DNA and pacific commensal models : applications, construction, limitations, and future prospects

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with humans have contributed to understanding prehistoric migration, trade, exchange, and sometimes revealed the geographic origins of particular plants and animals. This paper presents the basic elements of a DNA-based commensal model and discusses the phylogenetic and population genetic approaches these models employ. A clear delineation of the underlying assumptions of these models and the background information required to construct them have yet to appear in the literature. This not only provides a framework with which to construct a commensal model but also highlights gaps in current knowledge. The ways in which commensal models have enriched archaeological reconstructions will be highlighted, as will their current limitations. With these limitations in mind, options will be outlined for augmenting commensal models through the application of established techniques and new technologies in order to provide the best tools for reconstructing ancient human mobility and behavior in the Pacific and beyond

Characterisation of Equine Synovial Fluid Derived Extracellular Vesicles from Young and Old Horses.

Equine osteoarthritis is a disease that impacts the welfare and performance of horses from all disciplines. Similar to its effect on human joints, osteoarthritis in horses is a painful joint condition that leads to lameness and decreased range of movement. This study compared the lubricating synovial joint fluid from eight young and seven old horses, specifically looking for differences in the extracellular vesicles (EVs). EVs are small nanoparticles present in the joint synovial fluid. EVs contain a type of ribonucleic acid (RNA) called microRNAs (miRNA), which can alter expression of genes and therefore influence the environment of a joint as some gene changes may promote or prevent osteoarthritic changes. This study was investigating whether there was a difference in the miRNAs present between old and young horses, as well as whether other characteristics of the EVs differ. Our study aimed to add to ongoing research into the role of EVs in the progression of osteoarthritis, and whether they could be used as biomarkers to diagnose joint changes. Our study did not find any significant differences in the size, concentration or miRNA expression of three miRNAs tested which suggests that their characteristics remain similar as a horse ages. However, a trend of decreased expression of these miRNAs was found, and while not statistically significant, this suggests that older horses may have lower levels of expression of certain osteoarthritis and inflammation related miRNAs. Additional work is required to confirm these findings

Epibenthic and mobile species colonisation of a geotextile artificial surf reef on the south coast of England

With increasing coastal infrastructure and use of novel materials there is a need to investigate the colonisation of assemblages associated with new structures, how these differ to natural and other artificial habitats and their potential impact on regional biodiversity. The colonisation of Europe’s first artificial surf reef (ASR) was investigated at Boscombe on the south coast of England (2009–2014) and compared with assemblages on existing natural and artificial habitats. The ASR consists of geotextile bags filled with sand located 220m offshore on a sandy sea bed at a depth of 0-5m. Successional changes in epibiota were recorded annually on differently orientated surfaces and depths using SCUBA diving and photography. Mobile faunal assemblages were sampled using Baited Remote Underwater Video (BRUV). Distinct stages in colonisation were observed, commencing with bryozoans and green algae which were replaced by red algae, hydroids and ascidians, however there were significant differences in assemblage structure with depth and orientation. The reef is being utilised by migratory, spawning and juvenile life-history stages of fish and invertebrates. The number of non-native species was larger than on natural reefs and other artificial habitats and some occupied a significant proportion of the structure. The accumulation of 180 benthic and mobile taxa, recorded to date, appears to have arisen from a locally rich and mixed pool of native and non-native species. Provided no negative invasive impacts are detected on nearby protected reefs the creation of novel yet diverse habitats may be considered a beneficial outcome

The Warped Circumstellar Disk of HD100546

We propose that the two armed spiral features seen in visible Hubble Space Telescope images of scattered light in HD100546's circumstellar disk are caused by the illumination of a warped outer disk. A tilt of 6-15 degrees from the symmetry plane can cause the observed surface brightness variations providing the disk is very twisted (highly warped) at radii greater than 200 AU where the spiral features are seen. Dust lanes are due in part to shadowing in the equatorial plane from the inner disk within a radius of 100 AU. HD100546's outer disk, if viewed edge-on, would appear similar to that of Beta Pictorus. A disk initially misaligned with a planetary system, becomes warped due to precession induced by planetesimal bodies and planets. However, the twistedness of HD100546's disk cannot be explained by precession during the lifetime of the system induced by a single Jovian mass planet within the clearing at ~13 AU. One possible explanation for the corrugated disk is that precession was induced by massive of bodies embedded in the disk at larger radius. This would require approximately a Jupiter mass of bodies well outside the central clearing at 13 AU and within the location of the spiral features or at radii approximately between 50-200 AU.Comment: submitted to Ap

The association of physical function and physical activity with all-cause mortality and adverse clinical outcomes in non-dialysis chronic kidney disease : a systematic review

Objective: People with nondialysis-dependent chronic kidney disease (CKD) and renal transplant recipients (RTRs) have compromised physical function and reduced physical activity (PA) levels. Whilst established in healthy older adults and other chronic diseases, this association remains underexplored in CKD. We aimed to review the existing research investigating poor physical function and PA with clinical outcome in nondialysis CKD. Data sources: Electronic databases (PubMed, MEDLINE, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials) were searched until December 2017 for cohort studies reporting objective or subjective measures of PA and physical function and the associations with adverse clinical outcomes and all-cause mortality in patients with nondialysis CKD stages 1–5 and RTRs. The protocol was registered on the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42016039060). Review methods: Study quality was assessed using the Newcastle-Ottawa Scale and the Agency for Healthcare and Research Quality (AHRQ) standards. Results: A total of 29 studies were included; 12 reporting on physical function and 17 on PA. Only eight studies were conducted with RTRs. The majority were classified as ‘good’ according to the AHRQ standards. Although not appropriate for meta-analysis due to variance in the outcome measures reported, a coherent pattern was seen with higher mortality rates or prevalence of adverse clinical events associated with lower PA and physical function levels, irrespective of the measurement tool used. Sources of bias included incomplete description of participant flow through the study and over reliance on self-report measures. Conclusions: In nondialysis CKD, survival rates correlate with greater PA and physical function levels. Further trials are required to investigate causality and the effectiveness of physical function and PA interventions in improving outcomes. Future work should identify standard assessment protocols for PA and physical function

Impact and amelioration of sediment pollution on coral reefs of St. Lucia, West Indies

Includes Policy and Management Brief 1: Annex A2.# Appendix 1 of the Final Technical Report of project R766

Twelve weeks of supervised exercise improves self-reported symptom burden and fatigue in chronic kidney disease : a secondary analysis of the ‘ExTra CKD’ trial

Background Chronic kidney disease (CKD) patients experience a high symptom burden including fatigue, sleep difficulties, muscle weakness and pain. These symptoms reduce levels of physical function (PF) and activity, and contribute to poor health-related quality of life (HRQoL). Despite the gathering evidence of positive physiological changes following exercise in CKD, there is limited evidence on its effect on self-reported symptom burden, fatigue, HRQoL and physical activity. Methods Thirty-six patients [mean ± SD 61.6 ± 11.8 years, 22 (61%) females, estimated glomerular filtration rate: 25.5 ± 7.8 mL/min/1.73 m2] not requiring renal replacement therapy underwent 12 weeks (3 times/week) of supervised aerobic exercise (AE), or a combination (CE) of AE plus resistance training. Outcomes included self-reported symptom burden, fatigue, HRQoL and physical activity. Results Exercise reduced the total number of symptoms reported by 17% and had favourable effects on fatigue in both groups. AE reduced the frequency of ‘itching’, ‘impotence’ and ‘shortness of breath’ symptoms, and the intrusiveness for symptoms of ‘sleep disturbance’, ‘loss of muscular strength/power’, ‘muscle spasm/stiffness’ and ‘restless legs’. The addition of resistance exercise in the CE group saw a reduction in ‘loss of muscular strength/power’. No changes were seen in subjective PF or physical activity levels. AE increased self-efficacy for physical activity. Conclusions Supervised exercise had favourable effects on symptom frequency and intrusiveness, including substantial improvements in fatigue. Although the intervention did not improve self-reported physical activity levels, AE increased patients’ self-efficacy for physical activity. These favourable changes in self-reported outcomes support the important role of exercise in CKD

The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies

The third complementary‐determining regions of the heavy‐chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β‐ribbon stalks that protrude from the surface of the antibody with a disulfide cross‐linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B‐cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen‐unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing

Barriers, motivators and facilitators of physical activity in people with dementia and their family carers in England: dyadic interviews

Introduction: Physical activity may have a number of physical and mental health benefits for people with dementia and their carers. However, there is limited evidence about factors that influence physical activity participation in these groups. This study therefore looks at the barriers, facilitators and motivators of physical activity in people with dementia, from both the perspective of the person with dementia and their carer. Method: Thirty participants (15 sets of community-dwelling people with dementia and their family carers) were recruited from the South East of England. The participants took part in semi-structured dyadic interviews about their views of physical activity. Interviews were analysed using inductive thematic analysis at an individual level and comparisons were made between the groups. Results: Common motivator themes across persons with dementia and family carers were emotional and physical wellbeing, and social connectedness. Physical health was seen as a common barrier in both groups. Physical activity in the person with dementia was encouraged and supported by the family carer. For the carer, their caring role, and limited time acted as barriers to their participation. Conclusion: Themes such as social connectedness, positive emotion and health were seen as key motivators to physical activity, which indicate that people with dementia and carers use physical activity as a means to maintain and improve their quality of life. Supporting family members to better facilitate such activities could encourage physical activity in people with dementia