The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate

Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as ‘minicircles’. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any ‘empty’ minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic

Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid.

The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.CNRS Investissements de l'avenir programme Gordon and Betty Moore Foundatio

Assessing Symbiodinium diversity in scleractinian corals via next-generation sequencing-based genotyping of the ITS2 rDNA region.

The persistence of coral reef ecosystems relies on the symbiotic relationship between scleractinian corals and intracellular, photosynthetic dinoflagellates in the genus Symbiodinium. Genetic evidence indicates that these symbionts are biologically diverse and exhibit discrete patterns of environmental and host distribution. This makes the assessment of Symbiodinium diversity critical to understanding the symbiosis ecology of corals. Here, we applied pyrosequencing to the elucidation of Symbiodinium diversity via analysis of the internal transcribed spacer 2 (ITS2) region, a multicopy genetic marker commonly used to analyse Symbiodinium diversity. Replicated data generated from isoclonal Symbiodinium cultures showed that all genomes contained numerous, yet mostly rare, ITS2 sequence variants. Pyrosequencing data were consistent with more traditional denaturing gradient gel electrophoresis (DGGE) approaches to the screening of ITS2 PCR amplifications, where the most common sequences appeared as the most intense bands. Further, we developed an operational taxonomic unit (OTU)-based pipeline for Symbiodinium ITS2 diversity typing to provisionally resolve ecologically discrete entities from intragenomic variation. A genetic distance cut-off of 0.03 collapsed intragenomic ITS2 variants of isoclonal cultures into single OTUs. When applied to the analysis of field-collected coral samples, our analyses confirm that much of the commonly observed Symbiodinium ITS2 diversity can be attributed to intragenomic variation. We conclude that by analysing Symbiodinium populations in an OTU-based framework, we can improve objectivity, comparability and simplicity when assessing ITS2 diversity in field-based studies.We would like to thank the KAUST BioScience Core Lab and S. Neelamegam for 454 library generation and sequencing. We would also like to thank Y. Sawall and A. Al-Sofyani for provision and collection of coral samples, and three anonymous reviewers for helpful comments. This project was funded by a KAUST Academic Excellence Alliance (AEA) Award to CRV and CJH, baseline research funds to CRV and a National Science Foundation grant to TCL (OCE-09287664).This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1111/mec.12869/abstract

Trace.space: a psychogeographical community project with members of an arts and health organisation

In this paper we theorise a situationist psychogeographical community group work project, conducted with members of an arts and health organization. Using creative ways to improve the mental health and well-being of individuals, we draw on the concepts of trace and spaces both to map relationships between researchers and group members and project implications. This project was driven by three aims which were: to do community group-work in order to produce contributions both inside and outside of the University; to use a psychogeographical approach to playfully critique everyday life in consumer capitalist society and finally, to consider the extent to which wider personal and political changes could be enabled. To realise these aims, we put into practice a range of architectural, critical community psychological and psychogeographical methods including photo-elicitation, dice walking and site specific investigations. We also facilitated participatory workshops via the creation of artistic and reflective maps and writing poems and stories. Reflections from all the stakeholders, conclusions and implications of this work are considered in terms of individual, group and societal changes. We argue for more psychogeographically inspired work

From Stop to Start: Tandem Gene Arrangement, Copy Number and Trans-Splicing Sites in the Dinoflagellate Amphidinium carterae

Dinoflagellate genomes present unique challenges including large size, modified DNA bases, lack of nucleosomes, and condensed chromosomes. EST sequencing has shown that many genes are found as many slightly different variants implying that many copies are present in the genome. As a preliminary survey of the genome our goal was to obtain genomic sequences for 47 genes from the dinoflagellate Amphidinium carterae. A PCR approach was used to avoid problems with large insert libraries. One primer set was oriented inward to amplify the genomic complement of the cDNA and a second primer set would amplify outward between tandem repeats of the same gene. Each gene was also tested for a spliced leader using cDNA as template. Almost all (14/15) of the highly expressed genes (i.e. those with high representation in the cDNA pool) were shown to be in tandem arrays with short intergenic spacers, and most were trans-spliced. Only two moderately expressed genes were found in tandem arrays. A polyadenylation signal was found in genomic copies containing the sequence AAAAG/C at the exact polyadenylation site and was conserved between species. Four genes were found to have a high intron density (>5 introns) while most either lacked introns, or had only one to three. Actin was selected for deeper sequencing of both genomic and cDNA copies. Two clusters of actin copies were found, separated from each other by many non-coding features such as intron size and sequence. One intron-rich gene was selected for genomic walking using inverse PCR, and was not shown to be in a tandem repeat. The first glimpse of dinoflagellate genome indicates two general categories of genes in dinoflagellates, a highly expressed tandem repeat class and an intron rich less expressed class. This combination of features appears to be unique among eukaryotes

Marx’s "Capital"in the Information Age

This article argues that a media and communication studies perspective on reading Marx’s Capital has thus far been missing, but is needed in the age of information capitalism and digital capitalism. Two of the most popular contemporary companions to Marx’s Capital, the ones by David Harvey and Michael Heinrich, present themselves as general guidebooks on how to read Marx, but are actually biased towards particular schools of Marxist thought. A contemporary reading of Marx needs to be mediated with contemporary capitalism’s structures and the political issues of the day. Media, communications and the Internet are important issues for such a reading today. It is time to see Marx not just as a critic of capitalism but also as a critic of capitalist communications

The Web will kill them all: new media, digital utopia, and political struggle in the Italian 5-Star Movement

This article examines the role of discourses about new media technology and the Web in the rise of the 5-Star Movement (Movimento 5 Stelle, or M5S) in Italy. Founded by comedian and activist Beppe Grillo and Web entrepreneur Gianrobe rto Casaleggio in 2009, this movement succeeded in becoming the second largest party at t he 2013 national elections in Italy. This article aims to discuss how elements of digital uto pia and Web-centric discourses have been inserted into the movement’s political message, and how the construction of the Web as a myth has shaped the movement’s discourse and political p ractice. The 5-Star Movement is compared and contrasted with other social and political move ments in Western countries which have displayed a similar emphasis on new media, such as the Occupy movement, the Indignados movement, and the Pirate Parties in Sweden and Germ any. By adopting and mutating cyber- utopian discourses from the so-called Californian i deology, the movement symbolically identifies itself with the Web. The traditional political esta blishment is associated with “old” media (television, radio, and the printed press), and rep resented as a “walking dead,” doomed to be superseded and buried by a Web-based direct democra cy

‘Contextualizing and Critiquing the Fantastic Prosumer: Power, Alienation and Hegemony’

Abstract The ‘prosumer’ has emerged to become a central figure in contemporary culture. Through the melding of production with consumption, both mainstream and progressive analysts conceptualize prosumption to be a liberating, empowering and, for some, a prospectively revolutionary institution. In this article, these fantastic associations are critically assessed using an approach that situates prosumption activities, including contemporary online applications often referred to as ‘cocreation’, in three social-historical contexts: capitalism as a political economy dominated by mediated abstractions; capitalist society as a hierarchical order; and alienation as a pervasive norm. Among other conclusions, we find that prosumption (particularly its Web 2.0 iterations), constitutes an emerging hegemonic institution; one that effectively frames and contains truly radical imaginations while also tapping into existing predilections for commodity-focused forms of self-realization