Measuring specialization in species interaction networks

BACKGROUND: Network analyses of plant-animal interactions hold valuable biological information. They are often used to quantify the degree of specialization between partners, but usually based on qualitative indices such as 'connectance' or number of links. These measures ignore interaction frequencies or sampling intensity, and strongly depend on network size. RESULTS: Here we introduce two quantitative indices using interaction frequencies to describe the degree of specialization, based on information theory. The first measure (d') describes the degree of interaction specialization at the species level, while the second measure (H(2)') characterizes the degree of specialization or partitioning among two parties in the entire network. Both indices are mathematically related and derived from Shannon entropy. The species-level index d' can be used to analyze variation within networks, while H(2)' as a network-level index is useful for comparisons across different interaction webs. Analyses of two published pollinator networks identified differences and features that have not been detected with previous approaches. For instance, plants and pollinators within a network differed in their average degree of specialization (weighted mean d'), and the correlation between specialization of pollinators and their relative abundance also differed between the webs. Rarefied sampling effort in both networks and null model simulations suggest that H(2)' is not affected by network size or sampling intensity. CONCLUSION: Quantitative analyses reflect properties of interaction networks more appropriately than previous qualitative attempts, and are robust against variation in sampling intensity, network size and symmetry. These measures will improve our understanding of patterns of specialization within and across networks from a broad spectrum of biological interactions

Mathematical models in mammalian cell biology

A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008

Tropical parabiotic ants: Highly unusual cuticular substances and low interspecific discrimination

<p>Abstract</p> <p>Background</p> <p>Associations between animal species require that at least one of the species recognizes its partner. Parabioses are associations of two ant species which co-inhabit the same nest. Ants usually possess an elaborate nestmate recognition system, which is based on cuticular hydrocarbons and allows them to distinguish nestmates from non-nestmates through quantitative or qualitative differences in the hydrocarbon composition. Hence, living in a parabiotic association probably necessitates changes of the nestmate recognition system in both species, since heterospecific ants have to be accepted as nestmates.</p> <p>Results</p> <p>In the present study we report highly unusual cuticular profiles in the parabiotic species <it>Crematogaster modiglianii </it>and <it>Camponotus rufifemur </it>from the tropical rainforest of Borneo. The cuticle of both species is covered by a set of steroids, which are highly unusual surface compounds. They also occur in the Dufour gland of <it>Crematogaster modiglianii </it>in high quantities. The composition of these steroids differed between colonies but was highly similar among the two species of a parabiotic nest. In contrast, hydrocarbon composition of <it>Cr. modiglianii </it>and <it>Ca. rufifemur </it>differed strongly and only overlapped in three regularly occurring and three trace compounds. The hydrocarbon profile of <it>Camponotus rufifemur </it>consisted almost exclusively of methyl-branched alkenes of unusually high chain lengths (up to C₄₉). This species occurred in two sympatric, chemically distinct varieties with almost no hydrocarbons in common. <it>Cr. modiglianii </it>discriminated between these two varieties. It only tolerated workers of the <it>Ca. rufifemur </it>variety it was associated with, but attacked the respective others. However, <it>Cr. modiglianii </it>did not distinguish its own <it>Ca. rufifemur </it>partner from allocolonial <it>Ca. rufifemur </it>workers of the same variety.</p> <p>Conclusion</p> <p>We conclude that there is a mutual substance transfer between <it>Cr. modiglianii </it>and <it>Ca. rufifemur</it>. <it>Ca. rufifemur </it>actively or passively acquires cuticular steroids from its <it>Cr. modiglianii </it>partner, while the latter acquires at least two cuticular hydrocarbons from <it>Ca. rufifemur</it>. The cuticular substances of both species are highly unusual regarding both substance classes and chain lengths, which may cause the apparent inability of <it>Cr. modiglianii </it>to discriminate <it>Ca. rufifemur </it>nestmates from allocolonial <it>Ca. rufifemur </it>workers of the same chemical variety.</p

In search of cues: dung beetle attraction and the significance of volatile composition of dung

Volatile organic compounds (VOCs) provide animals with multiple cues about location, type, and condition of valuable resources such as food. In particular, odour cues are often essential for the localization and discrimination of resources with patchy distribution. Dung beetles (Scarabaeoidea) rely on such scented resources to locate food for their own diet and to provision their progeny. Despite the beetles’ mostly generalist choice across dung types, several studies showed that the beetles prefer some dung types over others. Yet, the importance of VOCs for dung localization and differentiation remains unclear. In this study, we used six single chemical components (indole, skatole, phenol, butyric acid, 2-butanone, and p-cresol), two different blends of these components, and six different dung types for a detailed behavioural analysis of dung beetles. We found very little specialization of beetle species towards specific VOCs. We found that dung baits and baits with synthetic compounds attracted similar communities of dung beetles, but the visitors of synthetic baits exhibited much lower diversity and abundance. The analysis of dung scent profiles of six types of dung revealed both, unique patterns in composition and ubiquitous components such as p-cresol. However, when we used a six-component blend of synthetic compounds, it turned out to be as attractive as three of the most attractive dung types in the field. Our findings highlight the significance of key VOCs, but, moreover, that dung beetles use a blend of specific components for resource localization

Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability

The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether cytochrome c released from mitochondria induces caspase activation gradually or in an all-or-none fashion, and whether caspase activation irreversibly commits cells to apoptosis. By analyzing a quantitative kinetic model, we show that inhibition of caspase-3 (Casp3) and Casp9 by inhibitors of apoptosis (IAPs) results in an implicit positive feedback, since cleaved Casp3 augments its own activation by sequestering IAPs away from Casp9. We demonstrate that this positive feedback brings about bistability (i.e., all-or-none behaviour), and that it cooperates with Casp3-mediated feedback cleavage of Casp9 to generate irreversibility in caspase activation. Our calculations also unravel how cell-specific protein expression brings about the observed qualitative differences in caspase activation (gradual versus all-or-none and reversible versus irreversible). Finally, known regulators of the pathway are shown to efficiently shift the apoptotic threshold stimulus, suggesting that the bistable caspase cascade computes multiple inputs into an all-or-none caspase output. As cellular inhibitory proteins (e.g., IAPs) frequently inhibit consecutive intermediates in cellular signaling cascades (e.g., Casp3 and Casp9), the feedback mechanism described in this paper is likely to be a widespread principle on how cells achieve ultrasensitivity, bistability, and irreversibility

An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging

Digitization of natural history collections is a major challenge in archiving biodiversity. In recent years, several approaches have emerged, allowing either automated digitization, extended depth of field (EDOF) or multi-view imaging of insects. Here, we present DISC3D: a new digitization device for pinned insects and other small objects that combines all these aspects. A PC and a microcontroller board control the device. It features a sample holder on a motorized two-axis gimbal, allowing the specimens to be imaged from virtually any view. Ambient, mostly reflection-free illumination is ascertained by two LED-stripes circularly installed in two hemispherical white-coated domes (front-light and back-light). The device is equipped with an industrial camera and a compact macro lens, mounted on a motorized macro rail. EDOF images are calculated from an image stack using a novel calibrated scaling algorithm that meets the requirements of the pinhole camera model (a unique central perspective). The images can be used to generate a calibrated and real color texturized 3Dmodel by ‘structure from motion’ with a visibility consistent mesh generation. Such models are ideal for obtaining morphometric measurement data in 1D, 2D and 3D, thereby opening new opportunities for trait-based research in taxonomy, phylogeny, eco-physiology, and functional ecology