Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

We have mapped sequence-directed nucleosome positioning on genomic DNA molecules using high-throughput sequencing. Chromatins, prepared by reconstitution with either chicken or frog histones, were separately digested to mononucleosomes using either micrococcal nuclease (MNase) or caspase-activated DNase (CAD). Both enzymes preferentially cleave internucleosomal (linker) DNA, although they do so by markedly different mechanisms. MNase has hitherto been very widely used to map nucleosomes, although concerns have been raised over its potential to introduce bias. Having identified the locations and quantified the strength of both the chicken or frog histone octamer binding sites on each DNA, the results obtained with the two enzymes were compared using a variety of criteria. Both enzymes displayed sequence specificity in their preferred cleavage sites, although the nature of this selectivity was distinct for the two enzymes. In addition, nucleosomes produced by CAD nuclease are 8–10 bp longer than those produced with MNase, with the CAD cleavage sites tending to be 4–5 bp further out from the nucleosomal dyad than the corresponding MNase cleavage sites. Despite these notable differences in cleavage behaviour, the two nucleases identified essentially equivalent patterns of nucleosome positioning sites on each of the DNAs tested, an observation that was independent of the histone type. These results indicate that biases in nucleosome positioning data collected using MNase are, under our conditions, not significant

Age and Age-related Diseases: Role of Inflammation Triggers and Cytokines

Cytokine dysregulation is believed to play a key role in the remodeling of the immune system at older age, with evidence pointing to an inability to fine-control systemic inflammation, which seems to be a marker of unsuccessful aging. This reshaping of cytokine expression pattern, with a progressive tendency toward a pro-inflammatory phenotype has been called “inflamm-aging.” Despite research there is no clear understanding about the causes of “inflamm-aging” that underpin most major age-related diseases, including atherosclerosis, diabetes, Alzheimer’s disease, rheumatoid arthritis, cancer, and aging itself. While inflammation is part of the normal repair response for healing, and essential in keeping us safe from bacterial and viral infections and noxious environmental agents, not all inflammation is good. When inflammation becomes prolonged and persists, it can become damaging and destructive. Several common molecular pathways have been identified that are associated with both aging and low-grade inflammation. The age-related change in redox balance, the increase in age-related senescent cells, the senescence-associated secretory phenotype (SASP) and the decline in effective autophagy that can trigger the inflammasome, suggest that it may be possible to delay age-related diseases and aging itself by suppressing pro-inflammatory molecular mechanisms or improving the timely resolution of inflammation. Conversely there may be learning from molecular or genetic pathways from long-lived cohorts who exemplify good quality aging. Here, we will discuss some of the current ideas and highlight molecular pathways that appear to contribute to the immune imbalance and the cytokine dysregulation, which is associated with “inflammageing” or parainflammation. Evidence of these findings will be drawn from research in cardiovascular disease, cancer, neurological inflammation and rheumatoid arthritis

How to measure response diversity

The insurance effect of biodiversity—that diversity enhances and stabilises aggregate ecosystem properties—is mechanistically underlain by inter- and intraspecific trait variation in organismal responses to environmental change. This variation, termed response diversity, is therefore a potentially critical determinant of ecological stability. However, response diversity has yet to be widely quantified, possibly due to difficulties in its measurement. Even when it has been measured, approaches have varied.Here, we review methods for measuring response diversity and from them distil a methodological framework for quantifying response diversity from experimental and/or observational data, which can be practically applied in lab and field settings across a range of taxa.Previous empirical studies on response diversity most commonly invoke functional response traits as proxies aimed at capturing functional responses to the environment. Our approach, which is based on environment-dependent functional responses to any biotic or abiotic environmental variable, is conceptually simple and robust to any form of environmental response, including nonlinear responses. Given its derivation from empirical data on functional responses, this approach should more directly reflect response diversity than the trait-based approach dominant in the literature.By capturing even subtle inter- or intraspecific variation in environmental responses, and environment-dependencies in response diversity, we hope this framework will motivate tests of the diversity-stability relationship from a new perspective, and provide an approach for mapping, monitoring, and conserving this critical dimension of biodiversity

How to measure response diversity

The insurance effect of biodiversity—that diversity stabilises aggregate ecosystem properties—is mechanistically underlain by inter‐ and intraspecific trait variation in organismal responses to the environment. This variation, termed response diversity, is therefore a potentially critical determinant of ecological stability. However, response diversity has yet to be widely quantified, possibly due to difficulties in its measurement. Even when it has been measured, approaches have varied. Here, we review methods for measuring response diversity and from them distil a methodological framework for quantifying response diversity from experimental and/or observational data, which can be practically applied in laboratory and field settings across a range of taxa. Previous empirical studies on response diversity most commonly invoke response traits as proxies aimed at capturing species' ecological responses to the environment. Our approach, which is based on environment‐dependent ecological responses to any biotic or abiotic environmental variable, is conceptually simple and robust to any form of environmental response, including nonlinear responses. Given its derivation from empirical data on species' ecological responses, this approach should more directly reflect response diversity than the trait‐based approach dominant in the literature. By capturing even subtle inter‐ or intraspecific variation in environmental responses, and environment dependencies in response diversity, we hope this framework will motivate tests of the diversity–stability relationship from a new perspective, and provide an approach for mapping, monitoring and conserving this critical dimension of biodiversity

Supporting the uptake of low cost resilience: Final report (FD2682)

Executive SummaryThe Defra research project FD2682 examined the technical, social and behavioural aspects of supporting low cost flood repairable measures designed to limit damage to buildings during and after flood events. Flood repairable measures (sometimes called ‘flood resilient measures’) applied to buildings are designed to limit damage, or speed up recovery where water has entered a property. They include strategies to keep water away from building elements (such as raising power sockets) and the internal use of waterproof or water resistant materials, including those capable of retaining their integrity and recovering quickly after inundation. These measures have traditionally been regarded as most useful when water exclusion approaches(measures to keep water out of the building, sometimes called ‘resistant measures’)are not practical or cost effective.The investigation took an action research approach, consulting widely and reflecting on findings on an ongoing basis. The research comprised the following stages:1. A rapid evidence assessment (REA) including a review of relevant academic and grey literature; consultation with a panel of experts; interviews with flood reinstatement and property protection professionals; and interviews with occupants of properties where flood repairable measures have been adopted.2. An assessment of the costs and benefits of selected low cost flood repairable measures, and illustrative packages of measures.3. A demonstration project to explore innovative approaches that could be used by local agencies and businesses to address some of the barriers to the use of flood repairable measures. This made use of a co-design process, via the formation of the Tewkesbury ‘Learning and Action Alliance’ (LAA).The REA concluded that (in contrast to previous perceptions of repairable measures as a last resort for properties at highest risk) low cost repairable measures are widely applicable as part of an integrated approach to limiting the residual risk to individual properties that may also include water exclusion measures. Interviews as part of theREA showed repairability to be a pragmatic approach that can be applied incrementally at various windows of opportunity with lower financial barriers to implementation than alternative strategies. The assessment of costs and benefits of selected low cost flood repairable measures, and illustrative packages of measures, confirmed their potential cost effectiveness in limiting flood damage.The REA concluded that the weight of evidence supports the effectiveness of an ever expanding list of low cost resilience measures in limiting flood damage.However, there are also major gaps in evidence, and in communication and sharing of available evidence, reducing the confidence in implementation of measures within relevant trades and professionals, as well as by owners and occupiers directly. Key areas in urgent need of additional scientific evidence include: the implications ofdebris and contaminants in floodwater; the effect of hydrodynamic and hydrostatic pressure on ‘waterproof’ materials; and durability of resilient measures afterprolonged flood exposure. However, attention should also be directed towards further understanding the real performance of flood repairable measures in a variety of types of building before, during and after flooding.The REA and demonstration project both concluded that, in order for the potential benefits of repairable measures to be realised in practice, there will need to be a shiftin the repair and reinstatement process. Improved protocols (and incentives) are required that include clarity regarding the autonomy and responsibility of differentactors within the repair process to recommend adoption of repairable measures. The inception of Flood Re offers both a challenge and an opportunity in this regard. The research finds that there could be benefits to placing the specification of negligible cost and cost neutral measures within the professional remit of surveyors and contractors on the ground. To support this, improved technical guidance and training is needed to raise levels of understanding and awareness within the industry. The surveyors’ checklist, designed within the project, was seen as a useful contribution to this requirement. Improved confidence in appropriate measures could also be fostered through provision of exemplars and factsheets.The REA and demonstration project highlighted the potential importance of other windows of opportunity (outside the recovery period) in the take up of low cost floodrepairable measures. Insurance renewal and property transfer represent opportunities to raise awareness of measures at very low cost with minimal upskillingof professionals and may provide direct triggers to action. Other building work and redecoration opportunities are harder to target in terms of awareness raising,therefore a well-informed and up-skilled local ‘property support network’ (PSN) is needed, in order to spot opportunities to support uptake on an individual basis.Evaluation of the demonstration project innovations indicated that implementation was most successful in those innovations driven by members of the LAA, or hadsignificant input from members of the local PSN. Increased awareness of low cost flood resilience measures amongst LAA members was also achieved. Therefore the LAA model was seen as a potential platform to engage relevant local propertyexperts and agencies, and to empower them to encourage property level approaches.However, the REA evidence and that from the LAA meetings together with the evaluation of the surveyor’s checklist suggest that emotional barriers to implementation of low cost resilience are important. Use of repairable measures is a difficult concept, as it requires an acceptance that water might enter the property (home or business) and changes within the living space that might feel abnormal.Interviews with practitioner experts, together with an assessment of current regulations, suggest that making small adjustments to building regulations, relevantto passive avoidance and resilience, could aid normalisation of such measures. A greater focus on design and aesthetics aspects, and clearer guidance on the ways todeal with perceived contamination is also seen as important by professionals, the PSN and in the demonstration project. Finally, a wider framing of property level flooddamage reduction, with suggested schemes including both water entry and water exclusion measures was indicated by the interviews with homeowners and professionals and discussed by the LAA as helpful in addressing emotional barriers

The only known cyclopygid–‘atheloptic’ trilobite fauna from North America: the upper Ordovician fauna of the Pyle Mountain Argillite and its palaeoenvironmental significance

The trilobite fauna of the upper Ordovician (middle Katian) Pyle Mountain Argillite comprises a mixture of abundant mesopelagic cyclopygids and other pelagic taxa and a benthic fauna dominated by trilobites lacking eyes. Such faunas were widespread in deep water environments around Gondwana and terranes derived from that continent throughout Ordovician time but this is the only known record of such a fauna from North America and thus from Laurentia. It probably reflects a major sea level rise (the ‘Linearis drowning events’) as does the development of coeval cyclopygid-dominated deep water trilobite faunas in terranes that were marginal to Laurentia and are now preserved in Ireland and Scotland. The Pyle Mountain Argillite trilobite fauna occurs with a deep water Foliomena brachiopod fauna and comprises 22 species. Pelagic trilobites (mostly cyclopygids) constitute 36% of the preserved sclerites, and 45% of the fauna is the remains of trilobites lacking eyes, including one new species, Dindymene whittingtoni sp. nov. Three species of cyclopygid are present, belonging in Cyclopyge, Symphysops and Microparia (Heterocyclopyge). Cyclopygids are widely thought to have been stratified in the water column in life and thus their taxonomic diversity reflects the relative depths of the sea-beds on which their remains accumulated. A tabulation of middle and upper Katian cyclopygid-bearing faunas from several palaeoplates and terranes arranged on the basis of increasing numbers of cyclopygid genera allows an assessment of the relative depth ranges of the associated benthic taxa. The Pyle Mountain Argillite fauna lies towards the deeper end of this depth spectrum

Targeting the LOX/hypoxia axis reverses many of the features that make pancreatic cancer deadly: inhibition of LOX abrogates metastasis and enhances drug efficacy

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer‐related mortality. Despite significant advances made in the treatment of other cancers, current chemotherapies offer little survival benefit in this disease. Pancreaticoduodenectomy offers patients the possibility of a cure, but most will die of recurrent or metastatic disease. Hence, preventing metastatic disease in these patients would be of significant benefit. Using principal component analysis (PCA), we identified a LOX/hypoxia signature associated with poor patient survival in resectable patients. We found that LOX expression is upregulated in metastatic tumors from Pdx1‐Cre KrasG12D/+ Trp53R172H/+ (KPC) mice and that inhibition of LOX in these mice suppressed metastasis. Mechanistically, LOX inhibition suppressed both migration and invasion of KPC cells. LOX inhibition also synergized with gemcitabine to kill tumors and significantly prolonged tumor‐free survival in KPC mice with early‐stage tumors. This was associated with stromal alterations, including increased vasculature and decreased fibrillar collagen, and increased infiltration of macrophages and neutrophils into tumors. Therefore, LOX inhibition is able to reverse many of the features that make PDAC inherently refractory to conventional therapies and targeting LOX could improve outcome in surgically resectable disease

Forest fire management, climate change, and the risk of catastrophic carbon losses

Approaches to management of fireprone forests are undergoing rapid change, driven by recognition that technological attempts to subdue fire at large scales (fire suppression) are ecologically and economically unsustainable. However, our current framework for intervention excludes the full scope of the fire management problem within the broader context of fire−vegetation−climate interactions. Climate change may already be causing unprecedented fire activity, and even if current fires are within the historical range of variability, models predict that current fire management problems will be compounded by more frequent extreme fire-conducive weather conditions (eg Fried et al. 2004)