Computational study of the mechanism of Bcl-2 apoptotic switch

Programmed cell death - apoptosis is one of the most studied biological phenomenon of recent years. Apoptotic regulatory network contains several significant control points, including probably the most important one - Bcl--2 apoptotic switch. There are two proposed hypotheses regarding its internal working - the indirect activation and direct activation models. Since these hypotheses form extreme poles of full continuum of intermediate models, we have constructed more general model with these two models as extreme cases. By studying relationship between model parameters and steady-state response ultrasensitivity we have found optimal interaction pattern which reproduces behavior of Bcl-2 apoptotic switch. Our results show, that stimulus-response ultrasensitivity is negatively related to spontaneous activation of Bcl-2 effectors - subgroup of Bcl-2 proteins. We found that ultrasensitivity requires effector's activation, mediated by another subgroup of Bcl-2 proteins - activators. We have shown that the auto-activation of effectors forms ultrasensitivity enhancing feedback loop, only if mediated by monomers, but not by oligomers. Robustness analysis revealed that interaction pattern proposed by direct activation hypothesis is able to conserve stimulus-response dependence and preserve ultrasensitivity despite large changes of its internal parameters. This ability is strongly reduced as for the intermediate to indirect side of the models. Computer simulation of the more general model presented here suggest, that stimulus-response ultrasensitivity is an emergent property of the direct activation model, that cannot originate within model of indirect activation. Introduction of indirect-model-specific interactions does not provide better explanation of Bcl-2 functioning compared to direct model

Resilience of ecosystem processes: a new approach shows that functional redundancy of biological control services is reduced by landscape simplification

Functional redundancy can increase the resilience of ecosystem processes by providing insurance against species loss and the effects of abundance fluctuations. However, due to the difficulty of assessing individual species' contributions and the lack of a metric allowing for a quantification of redundancy within communities, few attempts have been made to estimate redundancy for individual ecosystem processes. We present a new method linking interaction metrics with metabolic theory that allows for a quantification of redundancy at the level of ecosystem processes. Using this approach, redundancy in the predation on aphids and other prey by natural enemies across a landscape heterogeneity gradient was estimated. Functional redundancy of predators was high in heterogeneous landscapes, low in homogeneous landscapes and scaled with predator specialisation. Our approach allows quantifying functional redundancy within communities and can be used to assess the role of functional redundancy across a wide variety of ecosystem processes and environmental factors

The structure and robustness of nocturnal Lepidopteran pollen-transfer networks in a Biodiversity Hotspot

1. The role of nocturnal moths within plant-pollinator networks is poorly understood but could be important in the context of declining biodiversity and the ecosystem services they provide. 2. For the first time, this study examined the role of moths as pollen vectors in the Mediterranean Biodiversity Hotspot. Light traps were used to sample moths in SW Portugal in 2010. The pollen on moth head parts was collected, identified, and counted to construct a nocturnal pollen-transfer and flower-visitor network. 3. A total of 257 moths belonging to 95 species were captured in 11 trapping sessions in 2010; 196 moths (76%) carried pollen and the total number of pollen grains counted and identified was 9064. 4. The pollen-transfer network exhibited a high degree of selectivity (H20) but low robustness when the most-to-least connected plants were made extinct in the network. The flower-visitor network (based on the incidences of interactions by individual moths), however, exhibited high linkage density and was generally more robust to simulated plant or moth extinction. 5. Including nocturnal moths in plant–pollinator networks will provide a better understanding of their robustness to species extinctions due to environmental change as well as the impacts on ecosystem structure and functioning. Nocturnal pollen–transfer networks could be developed for identifying key species for targeted conservation

Global dung webs: High trophic generalism of dung beetles along the latitudinal diversity gradient

At the global scale, species diversity is known to strongly increase towards the equator for most taxa. According to theory, a higher resource specificity of consumers facilitates the coexistence of a larger number of species and has been suggested as an explanation for the latitudinal diversity gradient. However, only few studies support the predicted increase in specialization or even showed opposite results. Surprisingly, analyses for detritivores are still missing. Therefore, we performed an analysis on the degree of trophic specialization of dung beetles. We summarized 45 studies, covering the resource preferences of a total of 994503 individuals, to calculate the dung specificity in each study region. Our results highlighted a significant (4.3-fold) increase in the diversity of beetles attracted to vertebrate dung towards the equator. However, their resource specificity was low, unrelated to diversity and revealed a highly generalistic use of dung resources that remained similar along the latitudinal gradient

Targetfinder.org: a resource for systematic discovery of transcription factor target genes

Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13 000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the ‘seed’), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis

TransFind—predicting transcriptional regulators for gene sets

The analysis of putative transcription factor binding sites in promoter regions of coregulated genes allows to infer the transcription factors that underlie observed changes in gene expression. While such analyses constitute a central component of the in-silico characterization of transcriptional regulatory networks, there is still a lack of simple-to-use web servers able to combine state-of-the-art prediction methods with phylogenetic analysis and appropriate multiple testing corrected statistics, which returns the results within a short time. Having these aims in mind we developed TransFind, which is freely available at http://transfind.sys-bio.net/

Global dung webs: high trophic generalism of dung beetles along the latitudinal diversity gradient

At the global scale, species diversity is known to strongly increase towards the equator for most taxa. According to theory, a higher resource specificity of consumers facilitates the coexistence of a larger number of species and has been suggested as an explanation for the latitudinal diversity gradient. However, only few studies support the predicted increase in specialisation or even showed opposite results. Surprisingly, analyses for detritivores are still missing. Therefore, we performed an analysis on the degree of trophic specialisation of dung beetles. We summarised 45 studies, covering the resource preferences of a total of 994503 individuals, to calculate the dung specificity in each study region. Our results highlighted a significant (4.3‐fold) increase in the diversity of beetles attracted to vertebrate dung towards the equator. However, their resource specificity was low, unrelated to diversity and revealed a highly generalistic use of dung resources that remained similar along the latitudinal gradient