Networks for systems biology: conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

‘Towards a Green New Deal on the Island of Ireland: from economic crisis to a new political economy of sustainability’

This article begins from the assumption (which may seem controversial to many) that anyone who thinks that our current economic crisis is a temporary blip until ‘normal service’ (i.e. a return to ‘business as usual’) is resumed, profoundly misunderstands the severity and significance of what’s happening to the global economy and its impacts on the future prosperity of the island of Ireland. The economic recession represents nothing short of a re-structuring of the global economy and the creation of a new dispensation between governments, markets and citizens. The full implications of the re-regulation of the market, with the state bailing out and part nationalising the financial sector in both jurisdictions on the island (as in other parts of the world) have yet to be seen, but what we are witnessing is the emergence of a new economic model. Those who think we can, or even ought to, return to the pre-2008 economic model, are gravely mistaken. The current economic downturn marks the end of the ‘neo-liberal’ model and the beginnings of the transition (an inevitable transition, this article will argue) towards a new low carbon, renewable, green and sustainable economy and society.

Metáforas Convencionais & Atribuição de Crenças

The article deals with a particular methodological problem: the interpretation of assertions containing conventional metaphors. Seeking inspiration in the cognitive sciences, seeks to provide some conceptual distinctions in order to make more efficacious the interpretative exercise of allocation dc beliefs is intrfnsceco the ethnographic work.

Measuring Inconsistency in a Network Intrusion Detection Rule Set Based on Snort

In this preliminary study, we investigate how inconsistency in a network intrusion detection rule set can be measured. To achieve this, we first examine the structure of these rules which are based on Snort and incorporate regular expression (Regex) pattern matching. We then identify primitive elements in these rules in order to translate the rules into their (equivalent) logical forms and to establish connections between them. Additional rules from background knowledge are also introduced to make the correlations among rules more explicit. We measure the degree of inconsistency in formulae of such a rule set (using the Scoring function, Shapley inconsistency values and Blame measure for prioritized knowledge) and compare the informativeness of these measures. Finally, we propose a new measure of inconsistency for prioritized knowledge which incorporates the normalized number of atoms in a language involved in inconsistency to provide a deeper inspection of inconsistent formulae. We conclude that such measures are useful for the network intrusion domain assuming that introducing expert knowledge for correlation of rules is feasible.

RNAi Effector Diversity in Nematodes

While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes.

Large-Range Movements of Neotropical Orchid Bees Observed via Radio Telemetry

Neotropical orchid bees (Euglossini) are often cited as classic examples of trapline-foragers with potentially extensive foraging ranges. If long-distance movements are habitual, rare plants in widely scattered locations may benefit from euglossine pollination services. Here we report the first successful use of micro radio telemetry to track the movement of an insect pollinator in a complex and forested environment. Our results indicate that individual male orchid bees (Exaerete frontalis) habitually use large rainforest areas (at least 42-115 ha) on a daily basis. Aerial telemetry located individuals up to 5 km away from their core areas, and bees were often stationary, for variable periods, between flights to successive localities. These data suggest a higher degree of site fidelity than what may be expected in a free living male bee, and has implications for our understanding of biological activity patterns and the evolution of forest pollinators.