A role for SUMO modification in transcriptional repression and activation

Since the discovery of the SUMO (small ubiquitin-like modifier) family of proteins just over a decade ago, a plethora of substrates have been uncovered including many regulators of transcription. Conjugation of SUMO to target proteins has generally been considered as a repressive modification. However, there are now a growing number of examples where sumoylation has been shown to activate transcription. Here we discuss whether there is something intrinsically repressive about sumoylation, or if the outcome of this modification in the context of transcription will prove to be largely substrate-dependent. We highlight some of the technical challenges that will be faced by attempting to answer this question

Herbivore effect traits and their impact on plant community biomass: an experimental test using grasshoppers

1. Using trait-based approaches to study trophic interactions may represent one of the most promising approaches to evaluate the impact of trophic interactions on ecosystem functioning. To achieve this goal, it is necessary to clearly identify which traits determine the impact of one trophic level on another.2. Using functionally contrasting grasshopper species, we tested the ability of multiple traits (morphological, chemical and biomechanical) to predict herbivore impact on the biomass of a diverse plant community. We set up a cage experiment in an old species rich grassland field and evaluated how multiple candidate grasshopper effect traits mediated herbivore impact on plant biomass.3. Grasshoppers had different impact on plant community biomass (consuming up to 60 % of plant community biomass). Grasshopper impact was positively correlated with their incisive strength while body size or grasshopper C:N ratio exhibited low predictive ability. Importantly, the strong relationship between the incisive strength and the impact was mediated by the grasshopper feeding niche, which was well predicted in our study by two simple plant traits (leaf dry matter content, leaf C:N ratio). Feeding niche differences between grasshoppers were explained by differences in incisive strength, highlighting the fundamental linkage between grasshopper effect traits and their niche.4. Our study contributes to the development of the trait-based approach in the study of trophic interactions by providing a first experimental test of the relationship between herbivore effect traits, their impact on plant community biomass, and in a larger extent on ecosystem functioning. By comparing the relative importance of multiple interacting grasshopper traits, our study showed that incisive strength was a key effect trait which determined grasshopper feeding niche and its relative impact on plant community biomass

Food Quality Affects Secondary Consumers Even at Low Quantities: An Experimental Test with Larval European Lobster

The issues of food quality and food quantity are crucial for trophic interactions. Although most research has focussed on the primary producer – herbivore link, recent studies have shown that quality effects at the bottom of the food web propagate to higher trophic levels. Negative effects of poor food quality have almost exclusively been demonstrated at higher food quantities. Whether these negative effects have the same impact at low food availability in situations where the majority if not all of the resources are channelled into routine metabolism, is under debate. In this study a tri-trophic food chain was designed, consisting of the algae Rhodomonas salina, the copepod Acartia tonsa and freshly hatched larvae of the European lobster Homarus gammarus. The lobster larvae were presented with food of two different qualities (C∶P ratios) and four different quantities to investigate the combined effects of food quality and quantity. Our results show that the quality of food has an impact on the condition of lobster larvae even at very low food quantities. Food with a lower C∶P content resulted in higher condition of the lobster larvae regardless of the quantity of food. These interacting effects of food quality and food quantity can have far reaching consequences for ecosystem productivity

Passive and active suicidal ideation in a population-based sample of older adults: Associations with polygenic risk scores of relevance for suicidal behavior

Introduction: There are few studies investigating genetic factors related to suicidal ideation or behavior in older adult populations. Our aim was to test associations between passive and active suicidal ideation and polygenic risk scores (PRSs) for suicidality and other traits of relevance for suicidality in old age (i.e. depression, neuroticism, loneliness, Alzheimer’s disease, cognitive performance, educational attainment, and several specified vascular diseases) in a population-based sample aged 70 years and older. / Methods: Participants in the prospective H70 study in Gothenburg, Sweden, took part in a psychiatric examination that included the Paykel questions on active and passive suicidal ideation. Genotyping was performed with the Neurochip (Illumina). After quality control of the genetic data the sample included 3467 participants. PRSs for suicidality and other related traits were calculated based on summary statistics from recent GWASs of relevance. Exclusion of persons with dementia or incomplete data on suicidal ideation yielded 3019 participants, age range 70–101 years. Associations between past year suicidal ideation (any level) and selected PRSs were analysed using general estimation equation (GEE) models, adjusted for sex and age. / Results: We observed associations between passive/active suicidal ideation and PRSs for depression (three versions), neuroticism, and general cognitive performance. After excluding individuals with current major depressive disorder (MDD), similar associations were seen with PRS for neuroticism, general cognitive performance and two PRSs for depression. No associations were found between suicidal ideation and PRSs for suicidality, loneliness, Alzheimer’s disease, educational attainment, or vascular disease. / Discussion: Our results could indicate which types of genetic susceptibility that are of importance for suicidality in old age, and these findings can help to shed light on potential mechanisms that may be involved in passive and active suicidal ideation in late-life, also in those with no current MDD. However, due to the limited sample size, the results need to be interpreted with caution until replicated in larger samples

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-depleted Murine Embryonic Stem Cells

Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly understood, but recent results point to a key role for epigenetic mechanisms. In this study, we focus on quantifying the impact of histone 3 acetylation (H3K9,14ac) on gene expression in murine embryonic stem cells. We analyze genome-wide histone acetylation patterns and gene expression profiles measured over the first five days of cell differentiation triggered by silencing Nanog, a key transcription factor in ESC regulation. We explore the temporal and spatial dynamics of histone acetylation data and its correlation with gene expression using supervised and unsupervised statistical models. On a genome-wide scale, changes in acetylation are significantly correlated to changes in mRNA expression and, surprisingly, this coherence increases over time. We quantify the predictive power of histone acetylation for gene expression changes in a balanced cross-validation procedure. In an in-depth study we focus on genes central to the regulatory network of Mouse ESC, including those identified in a recent genome-wide RNAi screen and in the PluriNet, a computationally derived stem cell signature. We find that compared to the rest of the genome, ESC-specific genes show significantly more acetylation signal and a much stronger decrease in acetylation over time, which is often not reflected in an concordant expression change. These results shed light on the complexity of the relationship between histone acetylation and gene expression and are a step forward to dissect the multilayer regulatory mechanisms that determine stem cell fate.Comment: accepted at PLoS Computational Biolog

Overcoming Public Resistance to Carbon Taxes

Carbon taxes represent a cost-effective way to steer the economy toward a greener future. In the real world, their application has however been limited. In this paper, we address one of the main obstacles to carbon taxes: public opposition. We identify drivers of and barriers to public support, and, under the form of stylized facts, provide general lessons on the acceptability of carbon taxes. We derive our lessons from a growing literature, as well as from a combination of policy “failures” and “successes.” Based on our stylized facts, we formulate a set of suggestions concerning the design of carbon taxes. We consider the use of trial periods, tax escalators, environmental earmarking, lump-sum transfers, tax rebates, and advanced communication strategies, among others. This paper contributes to the policy debate about carbon taxes, hopefully leading to more success stories and fewer policy failures

Reconceptualising adaptation to climate change as part of pathways of change and response

The need to adapt to climate change is now widely recognised as evidence of its impacts on social and natural systems grows and greenhouse gas emissions continue unabated. Yet efforts to adapt to climate change, as reported in the literature over the last decade and in selected case studies, have not led to substantial rates of implementation of adaptation actions despite substantial investments in adaptation science. Moreover, implemented actions have been mostly incremental and focused on proximate causes; there are far fewer reports of more systemic or transformative actions. We found that the nature and effectiveness of responses was strongly influenced by framing. Recent decision-oriented approaches that aim to overcome this situation are framed within a "pathways" metaphor to emphasise the need for robust decision making within adaptive processes in the face of uncertainty and inter-temporal complexity. However, to date, such "adaptation pathways" approaches have mostly focused on contexts with clearly identified decision-makers and unambiguous goals; as a result, they generally assume prevailing governance regimes are conducive for adaptation and hence constrain responses to proximate causes of vulnerability. In this paper, we explore a broader conceptualisation of "adaptation pathways" that draws on 'pathways thinking' in the sustainable development domain to consider the implications of path dependency, interactions between adaptation plans, vested interests and global change, and situations where values, interests, or institutions constrain societal responses to change. This re-conceptualisation of adaptation pathways aims to inform decision makers about integrating incremental actions on proximate causes with the transformative aspects of societal change. Case studies illustrate what this might entail. The paper ends with a call for further exploration of theory, methods and procedures to operationalise this broader conceptualisation of adaptation

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Capability in research on cognition and well-being in ageing and retirement

In this chapter, we outline our thoughts on capability in relation to previous and ongoing research projects conducted by the Adult Development and Ageing (ADA-Gero) Research Group located at the Department of Psychology, University of Gothenburg, Sweden. More specifically, we relate our research on cognitive ageing and subjective well-being to the overarching capability framework implemented as a theoretical platform in the AgeCap research consortium