The PRISM4 (mid-Piacenzian) paleoenvironmental reconstruction

The mid-Piacenzian is known as a period of relative warmth when compared to the present day. A comprehensive understanding of conditions during the Piacenzian serves as both a conceptual model and a source for boundary conditions and means of verification of global climate model experiments. In this paper we present the PRISM4 reconstruction, a palaeoenvironmental reconstruction of the mid-Piacenzian (~3 Ma) containing data for palaeogeography, land and sea-ice, sea-surface temperature, vegetation, soils and lakes. Our retrodicted palaeogeography takes into account glacial isostatic adjustments and changes in dynamic topography. Soils and lakes, both significant as land surface features, are introduced to the PRISM reconstruction for the first time. Sea-surface temperature and vegetation reconstructions are unchanged but now have confidence assessments. The PRISM4 reconstruction is being used as boundary condition data for the Pliocene Model Intercomparison Project, Phase 2 (PlioMIP2) experiments

Ecological risk assessments to guide decision-making: Methodology matters

Ecological risk assessment is often applied to guide the decision-making process that underpins ecosystem-based management and prioritisation of risk factors for management. Several studies have recently used ecological risk assessment approaches to identify risk factors of greatest concern, but rarely are the underlying methodological decisions discussed in terms of the effect that those decisions have on the outcome of the assessment and ultimately, how that affects prioritisation of risk factors for management. This study therefore evaluates the effect of methodological decisions involving (1) the choice and definition of risk factors, and (2) the calculation of risk scores, providing, where possible, recommendations on what should be the most appropriate methodologies. The definition of risk factors is often determined by the policy context and could result in the comparison of one broadly defined risk meta-factor (e.g. Food Production) with corresponding specific risk factors defined more narrowly (i.e. Oil and Gas production or Offshore Wind). Depending on the method to calculate risk this may result in a systematic bias prioritising any risk meta-factor. For the calculation of individual impact chain risk scores we compared weighted scores with ordinal scores, where the former allows more flexibility to represent the qualitative categories that determine risk and provided results better supported by scientific evidence. A consideration of different risk assessment applications in EBM showed there is no one-size-fits-all solution to this as these methodological decisions need to be considered in concert and the preferred methodology may depend on the context in which the risk assessment is applied. The outcome of the risk assessment should always be accompanied by an explicit consideration of these methodological issues and description of the resulting methodological choices

Predicting free-space occupancy on novel artificial structures by an invasive intertidal barnacle using a removal experiment.

Artificial structures can create novel habitat in the marine environment that has been associated with the spread of invasive species. They are often located in areas of high disturbance and can vary significantly in the area of free space provided for settlement of marine organisms. Whilst correlation between the amount of free space available and recruitment success has been shown in populations of several marine benthic organisms, there has been relatively little focus on invasive species, a group with the potential to reproduce in vast numbers and colonise habitats rapidly. Invasion success following different scales of disturbance was examined in the invasive acorn barnacle, Austrominiusmodestus, on a unique art installation located in Liverpool Bay. Population growth and recruitment success were examined by comparing recruitment rates within disturbance clearings of 4 different sizes and by contrasting population development with early recruitment rates over a 10 week period. Disturbed areas were rapidly recolonised and monocultures of A. modestus formed within 6 weeks. The size of patch created during disturbance had no effect on the rate of recruitment, while a linear relationship between recruit density and patch size was observed. Density-dependent processes mediated initial high recruitment resulting in population stability after 8-10 weeks, but densities continued to greatly exceed those reported in natural habitats. Given that artificial structures are likely to continue to proliferate in light of climate change projections, free-space is likely to become more available more frequently in the future supporting the expansion of fast-colonising species

Cytosolic thioredoxin reductase 1 is required for correct disulfide formation in the ER

Folding of proteins entering the secretory pathway in mammalian cells frequently requires the insertion of disulfide bonds. Disulfide insertion can result in covalent linkages found in the native structure as well as those that are not, so‐called non‐native disulfides. The pathways for disulfide formation are well characterized, but our understanding of how non‐native disulfides are reduced so that the correct or native disulfides can form is poor. Here, we use a novel assay to demonstrate that the reduction in non‐native disulfides requires NADPH as the ultimate electron donor, and a robust cytosolic thioredoxin system, driven by thioredoxin reductase 1 (TrxR1 or TXNRD1). Inhibition of this reductive pathway prevents the correct folding and secretion of proteins that are known to form non‐native disulfides during their folding. Hence, we have shown for the first time that mammalian cells have a pathway for transferring reducing equivalents from the cytosol to the ER, which is required to ensure correct disulfide formation in proteins entering the secretory pathway

The holistic phase model of early adult crisis

The objective of the current study was to explore the structural, temporal and experiential manifestations of crisis episodes in early adulthood, using a holistic-systemic theoretical framework. Based on an analysis of 50 interviews with individuals about a crisis episode between the ages of 25 and 35, a holistic model was developed. The model comprises four phases: (1) Locked-in, (2) Separation/Time-out, (3) Exploration and (4) Rebuilding, which in turn have characteristic features at four levels—person-in-environment, identity, motivation and affect-cognition. A crisis starts out with a commitment at work or home that has been made but is no longer desired, and this is followed by an emotionally volatile period of change as that commitment is terminated. The positive trajectory of crisis involves movement through an exploratory period towards active rebuilding of a new commitment, but ‘fast-forward’ and ‘relapse’ loops can interrupt Phases 3 and 4 and make a positive resolution of the episode less likely. The model shows conceptual links with life stage theories of emerging adulthood and early adulthood, and it extends current understandings of the transitional developmental challenges that young adults encounter

Differential expression analysis for sequence count data

*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq

Evaluation of ecosystem-based marine management strategies based on risk assessment

Abstract This study presents a comprehensive and generic framework that provides a typology for the identification and selection of consistently defined ecosystem-based management measures and allows a coherent evaluation of these measures based on their performance to achieve policy objectives. The performance is expressed in terms of their reduction of risk of an adverse impact on the marine ecosystem. This typology consists of two interlinked aspects of a measure, i.e. the “Focus” and the “Type”. The “Focus” is determined by the part of the impact chain (Driver–Pressure–State) the measure is supposed to mitigate or counteract. The “Type” represents the physical measure itself in terms of how it affects the impact chain directly; we distinguish Spatio-temporal distribution controls, Input and Output controls, Remediation and Restoration measures. The performance of these measures in terms of their reduction in risk of adverse impacts was assessed based on an explicit consideration of three time horizons: past, present and future. Application of the framework in an integrated management strategy evaluation of a suite of measures, shows that depending on the time horizon, different measures perform best. “Past” points to measures targeting persistent pressures (e.g. marine litter) from past activities. “Present” favors measures targeting a driver (e.g. fisheries) that has a high likelihood of causing adverse impacts. “Future” involves impacts that both have a high likelihood of an adverse impact, as well as a long time to return to pre-impacted condition after the implementation of appropriate management, e.g. those caused by permanent infrastructure or persistent pressures such as marine litter or specific types of pollution