presented CPD combines the quasi-continuous search (QCS) analogous to the steepest descent method with a random node swapping strategy for an enhanced calculation speed. The CPD depicts a network in an aesthetic manner by showing connection patterns between different parts of the network instead of detailed links between nodes. Global structural features of networks exhibited by CPD provide clues toward a comprehensive understanding of the network organizations. Availability: Software is freely available at http://www.cadlive.jp.     

Effect of a large city on the structure of coenoelements in a natural woodland in Warsaw

This paper reports on the anthropogenic degradation of natural forest vegetation in Warsaw (Reserve Las Bielaski). The degree and form of degradation was assessed on the basis of composition and distribution of forest and non-forest coenoelements (sensu Walter & Straka 1970).The total number of forest coenoelements was found to be three times lower than that of non-forest coenoelements; the former decidedly dominated only over 20% of the reserve area, the least accessible to town inhabitants. In the remaining area the vegetation was deformed to a various degree, indicated by the presence and local dominance of the species of: (1) brushwoods, clearings and shaded forest margins, (2) meadows and grasslands, (3) synanthropic communities. The distribution and proportions of above non-forest coenoelements in the vegetation composition reflected mainly the intensity and form of direct disturbance. The forest fragments defined as highly degraded on the basis of dominance of non-forest over forest coenoelements, were also the sites of anthropophyte concentration.The presented assessment method of the degree and form of degradation of natural vegetation can be especially useful when fragmentation and deformation of phytocoenoses make the application of phytosociological methods impossible.     

The topological differences between visitation and pollen transport networks: a comparison in species rich communities of the Himalaya–Hengduan Mountains

Pollination networks are usually constructed and assessed by direct field observations which commonly assume that all flower visitors are true pollinators. However, this assumption is often invalid and the use of data based on mere visitors to flowers may lead to a misunderstanding of intrinsic pollination networks. Here, using a large dataset by both sampling floral visitors and analyzing their pollen loads, we constructed 32 networks pairs (visitation versus pollen transport) across one flowering season at four elevation sites in the Himalaya–Hengduan Mountains region. Pollen analysis was conducted to determine which flower visitors acted as potential pollinators (pollen vectors) or as cheaters (those not carrying pollen of the visited plants). We tested whether there were topological differences between visitation and pollen transport networks and whether different taxonomic groups of insect visitors differed in their ability to carry pollen of the visited plants. Our results indicated that there was a significantly higher degree of specialization at both the network and species levels in the pollen transport networks in contrast to the visitation networks. Modularity was lower but nestedness was higher in the visitation networks compared to the pollen transport networks. All the cheaters were identified as peripheral species and most of them contributed positively to the nested structure. This may explain in part the differences in modularity and nestedness between the two network types. Bees carried the highest proportion of pollen of the visited plants. This was followed by Coleoptera, other Hymenoptera and Diptera. Lepidoptera carried the lowest proportion of pollen of the visited plants. Our study shows that the construction of pollen transport networks could provide a more in‐depth understanding of plant–pollinator interactions. Moreover, it suggests that detecting and removing cheater interactions when studying the topology of other mutualistic networks might be also important.     

Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties

Myosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350 nm vs. 1750 nm) transport by myoVa motors. Five thousand simulated liposomes transported within each network adopted one of three states: transport, tug-of-war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug-of-wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, N_c. N_c is a geometric property of the actin network that depends only on the position and polarity of the actin filaments, transport distance, and the liposome diameter, as evidenced by a fivefold increase in liposome diameter resulting in a fivefold decrease in N_c. Thus in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell’s physiological demands.     

Construction,validation, and application of nocturnal pollen transport networks in an agro‐ecosystem: a comparison using light microscopy and DNA metabarcoding

1. Moths are globally relevant as pollinators but nocturnal pollination remains poorly understood. Plant–pollinator interaction networks are traditionally constructed using either flower‐visitor observations or pollen‐transport detection using microscopy. Recent studies have shown the potential of DNA metabarcoding for detecting and identifying pollen‐transport interactions. However, no study has directly compared the realised observations of pollen‐transport networks between DNA metabarcoding and conventional light microscopy. 2. Using matched samples of nocturnal moths, we constructed pollen‐transport networks using two methods: light microscopy and DNA metabarcoding. Focussing on the feeding mouthparts of moths, we developed and provide reproducible methods for merging DNA metabarcoding and ecological network analysis to better understand species interactions. 3. DNA metabarcoding detected pollen on more individual moths, and detected multiple pollen types on more individuals than microscopy, although the average number of pollen types per individual was unchanged. However, after aggregating individuals of each species, metabarcoding detected more interactions per moth species. Pollen‐transport network metrics differed between methods because of variation in the ability of each to detect multiple pollen types per moth and to separate morphologically similar or related pollen. We detected unexpected but plausible moth–plant interactions with metabarcoding, revealing new detail about nocturnal pollination systems. 4. The nocturnal pollination networks observed using metabarcoding and microscopy were similar yet distinct, with implications for network ecologists. Comparisons between networks constructed using metabarcoding and traditional methods should therefore be treated with caution. Nevertheless, the potential applications of metabarcoding for studying plant–pollinator interaction networks are encouraging, especially when investigating understudied pollinators such as moths.     

Flower‐visitor networks only partially predict the function of pollen transport by bees

Mutualistic networks display distinct structural and organizational features such as nestedness, power‐law degree distribution and asymmetric dependencies. Attention is now focused on how these structural properties influence network function. Most plant‐pollinator networks are constructed using records of animals contacting flowers, which is based on the assumption that all visitors to flowers are pollinators; however, animals may visit flowers as nectar robbers, florivores, or to prey upon other visitors. To differentiate potential pollinator interactions from other interaction types, we examined individual bees that had visited flowers to detect if they carried pollen. Using these data, we constructed visitation and pollen‐transport networks for a spinifex‐dominated arid zone grassland. To determine how the structure of the visitation network reflects pollen transport, we compared the two networks using a null model approach to account for differences in network size. Differences in number of species, nestedness and connectance observed between the visitation and pollen‐transport networks were within expected ranges generated under the null model. The pollen‐transport network was more specialized, had lower interaction evenness, and fewer links compared to the visitation network. Almost half the number of species of the visitation network participated in the pollen‐transport network, and one‐third of unique visitation interactions resulted in pollen transport, highlighting that visitation does not always result in pollination. Floral visitor data indicate potential pollen transporters, but inferring pollination function from visitation networks needs to be performed cautiously as pollen transport resulted from both common and rare interactions, and depended on visitor identity. Although visitation and pollen‐transport networks are structurally similar, the function of all species cannot be predicted from the visitation network alone. Considering pollen transport in visitation networks is a simple first step towards determining pollinators from non‐pollinators. This is fundamental for understanding how network structure relates to network function.     

Live pine pollen in rainwater: reconstructing its long-range transport

Raindrops brim with pollen even when there is no ambient local pollen. How does this nonlocal pollen get inside rain? The likely answer is long-range transport beneath or inside clouds. To test this hypothesis, we captured rain-delivered pollen on Ocracoke Island, NC, USA over a 12-day interval before local pine pollen release then reconstructed its trajectory and its atmospheric exposure conditions. Findings were as follows: four rain episodes yielded a total of 632 pollen grains of which 6.7% germinated. To find pollen sources, we first identified pollen-releasing forested areas using a predictive heat sum equation for each rain episode. Next, we constructed the backward trajectory for air parcels carrying rain-delivered pollen from those forests using the MLDP atmospheric transport and dispersion model. Nonlocal sources were located at distances up to 300 km from Ocracoke Island and distances lessened with each successive episode. Below-cloud transport time was 8 and 17 h for Episodes A and B, respectively. Pollen grains were exposed to harsh atmospheric conditions during below-cloud transport, yet some grains still germinated. Atmospheric turbulence patterns changed for each episode, so distance from pollen source was poorly correlated with pollen transport time. Pollen germination was not closely correlated with either distances or transport time. In-cloud transport was more likely for pollen sampled during Episodes C and D. Pine pollen, although rarely allergenic, brings fresh insights into how atmospheric events can trigger human respiratory distress.

     

Parietaria pollen a new aeroallergen in the city of Valparaiso, Chile

Parietaria pollen has never been considered as a significant cause of pollinosis in Chile; therefore, the sensitization to Parietaria study has never been included in the study of patients with clinical suspicion of pollinosis in this region. The objective of this study was to describe the clinical characteristics of pollinosis caused by Parietaria in the Valparaíso region, related to air concentrations of this kind of pollen. A cross-sectional study was performed in the city of Valparaíso. It consisted of two stages: In the first, pollen grains were counted between 1999 and 2001. In the second, a sensitization profile on a patient population diagnosed with ARC (allergic rhinoconjunctivitis) was evaluated. Parietaria judaica (P. judiaca) presented pollination all year long, with aggravation in the spring and summer, and with values reaching 80 grains/m³ (weekly average). These findings determined the transience of the symptoms in this population, which is mainly perennial with seasonal aggravations. A total of 72 atopic subjects were obtained during the whole sample recollection period. P. judaica was the second most frequent cause of sensitization (60 %) after Dermatophagoides in the sample overall. Also, in monosensitized subjects, it was the first cause of pollen sensitization. P. judaica represents the second cause of allergy in Valparaíso and the first cause of pollinosis. These findings suggest the importance of quantifying Parietaria in Valparaíso and near cities, plus investigating the presence of sensitization and symptoms to allergies in a significant proportion of patients in this region.     

The Golgi ribbon structure facilitates anterograde transport of large cargoes

In mammalian cells, individual Golgi stacks fuse laterally to form the characteristic perinuclear ribbon structure. Yet the purpose of this remarkable structure has been an enigma. We report that breaking down the ribbon of mammalian cells strongly inhibits intra-Golgi transport of large cargoes without altering the rate of transport of smaller cargoes. In addition, insect cells that naturally harbor dispersed Golgi stacks have limited capacity to transport artificial oversized cargoes. These results imply that the ribbon structure is an essential requirement for transport of large cargoes in mammalian cells, and we suggest that this is because it enables the dilated rims of cisternae (containing the aggregates) to move across the stack as they transfer among adjacent stacks within the ribbon structure.     

Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure

Patterns of pollen dispersal are central to both the ecology and evolution of plant populations. However, the mechanisms controlling either the dispersal process itself or our estimation of that process may be influenced by site-specific factors such as local forest structure and nonuniform adult genetic structure. Here, we present an extension of the AMOVA model applied to the recently developed TWOGENER analysis of pollen pool structure. This model, dubbed the Stepwise AMOVA (StAMOVA), focuses on determining to what extent ecological, demographic, and/or environmental factors influence the observed genetic variation in spatially separated pollen pools. The analysis is verified for efficacy, using an extensive battery of simulations, illustrating: (1) how nonuniform adult genetic structure influences the differentiation of spatially separated pollen pools, and (2) how effectively the Stepwise analysis performs in carrying out the appropriate corrections. Finally, the model is applied to a Quercus alba data set, from which we have prior evidence that the adult genetic structure is nonuniformly distributed across the sampling landscape. From this data set, we show how the Stepwise model can be applied to remove the effects of spatial adult genetic structure on pollen pool differentiation and contrast these results with those derived from the original TWOGENER analysis.     

Long-distance transport ofBetula pollen grains and allergic symptoms

Summary An example of the potential importance of air masses as carriers of aero-allergens from distant source areas is provided. Considerable amount ofBetula pollen is relatively often transported to Fennoscandia before the local birch flowering period, mainly by southeastern air masses from eastern part of central Europe. Although the distance and the transport time in some cases can be extensive, the pollen grains seem to cause allergic reactions among sensitive persons.A comparison between the clinical results andBetula pollen counts from the time before the local flowering season in Stockholm in 1989 is presented.     

Allergenic pollen in the atmosphere of Rohtak city,Haryana (India): a pioneer study

An attempt has been made in the present study to assess the allergenicity of dominant pollen types recorded from the atmosphere of Rohtak city. Skin prick test was performed with the antigenic extracts of 22 pollen types on 150 local patients who visited Asthma Clinic, University of Health Sciences, Rohtak. Markedly positive skin reactions (2+ and above) varied from 4.6 to 20.6 % to various pollen antigens. Cenchrus ciliaria (20.6 %), Zea mays (20 %) and Pennisetum typhoides (19.3 %) were the pollen allergens exhibiting maximum sensitivity. Antigenic extract of Cassia occidentalis, Cynodon dactylon and Ricinus communis showed marked skin reactivity in 18.6 % of patients. Prosopis juliflora, Chenopodium murale, Amaranthus spinosus, Cassia fistula and Cassia siamea showed 2+ and above reactions in 16.6, 15.3, 14.6 and 14.0 % of the local patients, respectively. Least reactivity (4.6 %) was shown to the antigenic extract of Cyperus rotundus. Out of 52 sera screened for the presence of specific IgE antibodies against different antigenic extracts, only 5.5 % showed >60 % binding. About 30 % and above binding was shown to the antigenic extracts of Z. mays, A. spinosus, R. communis and Xanthium strumarium. The concordance between positive skin reaction and serum-specific IgE antibodies ranged from 15 to 69 %.     

gener: a server‐based analysis of pollen pool structure

The server‐based program gener performs the two‐generation analysis of pollen flow for data consisting of mother/offspring arrays using genetic markers. The gener program decomposes the genetic variance sampled by maternal individuals within and among pollen pool components of genetic variance and is accessible from http://dyerlab.bio.vcu.edu . These estimates are used to construct the test statistic, Φ_ft , whose significance is tested via permutation. The Φ_ft statistic can subsequently be used to quantify genetic effective pollen donor population size (N_ep), effective mating area and dispersal distance. Furthermore, the gener program can calculate Φ_ft values for all pairs of substrata within the data set.     

Modern surface pollen assemblages from the Middle and High Atlas,Morocco: insights into pollen representation and transport

Thirty-three modern surface samples were collected in the environmentally and climatologically contrasting regions of the Middle and High Atlas Mountains, Morocco. Samples representing forest and steppe montane environments (1935–2760 m above sea level) are clustered around study sites at Lake Tislit (High Atlas, semi-arid oro-Mediterranean bioclime) and Lake Sidi Ali and Michliffen (Middle Atlas, sub-humid montane Mediterranean bioclime). Good discrimination between regional pollen spectra is evident, with Middle Atlas samples reflecting higher arboreal cover (Cedrus and evergreen Quercus) and High Atlas samples with high abundances of non-arboreal taxa, including Artemisia and Fabaceae. These four taxa (Cedrus, evergreen Quercus, Artemisia and Fabaceae) are furthermore shown to be reliable indicators of local source vegetation within a 100 m² quadrat, taking into account threshold abundances of 7%, 20%, 4% and 10%, respectively. Deciduous Quercus, Olea and Phillyrea show long-distance pollen dispersal across both regions, contributing to non-trivial arboreal pollen (AP) values of up to 35% (typically 20–30%) in the High Atlas spectra. In the Middle Atlas, AP values of 40 to 50% occur in open sampling locations and > 60% under forest canopy cover. These insights should be taken into account when interpreting ancient pollen spectra from regional lakes and bogs for palaeoenvironmental reconstruction.     

Elements for a general memory structure: properties of recurrent neural networks used to form situation models

We study how individual memory items are stored assuming that situations given in the environment can be represented in the form of synaptic-like couplings in recurrent neural networks. Previous numerical investigations have shown that specific architectures based on suppression or max units can successfully learn static or dynamic stimuli (situations). Here we provide a theoretical basis concerning the learning process convergence and the network response to a novel stimulus. We show that, besides learning “simple” static situations, a nD network can learn and replicate a sequence of up to n different vectors or frames. We find limits on the learning rate and show coupling matrices developing during training in different cases including expansion of the network into the case of nonlinear interunit coupling. Furthermore, we show that a specific coupling matrix provides low-pass-filter properties to the units, thus connecting networks constructed by static summation units with continuous-time networks. We also show under which conditions such networks can be used to perform arithmetic calculations by means of pattern completion.     

Comparative structure of the pollen in species of Passiflora: insights from the pollen wall and cytoplasm contents

Pollen grains of three Brazilian species of Passiflora (P. elegans, P. suberosa and P. haematostigma) belonging to different subgenera were studied with respect to the wall and cytoplasm. New data were obtained on pollen wall histochemistry, cytoplasm contents and organelle inheritance. The structure of the pollen wall layers differed in all the species; P. elegans shares characters with those found in other species from the same subgenus. The exine foot layer is structured and evident only in P. haematostigma and is not structured in P. elegans. The pollen grains have pollenkitt with lipid components. The cytoplasm of the vegetative cell contains dissolved and non-dissolved polysaccharides. The generative cell contains plastids and mitochondria in all the species analyzed, and consequently has the potential for paternal or biparental extranuclear inheritance. Aspects of the evolution of the characters of the species are discussed in the light of a recent phylogeny of the group, with a focus on the three subgenera.     

Preparation and properties of pollen sporoplasts

Summary Methods for the removal of exine from mature, ungerminatedLilium longiflorum pollen and release of intact gametophytes (sporoplasts) have been developed. These methods rely on the low temperature solvolytic activity of 4-methylmorpholine N-oxide (MMNO), which allows partial or complete detachment of exine from intine during subsequent washing procedures. These methods are: aqueous MMNO combined with cyclohexylamine (method I), aqueous MMNO at alkaline pH (method II), and aqueous MMNO containing a high Ca²⁺ concentration with added cellulysin and macerase (method III). Sporoplasts produced by methods I and II are most frequently completely separated from exine and, as shown by histochemical tests, enveloped by the intine layer. Selected enzyme activities in method II sporoplasts are measurable but, as indicated by other tests, considerable damage to the plasma membrane accompanies this treatment. Sporoplasts produced by melhod III largely remain attached to their ruptured exine layer and retain substantial biological competence in terms of extractable enzyme activities, membrane integrity, and respiration.Abbreviations MMNO 4-methylmorpholine N-oxide - SEM scanning electron microscope - TEM transmission electron microscope