Pattern of functional extinctions in ecological networks with a variety of interaction types

There is a strong trend of declining populations in many species of both animals and plants. Dwindling numbers of species can eventually lead to their functional extinction. Functional, or ecological, extinction occurs when a species becomes too rare to fulfill its ecological, interactive role in the ecosystem, leading to true (numerical) extinction of other depending species. Recent theoretical work on food webs suggests that the frequency of functional extinction might be surprisingly high. However, little is known about the risk of functional species extinctions in networks with other types of interactions than trophic ones. Here, we explore the frequency of functional extinctions in model ecological networks having different proportions of antagonistic and mutualistic links. Furthermore, we investigate the topological relationship between functionally and numerically extinct species. We find that (1) the frequency of functional extinctions is higher in networks containing a mixture of antagonistic and mutualistic interactions than in networks with only one type of interaction, (2) increased mortality rate of species having both mutualistic and antagonistic links is more likely to lead to extinction of another species than to extinction of the species itself compared to species having only mutualistic or antagonistic links, and (3) trophic distance (shortest path) between functionally and numerically extinct species is, on average, longer than one, indicating the importance of indirect effects. These results generalize the findings of an earlier study on food webs, demonstrating the potential importance of functional extinction in a variety of ecological network types.     

The effects of space and diversity of interaction types on the stability of complex ecological networks

The relationship between structure and stability in ecological networks and the effect of spatial dynamics on natural communities have both been major foci of ecological research for decades. Network research has traditionally focused on a single interaction type at a time (e.g. food webs, mutualistic networks). Networks comprising different types of interactions have recently started to be empirically characterized. Patterns observed in these networks and their implications for stability demand for further theoretical investigations. Here, we employed a spatially explicit model to disentangle the effects of mutualism/antagonism ratios in food web dynamics and stability. We found that increasing levels of plant-animal mutualistic interactions generally resulted in more stable communities. More importantly, increasing the proportion of mutualistic vs. antagonistic interactions at the base of the food web affects different aspects of ecological stability in different directions, although never negatively. Stability is either not influenced by increasing mutualism—for the cases of population stability and species’ spatial distributions—or is positively influenced by it—for spatial aggregation of species. Additionally, we observe that the relative increase of mutualistic relationships decreases the strength of biotic interactions in general within the ecological network. Our work highlights the importance of considering several dimensions of stability simultaneously to understand the dynamics of communities comprising multiple interaction types.     

A genetic interaction network model of a complex neurological disease

Absence epilepsy (AE) is a complex, heritable disease characterized by a brief disruption of normal behavior and accompanying spike‐wave discharges (SWD) on the electroencephalogram. Only a handful of genes has been definitively associated with AE in humans and rodent models. Most studies suggest that genetic interactions play a large role in the etiology and severity of AE, but mapping and understanding their architecture remains a challenge, requiring new computational approaches. Here we use combined analysis of pleiotropy and epistasis (CAPE) to detect and interpret genetic interactions in a meta‐population derived from three C3H × B6J strain crosses, each of which is fixed for a different SWD‐causing mutation. Although each mutation causes SWD through a different molecular mechanism, the phenotypes caused by each mutation are exacerbated on the C3H genetic background compared with B6J, suggesting common modifiers. By combining information across two phenotypic measures – SWD duration and frequency – CAPE showed a large, directed genetic network consisting of suppressive and enhancing interactions between loci on 10 chromosomes. These results illustrate the power of CAPE in identifying novel modifier loci and interactions in a complex neurological disease, toward a more comprehensive view of its underlying genetic architecture.     

Role of Mg++ in the mithramycin-DNA interaction: evidence for two types of mithramycin-Mg++ complex

Mithramycin(MTR, structure shown in Figure 1) [and the related compound Chromomycin A3(CHRA3)] are antitumor antibiotics which inhibit DNA dependent RNA polymerase activity via reversible interaction with DNA only in the presence of divalent metal ion such as Mg++. In order to understand the role of Mg++ in MTR-DNA interaction, absorbance and CD spectroscopic techniques are employed to study the binding of MTR to Mg++. These studies show: i) the drug alone binds to Mg++ and ii) two different types of drug-Mg++ complexes are formed at low(Complex I) and high(Complex II) ratios of the concentration of Mg++ and MTR. We propose that these two complexes would bind to the same DNA with different affinities and rates. This result suggests that the relative concentration of Mg++ is an important factor to be taken into account to understand the molecular basis of MTR-DNA interaction.     

The complex interaction network among multiple invasive bird species in a cavity-nesting community

Alien invasive species have detrimental effects on invaded communities. Aliens do not invade a vacuum, but rather a community consisting of native and often other alien species. Our current understanding of the pathways and network of interactions among multiple invasive species within whole communities is limited. Eradication efforts often focus on a single target species, potentially leading to unexpected outcomes on interacting non-target species. We aimed to examine the interaction network in a cavity-nesting community consisting of native and invasive birds. We studied the nesting cavities in the largest urban park in Israel over two breeding seasons. We found evidence for a complex interaction network that includes negative, neutral and positive interactions, but no synergistic positive interactions among aliens. Three major factors shaped the interaction network: breeding timing, nesting preferences and the ability to excavate or widen the cavities, which were found to be a limited resource. Cavity enlargement by the early-breeding invasive rose-ringed parakeet may enhance breeding of the invasive common myna in previously unavailable holes. The myna excludes the smaller invasive vinous-breasted starling, a direct competitor of the primary nest excavator, the native Syrian woodpecker. Therefore, management and eradication efforts directed towards the common myna alone may actually release the vinous-breasted starling from competitive exclusion by the common myna, increasing the negative impact of the vinous-breasted starling on the native community. As found here, interactions among multiple alien species can be crucial in shaping invasion success and should be carefully considered when aiming to effectively manage biological invasions.     

The microbiome associated with two Synechococcus ribotypes at different levels of ecological interaction

Planktonic cyanobacteria belonging to the genus Synechococcus are ubiquitously distributed in marine and fresh waters, substantially contributing to total carbon fixation on a global scale. While their ecological relevance is acknowledged, increasing resolution in molecular techniques allows disentangling cyanobacteria's role at the micro‐scale, where complex microbial interactions may drive the overall community assembly. The interplay between phylogenetically different Synechococcus clades and their associated bacterial communities can affect their ecological fate and susceptibility to protistan predation. In this study, we experimentally promoted different levels of ecological interaction by mixing two Synechococcus ribotypes (MW101C3 and LL) and their associated bacteria, with and without a nanoflagellate grazer (Poterioochromonas sp.) in laboratory cultures. The beta‐diversity of the Synechococcus‐associated microbiome in laboratory cultures indicated that the presence of the LL ribotype was the main factor determining community composition changes (41% of total variance), and prevailed over the effect of protistan predation (18% of total variance). Our outcomes also showed that species coexistence and predation may promote microbial diversity, thus highlighting the underrated ecological relevance of such micro‐scale factors.     

Crystal structure of a heterodimer of editosome interaction proteins in complex with two copies of a cross-reacting nanobody

The parasite Trypanosoma brucei, the causative agent of sleeping sickness across sub-Saharan Africa, depends on a remarkable U-insertion/deletion RNA editing process in its mitochondrion. A approximately 20 S multi-protein complex, called the editosome, is an essential machinery for editing pre-mRNA molecules encoding the majority of mitochondrial proteins. Editosomes contain a common core of twelve proteins where six OB-fold interaction proteins, called A1-A6, play a crucial role. Here, we report the structure of two single-strand nucleic acid-binding OB-folds from interaction proteins A3 and A6 that surprisingly, form a heterodimer. Crystal growth required the assistance of an anti-A3 nanobody as a crystallization chaperone. Unexpectedly, this anti-A3 nanobody binds to both A3(OB) and A6, despite only ~40% amino acid sequence identity between the OB-folds of A3 and A6. The A3(OB)-A6 heterodimer buries 35% more surface area than the A6 homodimer. This is attributed mainly to the presence of a conserved Pro-rich loop in A3(OB). The implications of the A3(OB)-A6 heterodimer, and of a dimer of heterodimers observed in the crystals, for the architecture of the editosome are profound, resulting in a proposal of a 'five OB-fold center' in the core of the editosome.     

Acetic acid bacteria encode two levansucrase types of different ecological relationship

Acetic acid bacteria (AAB) are associated with plants and insects. Determinants for the targeting and occupation of these widely different environments are unknown. However, most of these natural habitats share plant-derived sucrose, which can be metabolized by some AAB via polyfructose building levansucrases (LS) known to be involved in biofilm formation. Here, we propose two LS types (T) encoded by AAB as determinants for habitat selection, which emerged from vertical (T1) and horizontal (T2) lines of evolution and differ in their genetic organization, structural features and secretion mechanism, as well as their occurrence in proteobacteria. T1-LS are secreted by plant-pathogenic α- and γ-proteobacteria, while T2-LS genes are common in diazotrophic, plant-growth-promoting α-, β- and γ-proteobacteria. This knowledge may be exploited for a better understanding of microbial ecology, plant health and biofilm formation by sucrase-secreting proteobacteria in eukaryotic hosts.     

Experimental immune complex glomerulonephritis in the mouse with two types of immune complexes.

Immune complex glomerulonephritis was induced in three groups of mice by long-term immunization. Two antigens of similar molecular weight were used. The first group was immunized with ferritin (mol wt 480,000). In altered glomeruli deposits of immune complexes were seen in the subendothelial and subepithelial spaces of the glomerular basement membrane (GBM) and in the mesangium. The immune complex deposits were formed by amorphous matrix with marked dense molecules of ferritin. The second group was immunized with human fibrinogen (mol wt 450,000). The immune complex deposits were present in the intramembranous, subepithelial and subendothelial spaces of the GBM and in the mesangium. These deposits were relatively less electron-dense and had a fine granular structure. The third group of mice were immunized with both ferritin and fibrinogen simultaneously. Two types of deposits situated subendothelially in the GBM and in the mesangium were seen in one animal of this group. One type of deposit resembled structurally the ferritin-antiferritin complex deposits, the other resembled the fibrinogen-antifibrinogen complex deposits. The individual deposits in the GBM and in the mesangium formed discrete homogeneous masses. The two types of deposit were occassionally in direct contact with one another, but were more often completely separate and were never mixed. It can be assumed that in at least some phase of the experiment both types of complex were present in the circulating blood simultaneously. However, since none of the complexes deposited in the GBM or in the mesangium were mixed, it seems probable that each type of complex is deposited separately in the form of "clusters" composed of a single type of complex. The phagocytic activity of mesangial cells of animals with complex glomerulonephritis was not increased when compared with control animals.     

Diversity and plastid types in Dinophysis acuminata complex (Dinophyceae) in Scottish waters

Dinophysis acuminata produces lipophilic shellfish toxins (LSTs) that have economic and ecological impact on marine invertebrates in NE Atlantic where aquaculture farming is prevalent. Identification of D. acuminata can be complex. Cells exhibit a variety of morphotypes that overlap between species making identification using routine light microscopy difficult. These cells are mixotrophic and their population size is influenced by hydrographic conditions and prey populations. Dinophysis cells are able to acquire and temporarily keep prey plastids from a variety of photosynthetic unicellular sources. The Dinophysis community in Scottish waters tend to be dominated by cells with morphologies that appear to be variants of D. acuminata/norvegica complex particularly during late spring/early summer. To determine the identity of these morphotypes, DNA barcoding was performed on 32 single cell isolates from sites around the Scottish coast using the ribosomal internal transcribed spacer 1 (ITS1) and a partial cytochrome oxidase I (COI) fragment on the same single cells. Although the cells exhibited a variety of morphotypes, most were restricted to one cluster containing D. acuminata and three grouped with Dinophysis ovum. This is the first molecular confirmation of the presence of D. ovum in Scottish waters. Two isolates showed considerable divergence – one was unidentifiable from the public databases, whilst the other matched a Dinophysis cf. acuta isolate from Canada. To investigate prey plastids, molecular analysis of these Dinophysis single cells was conducted with a partial fragment of the plastid ribosomal marker (16S). Most cells harboured plastids from the cryptophyte Teleaulax – the most commonly reported plastid type, however one cell harboured a Rhodomonas/Storeatula derived plastid. This finding increases the range and variety of cryptophyte plastids found in Dinophysis and increases the range of prey-types.     

Stability of a diamond-shaped module with multiple interaction types

Indirect interactions among species emerge from the complexity of ecological networks and can strongly affect the response of communities to disturbances. To determine these indirect interactions and understand better community dynamics, ecologists focused on the interactions within small sets of species or modules. Thanks to their analytical tractability, modules bring insights on the mechanisms occurring in complex interaction networks. So far, most studies have considered modules with a single type of interaction although numerous species are involved in mutualistic and antagonistic interactions simultaneously. In this study, we analyse the dynamics of a diamond-shaped module with multiple interaction types: two resource species sharing a mutualist and a consumer. We describe the different types of indirect interaction occurring between the resource species and the conditions for a stable coexistence of all species. We show that the nature of indirect interactions between resource species (i.e. apparent facilitation, competition or antagonism), as well as stable coexistence, depend on the species generalism and asymmetry of interactions, or in other words, on the distribution of interaction strengths among species. We further unveil that a balance between mutualistic and antagonistic interactions at the level of resource species favours stable coexistence, and that species are more likely to coexist stably if there is apparent facilitation between the two resource species rather than apparent competition. Our results echo existing knowledge on the trophic diamond-shaped module, and confirm that our understanding of communities combining different interaction types can gain from module analyses.     

The protein interaction network of the epithelial junctional complex: a system-level analysis

To acquire system-level understanding of the intercellular junctional complex, protein–protein interactions occurring at the junctions of simple epithelial cells have been examined by network analysis. Although proper hubs (i.e., very rare proteins with exceedingly high connectivity) were absent from the junctional network, the most connected (albeit nonhub) proteins displayed a significant association with essential genes and contributed to the “small world” properties of the network (as shown by in vivo and in silico deletion, respectively). In addition, compared with a random network, the junctional network had greater tendency to form modules and subnets of densely interconnected proteins. Module analysis highlighted general organizing principles of the junctional complex. In particular, two major modules (corresponding to the tight junctions and to the adherens junctions/desmosomes) were linked preferentially to two other modules that acted as structural and signaling platforms.     

Predicting protein complex geometries with a neural network

A major challenge of the protein docking problem is to define scoring functions that can distinguish near‐native protein complex geometries from a large number of non‐native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom‐pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near‐native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge‐based energy functions for scoring. We show that a distance‐dependent atom pair potential performs much better than a simple atom‐pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge‐based scoring functions such as ZDOCK 3.0, ZRANK, ITScore‐PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network‐based scoring function achieves a reasonable performance in rigid‐body unbound docking of proteins. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Diversity in riverine metacommunities: a network perspective

The influence of spatial processes on diversity and community dynamics is generally recognized in ecology and also applied to conservation projects involving forest and grassland ecosystems. Riverine ecosystems, however, have been for a long time viewed from a local or linear perspective, even though the treelike branching of river networks is universal. River networks (so-called dendritic networks) are not only structured in a hierarchic way, but the dendritic landscape structure and physical flows often dictate distance and directionality of dispersal. Theoretical models suggest that the specific riverine network structure directly affects diversity patterns. Recent experimental and comparative data are supporting this idea. Here, I provide an introduction on theoretical findings suggesting that genetic diversity, heterozygosity and species richness are higher in dendritic systems compared to linear or two-dimensional lattice landscapes. The characteristic diversity patterns can be explained in a network perspective, which also offers universal metrics to better understand and protect riverine diversity. I show how appropriate metrics describing network centrality and dispersal distances are superior to classic measures still applied in aquatic ecology, such as Strahler order or Euclidian distance. Finally, knowledge gaps and future directions of research are identified. The network perspective employed here may help to generalize findings on riverine biodiversity research and can be applied to conservation and river restoration projects.     

Spread of two linked social norms on complex interaction networks

In this paper, we study the spread of social norms, such as rules and customs that are components of human cultures. We consider the spread of two social norms, which are linked through individual behaviors. Spreading social norms depend not only on the social network structure, but also on the learning system. We consider four social network structures: (1) complete mixing, in which each individual interacts with the others at random, (2) lattice, in which each individual interacts with its neighbors with some probability and with the others at random, (3) power-law network, in which a few influential people have more social contacts than the others, and (4) random graph network, in which the number of contacts follows a Poisson distribution. Using the lattice model, we also investigate the effect of the small-world phenomenon on the dynamics of social norms. In our models, each individual learns a social norm by trial and error (individual learning) and also imitates the other's social norm (social learning). We investigate how social network structure and learning systems affect the spread of two linked social norms. Our main results are: (1) Social learning does not lead to coexistence of social norms. Individual learning produces coexistence, and the dynamics of coexistence depend on which social norms are learned individually. (2) Social norms spread fastest in the power-law network model, followed by the random graph model, the complete mixing model, the two-dimensional lattice model and the one-dimensional lattice. (3) We see a "small world effect" in the one-dimensional model, but not in two dimensions.     

Effect and potential ecological significance of the interaction of humic acids with two aquatic extracellular proteases

1. The effects of humic acids and fulvic acids on an extracellular serine and metalloprotease purified from a strain of Aeromonas hydrophila isolated from a freshwater wetland were examined. The serine protease was inhibited by humic acids at pH and humic acid concentrations found naturally in the wetland where this strain of A. hydrophila was isolated. The metalloprotease was not inhibited by humic acids at any pH investigated. Fulvic acids had no effect upon either protease. 2. Inhibition of serine protease activity by humic acids was reversed by increasing the pH to 9, as well as increasing the ionic strength by addition of CaCl₂- It was concluded that the interaction between humic acids and the serine protease was primarily ionic. 3. The formation of a humic acid-serine protease complex increased the half-life of enzymatic activity in dilute solutions. Humic acids had no effect on the stability of the metalloprotease. 4. There was no clear effect of humic acids on the growth of A. hydrophila, indicating that either the serine protease is not involved in the rate-limiting step of growth or that sufficient activity exists even when the serine protease is inhibited by humic acids. 5. Increasing the enzymatic lifetime through association with humic acids may be an adaptive mechanism which could result in energy conservation due to a decreased requirement for protein synthesis.     

Rare and spatially segregated release sites mediate a synaptic interaction between two identified network neurons

Laser‐scanning confocal microscopy (LSCM), electron microcopy (EM), and cellular electrophysiology were used in combination to study the structural basis of an inhibitory synapse between two identified neurons of the same network. To achieve this, we examined the chemical inhibitory synapse between identified neurons belonging to the lobster (Homarus gammarus) pyloric network: the pyloric dilator (PD) and the lateral pyloric (LP) neurons. In order to visualize simultaneously these two neurons, we used intrasomatic injection of Lucifer Yellow (LY) in one and rhodamine/horseradish peroxydase (HRP) in the other. Under LSCM, we found only two zones of close apposition in a restricted part of the neuritic tree of the two network neurons. Then, within these two zones, the synaptic release sites were searched using EM. To this end, photoconversion of LY with immunogold and development of HRP with DAB were performed on the previously observed preparations. Structural evidence was found for only one release site per zone. To confirm this result, and because the zones of contact were always segregated in a restricted part of the dendrites, we used laser photoablation to selectively delete, either pre‐ or postsynaptically, the branches on which the release sites were located. In both cases, such restrictive ablation completely abolished the functional interaction between these neurons. Our results therefore demonstrate that an inhibitory synapse that is essential for the operation of a neural network relies on only very few sites of contact localized in a highly restricted part of each neuron's dendritic arbor. © 2002 Wiley Periodicals, Inc. J Neurobiol 50: 150–163, 2002; DOI 10.1002/neu.10023     

交通网络空间互动视角下生态足迹驱动机制

长江中游城市群是中部崛起战略的重要区域,同时依托长江黄金水道面临发展和保护的困境。交通网络空间互动视角下的生态足迹驱动机制研究对统筹长江中游城市群经济社会高质量发展和生态文明高水平建设以实现可持续发展具有重要意义。基于生态足迹模型测度了长江中游城市群县域尺度的可持续发展状况,并在STIRPAT模型框架下基于交通网络空间互动关系挖掘生态足迹的驱动机制和空间效应,为交通网络扩张背景下的跨区域生态治理与可持续发展提供参考。研究结果显示：(1)2010—2017年,长江中游城市群县域生态足迹均值有所下降;(2)道路交通网络和铁路交通网络规模均有所扩大,但连通性略有下降;(3)在基于交通网络构建的空间互动媒介下,城镇化率和人均GDP对生态足迹具有显著的促进作用,而第三产业增加值占比对生态足迹产生抑制影响,且生态足迹表现出积极的空间外溢效应。基于以上研究结果,建议在基于交通网络加强区域生态协同发展的同时,建设产业互促、资源互通、技术互享的区域联动可持续发展新格局。