Experimental harvesting of fish populations drives genetically based shifts in body size and maturation

Size-selective harvesting in commercial fisheries can induce rapid changes in biological traits. While experimental and wild harvested populations often exhibit clear shifts in body size and maturation associated with fishing pressure, the relative contributions of genetic and environmental factors to these shifts remain uncertain and have been much debated. To date, observations of so-called fisheries-induced evolution (FIE) have been based solely on phenotypic measures, such as size data. Genetic data are hitherto lacking. Here, we quantify genetic versus environmental change in response to size-selective harvesting for small and large body size in guppies (Poecilia reticulata) across three generations of selection. We document for the first time significant changes at individual genetic loci, some of which have previously been associated with body size. In contrast, variation at neutral microsatellite markers was unaffected by selection, providing direct genetic evidence for rapid evolution induced by size-selective harvesting. These findings demonstrate FIE in an experimental system, with major implications for the sustainability of harvested populations, as well as impacts on size-structured communities and ecosystem processes. These findings highlight the need for scientists and managers to reconsider the capacity of harvested stocks to adapt to, and recover from, harvesting and predation. © 2013 The Ecological Society of America

Book Review: 1199: Of fiction and finance

Review of Daniel Defoe and the Bank of England: The Dark Arts of Projectors by Valerie Hamilton & Martin Parker. Zero Books, 2016, ISBN 9781782799528. Pages: 189. £11.99 (pbk

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Dynamic fluorescence microscopy of cellular uptake of intercalating model drugs by ultrasound-activated microbubbles

The combination of ultrasound and microbubbles can facilitate cellular uptake of (model) drugs via transient permeabilization of the cell membrane. By using fluorescent molecules, this process can be studied conveniently with confocal fluorescence microscopy. This study aimed to investigate the relation between cellular uptake and fluorescence intensity increase of intercalating model drugs. SYTOX Green, an intercalating fluorescent dye that displays > 500-fold fluorescence enhancement upon binding to nucleic acids, was used as a model drug for ultrasound-induced cellular uptake. SYTOX Green uptake was monitored in high spatiotemporal resolution to qualitatively assess the relation between uptake and fluorescence intensity in individual cells. In addition, the kinetics of fluorescence enhancement were studied as a function of experimental parameters, in particular, laser duty cycle (DC), SYTOX Green concentration and cell line. Ultrasound-induced intracellular SYTOX Green uptake resulted in local fluorescence enhancement, spreading throughout the cell and ultimately accumulating in the nucleus during the 9-min acquisition. The temporal evolution of SYTOX Green fluorescence was substantially influenced by laser duty cycle: continuous laser (100 % DC) induced a 6.4-fold higher photobleaching compared to pulsed laser (3.3 % DC), thus overestimating the fluorescence kinetics. A positive correlation of fluorescence kinetics and SYTOX Green concentration was found, increasing from 0.6 x 10(-3) to 2.2 x 10(-3) s(-1) for 1 and 20 mu M, respectively. Finally, C6 cells displayed a 2.4-fold higher fluorescence rate constant than FaDu cells. These data show that the temporal behavior of intracellular SYTOX Green fluorescence enhancement depends substantially on nuclear accumulation and not just on cellular uptake. In addition, it is strongly influenced by the experimental conditions, such as the laser duty cycle, SYTOX Green concentration, and cell line

The Body Dances: Carnival Dance and Organization

Building on the work of Pierre Bourdieu and Maurice Merleau-Ponty we seek to open up traditional categories of thought surrounding the relation `body-organization' and elicit a thought experiment: What happens if we move the body from the periphery to the centre? We pass the interlocking theoretical concepts of object-body/subject-body and habitus through the theoretically constructed empirical case of `carnival dance' in order to re-evaluate such key organizational concepts as knowledge and learning. In doing so, we connect with an emerging body of literature on `sensible knowledge'; knowledge that is produced and preserved within bodily practices. The investigation of habitual appropriation in carnival dance also allows us to make links between repetition and experimentation, and reflect on the mechanism through which the principles of social organization, whilst internalized and experienced as natural, are embodied so that humans are capable of spontaneously generating an infinite array of appropriate actions. This perspective on social and organizational life, where change and permanence are intricately interwoven, contrasts sharply with the dominant view in organization studies which juxtaposes change/ creativity and stability

Space of opposition: activism and deliberation in post-apartheid environmental politics

Drawing on recent political theory that examines the relationship between inclusive deliberation and oppositional activism in processes of democratisation, we develop a case study of environmental justice mobilisation in post-apartheid South Africa. We focus on the emergence of a network of social movement organisations embedded in particular localities in the city of Durban, connected into national and transnational campaigns, and centred on grievances around industrial air pollution. We analyse how the geographies of uneven industrial and urban development in Durban combine with sedimented place-based histories of activism to make particular locations spaces of democratic contention, in which the scope and operation of formal democratic procedures are challenged and transformed. We examine the range of strategic engagements adopted by social movement organisations in pursuing their objectives, looking in particular at the dynamic interaction between inclusion in deliberative forums and more adversarial, activist strategies of legal challenge and dramaturgical protest. We identify the key organisational features of groups involved in this environmental justice network, which both enable and constrain particular patterns of democratic engagement with the state and capital. We also identify a disjuncture between the interpretative frames of different actors involved in participatory policy making. These factors help to explain the difficulties faced by social movement organisations in opening up the space for legitimate nonparliamentary opposition in a political culture shaped by norms of conciliation and consensus

Sex-Specific Differences in Shoaling Affect Parasite Transmission in Guppies

Background: Individuals have to trade-off the costs and benefits of group membership during shoaling behaviour. Shoaling can increase the risk of parasite transmission, but this cost has rarely been quantified experimentally. Guppies (Poecilia reticulata) are a model system for behavioural studies, and they are commonly infected by gyrodactylid parasites, notorious fish pathogens that are directly transmitted between guppy hosts. Methodology/Principal Findings:Parasite transmission in single sex shoals of male and female guppies were observed using an experimental infection of Gyrodactylus turnbulli. Parasite transmission was affected by sex-specific differences in host behaviour, and significantly more parasites were transmitted when fish had more frequent and more prolonged contact with each other. Females shoaled significantly more than males and had a four times higher risk to contract an infection. Conclusions/Significance: Intersexual differences in host behaviours such as shoaling are driven by differences in natural and sexual selection experienced by both sexes. Here we show that the potential benefits of an increased shoaling tendency are traded off against increased risks of contracting an infectious parasite in a group-living species

The genetic organisation of prokaryotic two-component system signalling pathways

<p>Abstract</p> <p>Background</p> <p>Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and molecular mechanisms. However, there is currently little understanding of the relationships between domain architecture, gene organisation and TCS pathway structure.</p> <p>Results</p> <p>Here we classify the gene and domain organisation of TCS gene loci from 1405 prokaryotic replicons (>40,000 TCS proteins). We find that 200 bp is the most appropriate distance cut-off for defining whether two TCS genes are functionally linked. More than 90% of all TCS gene loci encode just one or two transmitter and/or receiver domains, however numerous other geometries exist, often with large numbers of encoded TCS domains. Such information provides insights into the distribution of TCS domains between genes, and within genes. As expected, the organisation of TCS genes and domains is affected by phylogeny, and plasmid-encoded TCS exhibit differences in organisation from their chromosomally-encoded counterparts.</p> <p>Conclusions</p> <p>We provide here an overview of the genomic and genetic organisation of TCS domains, as a resource for further research. We also propose novel metrics that build upon TCS gene/domain organisation data and allow comparisons between genomic complements of TCSs. In particular, '<it>percentage orphaned TCS genes</it>' (or 'Dissemination') and '<it>percentage of complex loci</it>' (or 'Sophistication') appear to be useful discriminators, and to reflect mechanistic aspects of TCS organisation not captured by existing metrics.</p