Taxonomic distinctness in the diet of two sympatric marine turtle species

Marine turtles are considered keystone consumers in tropical coastal ecosystems and their decline through overexploitation has been implicated in the deterioration of reefs and seagrass pastures in the Caribbean. In the present study, we analysed stomach contents of green (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata) harvested in the legal turtle fishery of the Turks and Caicos Islands (Caribbean) during 2008–2010. Small juveniles to adult-sized turtles were sampled. Together with data from habitat surveys, we assessed diet composition and the taxonomic distinctness (and other species diversity measures) in the diets of these sympatric marine turtle species. The diet of green turtles (n = 92) consisted of a total of 47 taxa: including three species of seagrass (present in 99% of individuals), 29 species of algae and eight sponge species. Hawksbill turtles (n = 45) consumed 73 taxa and were largely spongivorous (16 species; sponges present in 100% of individuals) but also foraged on 50 species of algae (present in 73% of individuals) and three species of seagrass. Plastics were found in trace amounts in 4% of green turtle and 9% of hawksbill turtle stomach samples. We expected to find changes in diet that might reflect ontogenetic shifts from small (oceanic-pelagic) turtles to larger (coastal-benthic) turtles. Dietary composition (abundance and biomass), however, did not change significantly with turtle size, although average taxonomic distinctness was lower in larger green turtles. There was little overlap in prey between the two turtle species, suggesting niche separation. Taxonomic distinctness routines indicated that green turtles had the most selective diet, whereas hawksbill turtles were less selective than expected when compared with the relative frequency and biomass of diet items. We discuss these findings in relation to the likely important trophic roles that these sympatric turtle species play in reef and seagrass habitats.This work was funded by Simon & Anne Notley, MCS, and Natural Environment Research Council (CASE PhD studentship to TS with MCS as CASE partners, Ref: NE/F01385X/1)

Audit of head injury management in Accident and Emergency at two hospitals: implications for NICE CT guidelines

BACKGROUND: The National Institute for Clinical Excellence (NICE) has produced guidelines on the early management of head injury. This study audits the process of the management of patients with head injury presenting at Accident and Emergency (A&E) departments and examines the impact upon resources of introducing NICE guidelines for eligibility of a CT scan. METHODS: A retrospective audit of consecutive patients of any age, presenting at A&E with a complaint of head injury during one month in two northern District General Hospitals forming part of a single NHS Trust. RESULTS: 419 patients presented with a median age of 15.5 years, and 61% were male. 58% had a Glasgow Coma Score (GCS) recorded and 33 (8%) were admitted. Only four of the ten indicators for a CT scan were routinely assessed, but data were complete for only one (age), and largely absent for another (vomiting). Using just three (incomplete) indicators showed a likely 4 fold increase in the need for a CT scan. CONCLUSIONS: The majority of patients who present with a head injury to Accident and Emergency departments are discharged home. Current assessment processes and associated data collection routines do not provide the information necessary to implement NICE guidelines for CT brain scans. The development of such clinical audit systems in a busy A&E department is likely to require considerable investment in technology and/or staff. The resource implications for radiology are likely to be substantial

Atmospheric Evolution

Earth's atmosphere has evolved as volatile species cycle between the atmosphere, ocean, biomass and the solid Earth. The geochemical, biological and astrophysical processes that control atmospheric evolution are reviewed from an "Earth Systems" perspective, with a view not only to understanding the history of Earth, but also to generalizing to other solar system planets and exoplanets.Comment: 34 pages, 3 figures, 2 tables. Accepted as a chapter in "Encyclopaedia of Geochemistry", Editor Bill White, Springer-Nature, 201

Chronic non-specific low back pain - sub-groups or a single mechanism?

Copyright 2008 Wand and O'Connell; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Low back pain is a substantial health problem and has subsequently attracted a considerable amount of research. Clinical trials evaluating the efficacy of a variety of interventions for chronic non-specific low back pain indicate limited effectiveness for most commonly applied interventions and approaches. Discussion: Many clinicians challenge the results of clinical trials as they feel that this lack of effectiveness is at odds with their clinical experience of managing patients with back pain. A common explanation for this discrepancy is the perceived heterogeneity of patients with chronic non-specific low back pain. It is felt that the effects of treatment may be diluted by the application of a single intervention to a complex, heterogeneous group with diverse treatment needs. This argument presupposes that current treatment is effective when applied to the correct patient. An alternative perspective is that the clinical trials are correct and current treatments have limited efficacy. Preoccupation with sub-grouping may stifle engagement with this view and it is important that the sub-grouping paradigm is closely examined. This paper argues that there are numerous problems with the sub-grouping approach and that it may not be an important reason for the disappointing results of clinical trials. We propose instead that current treatment may be ineffective because it has been misdirected. Recent evidence that demonstrates changes within the brain in chronic low back pain sufferers raises the possibility that persistent back pain may be a problem of cortical reorganisation and degeneration. This perspective offers interesting insights into the chronic low back pain experience and suggests alternative models of intervention. Summary: The disappointing results of clinical research are commonly explained by the failure of researchers to adequately attend to sub-grouping of the chronic non-specific low back pain population. Alternatively, current approaches may be ineffective and clinicians and researchers may need to radically rethink the nature of the problem and how it should best be managed

Crystal and melt inclusion timescales reveal the evolution of magma migration before eruption

Volatile element concentrations measured in melt inclusions are a key tool used to understand magma migration and degassing, although their original values may be affected by different re-equilibration processes. Additionally, the inclusion-bearing crystals can have a wide range of origins and ages, further complicating the interpretation of magmatic processes. To clarify some of these issues, here we combined olivine diffusion chronometry and melt inclusion data from the 2008 eruption of Llaima volcano (Chile). We found that magma intrusion occurred about 4 years before the eruption at a minimum depth of approximately 8 km. Magma migration and reaction became shallower with time, and about 6 months before the eruption magma reached 3–4 km depth. This can be linked to reported seismicity and ash emissions. Although some ambiguities of interpretation still remain, crystal zoning and melt inclusion studies allow a more complete understanding of magma ascent, degassing, and volcano monitoring data.NRF (Natl Research Foundation, S’pore)MOE (Min. of Education, S’pore)Published versio

Metabolic Factors Limiting Performance in Marathon Runners

Each year in the past three decades has seen hundreds of thousands of runners register to run a major marathon. Of those who attempt to race over the marathon distance of 26 miles and 385 yards (42.195 kilometers), more than two-fifths experience severe and performance-limiting depletion of physiologic carbohydrate reserves (a phenomenon known as ‘hitting the wall’), and thousands drop out before reaching the finish lines (approximately 1–2% of those who start). Analyses of endurance physiology have often either used coarse approximations to suggest that human glycogen reserves are insufficient to fuel a marathon (making ‘hitting the wall’ seem inevitable), or implied that maximal glycogen loading is required in order to complete a marathon without ‘hitting the wall.’ The present computational study demonstrates that the energetic constraints on endurance runners are more subtle, and depend on several physiologic variables including the muscle mass distribution, liver and muscle glycogen densities, and running speed (exercise intensity as a fraction of aerobic capacity) of individual runners, in personalized but nevertheless quantifiable and predictable ways. The analytic approach presented here is used to estimate the distance at which runners will exhaust their glycogen stores as a function of running intensity. In so doing it also provides a basis for guidelines ensuring the safety and optimizing the performance of endurance runners, both by setting personally appropriate paces and by prescribing midrace fueling requirements for avoiding ‘the wall.’ The present analysis also sheds physiologically principled light on important standards in marathon running that until now have remained empirically defined: The qualifying times for the Boston Marathon

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde