The risk of extinction for birds in Great Britain

t Over the last 20 years,species priorities for bird conservation in the UK have been guided by ‘Birds of Conservation Concern’ – an in-depth assessment made possible by the top-class data available on the status of the UK’s birds. For other wildlife, priorities tend to be informed by measures of extinction risk, generated by the IUCN Regional Red List process.We carried out the first formal IUCN assessment for birds in Great Britain. Of the 241 species assessed, 100 (43%) had at least one population (breeding and/or non-breeding) that qualified as Threatened using the standard IUCN Red List criteria and categories. Of 289 separate assessments of breeding or non-breeding populations, 39% qualified as Threatened (8% Critically Endangered, 14% Endangered, 17% Vulnerable) with a further 10% classified as Near Threatened. Both Golden Oriole Oriolus oriolus and Fieldfare Turdus pilaris were assessed as being Critically Endangered (Possibly Extinct) as breeding species, in addition to seven species that are already extinct (either Extinct or Regionally Extinct). The proportion of GB birds qualifying as Threatened was high compared with birds elsewhere in Europe and other taxonomic groups in GB. We believe that, if similar data were available, levels of extinction risk would be higher for other areas/taxa than is currently estimated

Developing a national indicator of functional connectivity

Habitat loss is a significant driver of biodiversity loss, causing fragmentation into small, isolated patches of suitable land cover. This reduces the permeability of landscapes to the movement of individuals and reduces the likelihood of metapopulation persistence. Quantifying functional connectivity, the ability of a focal species to move between resource patches, is therefore essential for conservation management. There is substantial evidence supporting a technique based on ‘population synchrony’- the degree of correlation in time-series of annual population growth rates between different long-term monitoring sites, to provide a measure of functional connectivity. However, synchronised population dynamics are not only driven by the movement of individuals between sites, but also shared environmental conditions which must be accounted for. Here, we use species survey data from over four decades to investigate average levels and temporal trends in population synchrony for 58 British bird and butterfly species. We first show that population synchrony is significantly associated with synchrony in some seasonal climatic variables. Once we accounted for spatiotemporal climatic patterns, we found that synchrony in butterflies declined over time by 71% between 1985 and 2000 but increased by 64% in recent years. Synchrony in birds showed some decline between 1999 and 2005, after which there appears to being recovery, however most species (74%) show no significant overall change in synchrony. Our proposed indicator provides a ‘species-eye-view’ of functional connectivity using widely available abundance data. Developing such indicators of functional connectivity, which can be updated annually, is crucial to improve the effectiveness of land management strategies for conservation under increasing environmental change

The unusual occurrence of green algal balls of <i>Chaetomorpha linum</i> on a beach in Sydney, Australia.

In spring 2014, thousands of green algal balls were washed up at Dee Why Beach, Sydney, New South Wales, Australia. Reports of algal balls are uncommon in marine systems, and mass strandings on beaches are even more rare, sparking both public and scientific interest. We identified the algal masses as Chaetomorpha linum by using light microscopy and DNA sequencing. We characterize the size and composition of the balls from Dee Why Beach and compare them to previous records of marine algal balls. We describe the environmental conditions that could explain their appearance, given the ecophysiology of C. linum

Human dissemination of genes and microorganisms in Earth's Critical Zone

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms

Applying a genetic risk score for prostate cancer to men with lower urinary tract symptoms in primary care to predict prostate cancer diagnosis : a cohort study in the UK Biobank

Background Prostate cancer is highly heritable, with >250 common variants associated in genome-wide association studies. It commonly presents with non-specific lower urinary tract symptoms that are frequently associated with benign conditions. Methods Cohort study using UK Biobank data linked to primary care records. Participants were men with a record showing a general practice consultation for a lower urinary tract symptom. The outcome measure was prostate cancer diagnosis within 2 years of consultation. The predictor was a genetic risk score of 269 genetic variants for prostate cancer. Results A genetic risk score (GRS) is associated with prostate cancer in symptomatic men (OR per SD increase = 2.12 [1.86-2.41] P = 3.5e-30). An integrated risk model including age and GRS applied to symptomatic men predicted prostate cancer (AUC 0.768 [0.739-0.796]). Prostate cancer incidence was 8.1% (6.7-9.7) in the highest risk quintile. In the lowest quintile, prostate cancer incidence was Conclusions This study is the first to apply GRS in primary care to improve the triage of symptomatic patients. Men with the lowest genetic risk of developing prostate cancer could safely avoid invasive investigation, whilst those identified with the greatest risk could be fast-tracked for further investigation. These results show that a GRS has potential application to improve the diagnostic pathway of symptomatic patients in primary care.Peer reviewe

A comparison of common programming languages used in bioinformatics

<p>Abstract</p> <p>Background</p> <p>The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.</p> <p>Results</p> <p>Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found.</p> <p>Source code and additional information are available from <url>http://www.bioinformatics.org/benchmark/</url></p> <p>Conclusion</p> <p>This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.</p

Are Ethnic and Gender Specific Equations Needed to Derive Fat Free Mass from Bioelectrical Impedance in Children of South Asian, Black African-Caribbean and White European Origin? Results of the Assessment of Body Composition in Children Study

Background Bioelectrical impedance analysis (BIA) is a potentially valuable method for assessing lean mass and body fat levels in children from different ethnic groups. We examined the need for ethnic- and gender-specific equations for estimating fat free mass (FFM) from BIA in children from different ethnic groups and examined their effects on the assessment of ethnic differences in body fat. Methods Cross-sectional study of children aged 8–10 years in London Primary schools including 325 South Asians, 250 black African-Caribbeans and 289 white Europeans with measurements of height, weight and arm-leg impedance (Z; Bodystat 1500). Total body water was estimated from deuterium dilution and converted to FFM. Multilevel models were used to derive three types of equation {A: FFM = linear combination(height+weight+Z); B: FFM = linear combination(height2/Z); C: FFM = linear combination(height2/Z+weight)}. Results Ethnicity and gender were important predictors of FFM and improved model fit in all equations. The models of best fit were ethnicity and gender specific versions of equation A, followed by equation C; these provided accurate assessments of ethnic differences in FFM and FM. In contrast, the use of generic equations led to underestimation of both the negative South Asian-white European FFM difference and the positive black African-Caribbean-white European FFM difference (by 0.53 kg and by 0.73 kg respectively for equation A). The use of generic equations underestimated the positive South Asian-white European difference in fat mass (FM) and overestimated the positive black African-Caribbean-white European difference in FM (by 4.7% and 10.1% respectively for equation A). Consistent results were observed when the equations were applied to a large external data set. Conclusions Ethnic- and gender-specific equations for predicting FFM from BIA provide better estimates of ethnic differences in FFM and FM in children, while generic equations can misrepresent these ethnic differences

Soil biota, antimicrobial resistance and planetary health

The concept of planetary health acknowledges the links between ecosystems, biodiversity and human health and well-being. Soil, the critical component of the interconnected ecosystem, is the most biodiverse habitat on Earth, and soil microbiomes play a major role in human health and well-being through ecosystem services such as nutrient cycling, pollutant remediation and synthesis of bioactive compounds such as antimicrobials. Soil is also a natural source of antimicrobial resistance, which is often termed intrinsic resistance. However, increasing use and misuse of antimicrobials in humans and animals in recent decades has increased both the diversity and prevalence of antimicrobial resistance in soils, particularly in areas affected by human and animal wastes, such as organic manures and reclaimed wastewater, and also by air transmission. Antimicrobials and antimicrobial resistance are two sides of the sword, while antimicrobials are essential in health care; globally, antimicrobial resistance is jeopardizing the effectiveness of antimicrobial drugs, thus threatening human health. Soil is a crucial pathway through which humans are exposed to antimicrobial resistance determinants, including those harbored by human pathogens. In this review, we use the nexus of antimicrobials and antimicrobial resistance as a focus to discuss the role of soil in planetary health and illustrate the impacts of soil microbiomes on human health and well-being. This review examines the sources and dynamics of antimicrobial resistance in soils and uses the perspective of planetary health to track the movement of antimicrobial-resistance genes between environmental compartments, including soil, water, food and air

Paclitaxel resistance is associated with switch from apoptotic to autophagic cell death in MCF-7 breast cancer cells

Taxanes remain first line chemotherapy in management of metastatic breast cancer and have a key role in epithelial ovarian cancer, with increasingly common use of weekly paclitaxel dosing regimens. However, their clinical utility is limited by the development of chemoresistance. To address this, we modelled in vitro paclitaxel resistance in MCF-7 cells. We show that at clinically relevant drug doses, emerging paclitaxel resistance is associated with profound changes in cell death responses and a switch from apoptosis to autophagy as the principal mechanism of drug-induced cytotoxicity. This was characterised by a complete absence of caspase-mediated apoptotic cell death (using the pan-caspase-inhibitor Z-VAD) in paclitaxel-resistant MCF-7TaxR cells, compared with parent MCF-7 or MDA-MB-231 cell lines on paclitaxel challenge, downregulation of caspase-7, caspase-9 and BCl2-interacting mediator of cell death (BIM) expression. Silencing with small interfering RNA to BIM in MCF-7 parental cells was sufficient to confer paclitaxel resistance, inferring the significance in downregulation of this protein in contributing to the resistant phenotype of the MCF-7TaxR cell line. Conversely, there was an increased autophagic response in the MCF-7TaxR cell line with reduced phospho-mTOR and relative resistance to the mTOR inhibitors rapamycin and RAD001. In conclusion, we show for the first time that paclitaxel resistance is associated with profound changes in cell death response with deletion of multiple apoptotic factors balanced by upregulation of the autophagic pathway and collateral sensitivity to platinum