Andrew Turner

Further evidence for the development of photic-zone euxinic conditions during Mesozoic oceanic anoxic events

Periods in Earth history characterized by extensive organic carbon deposition, so-called oceanic anoxic events (OAEs), are the subject of considerable scrutiny. Insight into the extent of anoxic conditions in the water column has been provided by the reported occurrence of derivatives of isorenieratene, a carotenoid found only in green sulphur bacteria and thus indicative of photic-zone euxinia (i.e. a water column containing free H2S), in North Atlantic deep-sea sediments deposited during the Cenomanian–Turonian boundary OAE2 (Bonarelli Event). In this study, we have used the distributions of chlorophyll and bacteriochlorophyll degradation products, maleimides (1-H-pyrrole-2,5-diones) and high molecular weight porphyrins, to examine further the Cenomanian–Turonian boundary OAE2 as well as other OAEs of the early Toarcian (Posidonienschiefer Event) and early Aptian (Selli Event). In particular, methyl isobutyl (Me,i-Bu) maleimide, on structural grounds, appears to be diagnostic of green sulphur bacteria. This compound occurs in five of seven examined marls that record the early Toarcian OAE (Marche–Umbria, Italy), further expanding the geographical range of Toarcian sediments where evidence for photic-zone euxinic conditions has been found. Me,i-Bu maleimide occurs in three of six black shales spanning the Livello Selli (Marche–Umbria, Italy), the type locality for the Aptian OAE1a, providing the first evidence for photic-zone euxinic conditions during this event. With respect to the Cenomanian–Turonian OAE, maleimide evidence for photic-zone euxinic conditions was found in all the North Atlantic sites investigated, including those characterized by relatively organic-lean sediments, several Tethyan sites and one site off western Australia. These data indicate that euxinic conditions were common in the water column during Mesozoic oceanic anoxic events.

Capitalizing hope: the commercial development of umbilical cord blood stem cell banking

The creation of commercial cord blood banks rests on the promise of stem cell based regenerative medicine and marks the capitalization of human tissues within a future-oriented “regime of hope”. This paper will present data from a survey of the international cord blood banking industry and will explore: (a) the way firms seek to commercialize cord blood as a new set of commodities; (b) the expectations and moral economy that are being constructed around this technology; and (c) how firms are acting as mediators of hope in what might be called a “promissory bioeconomy”.

DataSHIELD: taking the analysis to the data, not the data to the analysis

Background: Research in modern biomedicine and social science requires sample sizes so large that they can often only be achieved through a pooled co-analysis of data from several studies. But the pooling of information from individuals in a central database that may be queried by researchers raises important ethico-legal questions and can be controversial. In the UK this has been highlighted by recent debate and controversy relating to the UK’s proposed ‘care.data’ initiative, and these issues reflect important societal and professional concerns about privacy, confidentiality and intellectual property. DataSHIELD provides a novel technological solution that can circumvent some of the most basic challenges in facilitating the access of researchers and other healthcare professionals to individual-level data. Methods: Commands are sent from a central analysis computer (AC) to several data computers (DCs) storing the data to be co-analysed. The data sets are analysed simultaneously but in parallel. The separate parallelized analyses are linked by non-disclosive summary statistics and commands transmitted back and forth between the DCs and the AC. This paper describes the technical implementation of DataSHIELD using a modified R statistical environment linked to an Opal database deployed behind the computer firewall of each DC. Analysis is controlled through a standard R environment at the AC. Results: Based on this Opal/R implementation, DataSHIELD is currently used by the Healthy Obese Project and the Environmental Core Project (BioSHaRE-EU) for the federated analysis of 10 data sets across eight European countries, and this illustrates the opportunities and challenges presented by the DataSHIELD approach. Conclusions: DataSHIELD facilitates important research in settings where: (i) a co-analysis of individual-level data from several studies is scientifically necessary but governance restrictions prohibit the release or sharing of some of the required data, and/or render data access unacceptably slow; (ii) a research group (e.g. in a developing nation) is particularly vulnerable to loss of intellectual property—the researchers want to fully share the information held in their data with national and international collaborators, but do not wish to hand over the physical data themselves; and (iii) a data set is to be included in an individual-level co-analysis but the physical size of the data precludes direct transfer to a new site for analysis.

Isolation and characterisation of a melon cDNA clone encoding phytoene synthase.

A cDNA clone (MEL5), encoding a protein homologous to phytoene synthase (PSY), has been isolated from a climacteric melon fruit cDNA library, using the tomato cDNA clone TOM5 [34] as a heterologous probe. MEL5 hybridised to a transcript of 1.65 kb which suggested that the 1.36 kb clone, isolated originally, was not full-length. The missing 5′ end was isolated by a reverse transcriptase-polymerase chain reaction (RT-PCR)-based method. This enabled the full sequence of the protein to be deduced and the cleavage site of the transit peptide for chromoplast import to be predicted. Northern analysis of RNA extracted from fruit samples of different ripening stages as well as from roots, leaves and flower petals was used to examine the expression pattern of the corresponding mRNA. The transcript corresponding to MEL5 is present at low quantities in unripe (green) fruit, reaches its highest levels when the fruit turns from green to orange and persists at lower levels during later ripening stages. A similar transcript was also detected in flower petals and in trace amounts in leaves and roots. Genomic Southern analysis indicates that the clone is homologous to a low-copy-number gene family. Sequence analysis showed a high degree of conservation among plant PSYs.

Fracking on YouTube: Exploring Risks, Benefits and Human Values

Shale gas is a novel source of fossil fuel which is extracted by induced hydraulic fracturing, or “fracking.” This article examines the the socio-political dimension of fracking as manifested in the UK press at three key temporal points in the debate on the practice. Three newspaper corpora were analysed qualitatively using Thematic Analysis and Social Representations Theory. Three overarching themes are discussed: “April-May 2011: From Optimism to Scepticism”; “November 2011: (De-)Constructing and Re-Constructing Risk and Danger; “April 2012: Consolidating Social Representations of Fracking.” In this article, we examine the emergence and inter-relations between competing social representations, discuss the dynamics of threat positioning and show how threat can be re-construed in order to serve particular socio-political ends in the debate on fracking.

Yeast 2 µm plasmid copy number is elevated by a mutation in the nuclear gene UBC4

The copy number of the Saccharomyces cerevisiae endogenous 2 µm plasmid is under strict control to ensure efficient propagation to the daughter cell without significantly reducing the growth rate of the mother or the daughter cell. A recessive mutation has been identified that resulted in an elevated but stable 2 µm plasmid copy number, which could be complemented by a genomic DNA clone containing the UBC4 gene, encoding an E2 ubiquitin‐conjugating enzyme. A ubc4::URA3 deletion resulted in the same elevated 2 µm plasmid copy number. An analysis of the endogenous 2 µm transcripts revealed that the steady‐state abundance of REP1, REP2, FLP and RAF were all increased 4–5‐fold in the mutant. Analysis of the mutant ubc4 allele identified a single base pair mutation within the UBC4 coding region, which would generate a glutamic acid to lysine amino acid substitution within a region of conserved tertiary structure located within the first α‐helix of Ubc4p. These investigations represent the first molecular characterization of a mutation within a Saccharomyces cerevisiae nuclear gene shown to affect 2 µm steady‐state plasmid copy number and implicate the ubiquitin‐dependent proteolytic pathway in host control of 2 µm plasmid copy number. Copyright

Grain-size dynamics beneath mid-ocean ridges: Implications for permeability and melt extraction.

Grain size is an important control on mantle viscosity and permeability, but is difficult or impossible to measure in situ. We construct a two-dimensional, single phase model for the steady state mean grain size beneath a mid-ocean ridge. The mantle rheology is modeled as a composite of diffusion creep, dislocation creep, dislocation accommodated grain boundary sliding, and a plastic stress limiter. The mean grain size is calculated by the paleowattmeter relationship of Austin and Evans (2007). We investigate the sensitivity of our model to global variations in grain growth exponent, potential temperature, spreading-rate, and mantle hydration. We interpret the mean grain-size field in terms of its permeability to melt transport. The permeability structure due to mean grain size may be approximated as a high permeability region beneath a low permeability region. The transition between high and low permeability regions occurs across a boundary that is steeply inclined toward the ridge axis. We hypothesize that such a permeability structure generated from the variability of the mean grain size may focus melt toward the ridge axis, analogous to Sparks and Parmentier (1991)-type focusing. This focusing may, in turn, constrain the region where significant melt fractions are observed by seismic or magnetotelluric surveys. This interpretation of melt focusing via the grain-size permeability structure is consistent with MT observation of the asthenosphere beneath the East Pacific Rise. Key Points: The grain-size field beneath MORs can vary over orders of magnitude The grain-size field affects the rheology and permeability of the asthenosphere The grain-size field may focus melt toward the ridge axis

Isolation of a Ripening and Wound-Induced cDNA from Cucumis Melo L.With Homology to the Ethylene Forming Enzyme

Ethylene is an important plant growth regulator which is synthesized naturally during climacteric fruit ripening [Yang and Hoffmann, 1984]. The ability to extend the storage life and prevent spoilage of climacteric fruit by inhibiting ethylene biosynthesis has already been demonstrated in transgenic tomato plants expressing antisense EFE [Hamilton et al., 1990] and ACC synthase [Oehler et al., 1991] genes. In order to try and extend the storage life of melon fruit by inhibiting ethylene synthesis our initial aim was to isolate an EFE clone from a climacteric melon fruit cDNA library, using the heterologous pTOM13 (EFE) probe from tomato.

DataSHIELD: An Ethically Robust Solution to Multiple-Site Individual-Level Data Analysis

Background: DataSHIELD (Data Aggregation Through Anonymous Summary-statistics from Harmonised Individual levEL Databases) has been proposed to facilitate the co-analysis of individual-level data from multiple studies without physically sharing the data. In a previous paper, we investigated whether DataSHIELD could protect participant confidentiality in accordance with UK law. In this follow-up paper, we investigate whether DataSHIELD addresses a broader range of ethics-related data-sharing concerns. Methods: Ethics-related data-sharing concerns of Institutional Review Boards, ethics experts, international research consortia and research participants were identified through a literature search and systematically examined at a multidisciplinary workshop to determine whether DataSHIELD proposes mechanisms which can address these concerns. Results: DataSHIELD addresses several ethics-related data-sharing concerns related to privacy, confidentiality, and the protection of the research participants rights while sharing data and after the data have been shared. The data remain entirely under the direct management of the study that collected them. Data processing commands are strictly supervised, and the data are queried in a protected environment. Issues related to the return of individual research results when data are shared are eliminated; the responsibility for return remains at the study of origin. Conclusion: DataSHIELD can provide an innovative and robust solution for addressing commonly encountered ethics-related data-sharing concerns.

The ECOUTER methodology for stakeholder engagement in translational research

BackgroundBecause no single person or group holds knowledge about all aspects of research, mechanisms are needed to support knowledge exchange and engagement. Expertise in the research setting necessarily includes scientific and methodological expertise, but also expertise gained through the experience of participating in research and/or being a recipient of research outcomes (as a patient or member of the public). Engagement is, by its nature, reciprocal and relational: the process of engaging research participants, patients, citizens and others (the many ‘publics’ of engagement) brings them closer to the research but also brings the research closer to them. When translating research into practice, engaging the public and other stakeholders is explicitly intended to make the outcomes of translation relevant to its constituency of users.MethodsIn practice, engagement faces numerous challenges and is often time-consuming, expensive and ‘thorny’ work. We explore the epistemic and ontological considerations and implications of four common critiques of engagement methodologies that contest: representativeness, communication and articulation, impacts and outcome, and democracy. The ECOUTER (Employing COnceptUal schema for policy and Translation Engagement in Research) methodology addresses problems of representation and epistemic foundationalism using a methodology that asks, “How could it be otherwise?” ECOUTER affords the possibility of engagement where spatial and temporal constraints are present, relying on saturation as a method of ‘keeping open’ the possible considerations that might emerge and including reflexive use of qualitative analytic methods.ResultsThis paper describes the ECOUTER process, focusing on one worked example and detailing lessons learned from four other pilots. ECOUTER uses mind-mapping techniques to ‘open up’ engagement, iteratively and organically. ECOUTER aims to balance the breadth, accessibility and user-determination of the scope of engagement. An ECOUTER exercise comprises four stages: (1) engagement and knowledge exchange; (2) analysis of mindmap contributions; (3) development of a conceptual schema (i.e. a map of concepts and their relationship); and (4) feedback, refinement and development of recommendations.ConclusionECOUTER refuses fixed truths but also refuses a fixed nature. Its promise lies in its flexibility, adaptability and openness. ECOUTER will be formed and re-formed by the needs and creativity of those who use it.