Lake sedimentary DNA accurately records 20th Century introductions of exotic conifers in Scotland

Summary:Sedimentary DNA (sedDNA) has recently emerged as a new proxy for reconstructing past vegetation, but its taphonomy, source area and representation biases need better assessment. We investigated how sedDNA in recent sediments of two small Scottish lakes reflects a major vegetation change, using well-documented 20th Century plantations of exotic conifers as an experimental system. We used next-generation sequencing to barcode sedDNA retrieved from subrecent lake sediments. For comparison, pollen was analysed from the same samples. The sedDNA record contains 73 taxa (mainly genus or species), all but one of which are present in the study area. Pollen and sedDNA shared 35% of taxa, which partly reflects a difference in source area. More aquatic taxa were recorded in sedDNA, whereas taxa assumed to be of regional rather than local origin were recorded only as pollen. The chronology of the sediments and planting records are well aligned, and sedDNA of exotic conifers appears in high quantities with the establishment of plantations around the lakes. SedDNA recorded other changes in local vegetation that accompanied afforestation. There were no signs of DNA leaching in the sediments or DNA originating from pollen

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.publishersversionPeer reviewe

The Immune System in Stroke

Stroke represents an unresolved challenge for both developed and developing countries and has a huge socio-economic impact. Although considerable effort has been made to limit stroke incidence and improve outcome, strategies aimed at protecting injured neurons in the brain have all failed. This failure is likely to be due to both the incompleteness of modelling the disease and its causes in experimental research, and also the lack of understanding of how systemic mechanisms lead to an acute cerebrovascular event or contribute to outcome. Inflammation has been implicated in all forms of brain injury and it is now clear that immune mechanisms profoundly influence (and are responsible for the development of) risk and causation of stroke, and the outcome following the onset of cerebral ischemia. Until very recently, systemic inflammatory mechanisms, with respect to common comorbidities in stroke, have largely been ignored in experimental studies. The main aim is therefore to understand interactions between the immune system and brain injury in order to develop novel therapeutic approaches. Recent data from clinical and experimental research clearly show that systemic inflammatory diseases -such as atherosclerosis, obesity, diabetes or infection - similar to stress and advanced age, are associated with dysregulated immune responses which can profoundly contribute to cerebrovascular inflammation and injury in the central nervous system. In this review, we summarize recent advances in the field of inflammation and stroke, focusing on the challenges of translation between pre-clinical and clinical studies, and potential anti-inflammatory/immunomodulatory therapeutic approaches

Prolonged diet-induced obesity in mice modifies the inflammatory response and leads to worse outcome after stroke

BACKGROUND: Obesity increases the risk for ischaemic stroke and is associated with worse outcome clinically and experimentally. Most experimental studies have used genetic models of obesity. Here, a more clinically relevant model, diet-induced obesity, was used to study the impact of obesity over time on the outcome and inflammatory response after stroke. METHODS: Male C57BL/6 mice were maintained on a high-fat (60% fat) or control (12% fat) diet for 2, 3, 4 and 6 months when experimental stroke was induced by transient occlusion of the middle cerebral artery (MCAo) for either 20 (6-month diet) or 30 min (2-, 3-, 4- and 6-month diet). Ischaemic damage, blood-brain barrier (BBB) integrity, neutrophil number and chemokine expression in the brain were assessed at 24 h. Plasma chemokine levels (at 4 and 24 h) and neutrophil number in the liver (at 24 h) were measured. Physiological parameters (body weight and blood glucose) were measured in naïve control- and high-fat-fed mice at all time points and blood pressure at 3 and 6 months. Blood cell counts were also assessed in naïve 6-month control- and high-fat-fed mice. RESULTS: Mice fed a high-fat diet for 6 months had greater body weight, blood glucose and white and red blood cell count but no change in systolic blood pressure. After 4 and 6 months of high-fat feeding, and in the latter group with a 30-min (but not 20-min) occlusion of the MCA, obese mice had greater ischaemic brain damage. An increase in blood-brain barrier permeability, chemokine expression (CXCL-1 and CCL3), neutrophil number and microglia/macrophage cells was observed in the brains of 6-month high-fat-fed mice after 30-min MCAo. In response to stroke, chemokine (CXCL-1) expression in the plasma and liver was significantly different in obese mice (6-month high-fat fed), and a greater number of neutrophils were detected in the liver of control but not obese mice. CONCLUSIONS: The detrimental effects of diet-induced obesity on stroke were therefore dependent on the severity of obesity and length of ischaemic challenge. The altered inflammatory response in obese mice may play a key role in its negative impact on stroke

Last Glacial Maximum environmental conditions at Andoya, northern Norway; evidence for a northern ice-edge ecological "hotspot"

Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA (sedaDNA), pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre Æråsvatnet. A total of 23 new dates and age-depth modelling suggests the lake has been ice-free since GI2 (<23.4 cal ka BP) and possibly GS3 (<26.7 cal ka BP). Pinus and Picea sedaDNA was found in all three cores but at such low frequencies that it could not be distinguished from background contamination. LGM samples have an exceptionally high organic matter content, with isotopic values indicating that carbon and nitrogen derive from a marine source. Along with finds of bones of the little auk (Alle alle), this indicates that the lake received guano from an adjacent bird colony. SedaDNA, pollen and macrofossil assemblages were dominated by Poaceae, Brassicaceae and Papaver, but scattered occurrence of species currently restricted to the Low Arctic Tundra Zone (July temperature of 8–9 °C) such as Apiaceae (sedaDNA, 8–9 °C), and Alchemilla alpina (macrofossil, 8–9 °C) were also recorded. The review of >14.7 cal ka BP data recorded 94 vascular plant taxa, of which 38% have a northern limit in Shrub Tundra or more southern vegetation zones. This unusual assemblage likely stems from a combination of proximity to ice-free water in summer, geographical isolation linked with stochastic long-distance dispersal events, and the presence of bird-fertilized habitats. The environmental reconstruction based on all records from the area does not preclude local growth of tree species, as the local climate combined with high nutrient input may have led to periodically suitable environmental ‘hotspot’ conditions

Perceptual abnormalities in clinical high risk youth and the role of trauma, cannabis use and anxiety

Recent research suggests that perceptual abnormalities are a group of diverse experiences, which have been associated with trauma, cannabis use, and anxiety. Of the attenuated psychotic symptoms that are present in youth at clinical high risk (CHR) of psychosis, perceptual abnormalities tend to be one of the most frequently endorsed symptoms. However, very few studies have explored perceptual abnormalities and their relationships with the above environmental and affective factors in a CHR sample. Four hundred and forty-one CHR individuals who met criteria for attenuated psychotic symptom syndrome (APSS) determined by the Structured Interview for Psychosis-risk Syndromes (SIPS) were assessed on the content of their perceptual abnormalities, early traumatic experience, cannabis use and self-reported anxiety. Logistic regression analyses suggested that both simple auditory and simple visual perceptual abnormalities were more likely to be reported by CHR who had early traumatic experiences, who are current cannabis users, and who have higher levels of anxiety. Multiple regression analysis revealed that only trauma and anxiety were independent predictors of both simple auditory and simple visual perceptual abnormalities. It is possible that examining subtypes of perceptual abnormalities in CHR leads to an improved understanding of the prevalence of such symptoms

A palaeoenvironmental context for Terminal Upper Palaeolithic and Mesolithic activity in the Colne Valley: Offsite records contemporary with occupation at Three Ways Wharf, Uxbridge

Multi-proxy analyses from floodplain deposits in the Colne Valley, southern England, have provided a palaeoenvironmental context for the immediately adjacent Terminal Upper Palaeolithic and Early Mesolithic site of Three Ways Wharf. These deposits show the transition from an open cool environment to fully developed heterogeneous floodplain vegetation during the Early Mesolithic. Several distinct phases of burning are shown to have occurred that are chronologically contemporary with the local archaeological record. The floodplain itself is shown to have supported a number of rare Urwaldrelikt insect species implying human manipulation of the floodplain at this time must have been limited or episodic. By the Late Mesolithic a reed-sedge swamp had developed across much of the floodplain, within which repeated burning of the in situ vegetation took place. This indicates deliberate land management practices utilising fire, comparable with findings from other floodplain sequences in southern Britain. With similar sedimentary sequences known to exist across the Colne Valley, often closely associated with contemporary archaeology, the potential for placing the archaeological record within a spatially explicit palaeoenvironmental context is great