Estimation of badger abundance using faecal DNA typing

1.Wildlife management and conservation programmes often require accurate information on population density, but this can be difficult to obtain, particularly when the species in question is nocturnal or cryptic. Badger populations in Britain are of intense management interest because they are a wildlife reservoir host of bovine tuberculosis (TB). Attempts to manage this infection in badgers, whether by population control or vaccination, require reliable methods of estimating population size. In addition, such estimates are also required to support research into badger ecology and TB epidemiology. Currently, the most accurate estimates of local badger population size are obtained from labour-intensive and time-consuming mark–recapture studies. 2. In recent years, DNA has been successfully extracted from the faeces of certain mammals, and used to generate a genetic profile of the defecating individual. Here we report on an application of this technology to estimate badger abundance.3.Faecal samples were collected on 10 consecutive days from every freshly deposited dropping at latrine sites close to occupied setts in three badger social groups. Badger DNA was extracted from 89% of samples, and 20 different individuals were reliably identified. The genotypes derived from the faecal samples were compared with those obtained from blood or samples from badgers live trapped at the same setts.4.The faecal genotypes from badgers with known trap histories revealed that latrines were used equally by males and females, and by badgers ranging in age from cubs(< 1 year old) to 9 years old. Individual badgers used the latrines on between one and six different nights. Rarefaction analysis produced abundance estimates that closely matched those obtained from live trapping. 5.Synthesis and applications. Systematic sampling and genetic typing of fresh faeces from badger latrines can provide data that can be used to estimate abundance accurately.This approach requires considerably less human resources than repeated live trapping and mark–recapture. The technique may be valuable for future badger research and management in relation to bovine TB, where accurate estimates of abundance at a local scale are required

Potential of Retrofitting Sustainable Urban Drainage Systems Using an Integrated Geographical Information System Remote Sensing Based Approach

Flooding is a major problem in urban areas worldwide. Methodologies that can rapidly assess the scale and identify the reasons causing these flooding events at minimal cost are urgently required. This study has used the City of Kingston-upon-Hull to evaluate the capability of an integrated remote sensing and geographical information system based approach to provide the critical information on the spatial extent of flooding and flood water volumes and overcome the limitations in current monitoring based on ground-based visual mapping and household flooding surveys. Airborne and Terrestrial LiDAR datasets were combined with digital aerial photography, flood assessment surveys, and maps of housing, infrastructure and the sewer network. The integration of these datasets provided an enhanced understanding of the sources and pathways of the flood water runoff, accurate quantification of the water volumes associated with each flooding event and the identification of the optimum locations and size of potential retrofit Sustainable Urban Drainage systems.n/

Cell and gene therapies at the forefront of innovative medical care: Implications for South Africa

The fields of cell and gene therapy are moving rapidly towards providing  innovative cures for incurable diseases. A current and highly topical  example is immunotherapies involving T-cells that express chimeric antigen receptors (CAR T-cells), which have shown promise in the treatment of leukaemia and lymphoma. These new medicines are indicative of the changes we can anticipate in the practice of medicine in the near future. Despite their promise, they pose challenges for introduction into the healthcare sector in South Africa (SA), including: (i) that they are  technologically demanding and their manufacture is resource intensive; (ii) that the regulatory system is underdeveloped and likely to be challenged by ethical, legal and social requirements that accompany these new therapies; and (iii) that costs are likely to be prohibitive, at least initially, and before economies of scale take effect. Investment should be made into finding novel and innovative ways to introduce these therapies into SA sooner rather than later to ensure that SA patients are not excluded from these exciting new opportunitie

Predicting the response of plates subjected to near-field explosions using an energy equivalent impulse

Recent experimental work by the current authors has provided highly spatially and temporally resolved measurements of the loading imparted to, and the subsequent dynamic response of, structures subjected to near-field explosive loading [1]. In this article we validate finite element models of plates subjected to near-field blast loads and perform a parametric study into the relationship between imparted load and peak and residual plate deformation. The energy equivalent impulse is derived, based on the theory of upper bound kinetic energy uptake introduced herein, which accounts for the additional energy imparted to a structure from a spatially non-uniform blast load. Whilst plate deflection is weakly correlated to total impulse, there is shown to be a strong positive correlation between deflection and energy equivalent impulse. The strength of this correlation is insensitive to loading distribution and mode of response. The method developed in this article has clear applications for the generation of fast-running engineering tools for the prediction of structural response to near-field explosions

Sustainability metrics for coal power generation in Australia

The basis of this work was to investigate the relative environmental impacts of various power generators knowing that all plants are located in totally different environments and that different receptors will experience different impacts. Based on IChemE sustainability metrics paradigm, we calculated potential environmental indicators (P-EI) that represent the environmental burden of masses of potential pollutants discharged into different receiving media. However, a P-EI may not be of significance, as it may not be expressed at all in different conditions, so to try and include some receiver significance we developed a methodology to take into account some specific environmental indicators (S-EI) that refer to the environmental attributes of a specific site. In this context, we acquired site specific environmental data related to the airsheds and water catchment areas in different locations for a limited number of environmental indicators such as human health (carcinogenic) effects, atmospheric acidification, photochemical (ozone) smog and eutrophication. The S-EI results from this particular analysis show that atmospheric acidification has highest impact value while health risks due to fly ash emissions are considered not to be as significant. This is due to the fact that many coal power plants in Australia are located in low population density air sheds. The contribution of coal power plants to photochemical (ozone) smog and eutrophication were not significant. In this study, we have considered emission related data trends to reflect technology performance (e.g., P-EI indicators) while a real sustainability metric can be associated only with the specific environmental conditions of the relevant sites (e.g., S-EI indicators)

Heterozygous mutations in HSD17B4 cause juvenile peroxisomal D-bifunctional protein deficiency

Objective: To determine the genetic cause of slowly progressive cerebellar ataxia, sensorineural deafness, and hypergonadotropic hypogonadism in 5 patients from 3 different families. Methods: The patients comprised 2 sib pairs and 1 sporadic patient. Clinical assessment included history, physical examination, and brain MRI. Linkage analysis was performed separately on the 2 sets of sib pairs using single nucleotide polymorphism microarrays, followed by analysis of the intersection of the regions. Exome sequencing was performed on 1 affected patient with variant filtering and prioritization undertaken using these intersected regions. Results: Using a combination of sequencing technologies, we identified compound heterozygous mutations in HSD17B4 in all 5 affected patients. In all 3 families, peroxisomal D-bifunctional protein (DBP) deficiency was caused by compound heterozygosity for 1 nonsense/deletion mutation and 1 missense mutation. Conclusions: We describe 5 patients with juvenile DBP deficiency from 3 different families, bringing the total number of reported patients to 14, from 8 families. This report broadens and consolidates the phenotype associated with juvenile DBP deficiency

The effects of traffic management systems on the yield and economics of crops grown in deep, shallow and zero tilled sandy loam soil over eight years.

This paper reports on a 3 × 3 factorial study to consider the effects of controlled traffic (CTF), low tyre inflation pressure (high flexion) tyres (LTP) and standard tyre inflation pressure (STP) farming systems for deep, shallow and zero tillage practices on the yield of wheat, barley, oats and field beans grown in a sandy loam soil in the UK. The main effect of tillage showed that the zero tillage option significantly (***P < 0.001) reduced crop yields in four out of the five of the first crop years, with no significant effect in years two, six and eight and exceeded the yield of the other tillage treatments in year seven. The specific costs of the alternative tillage systems were estimated, from which the cost saving for zero tillage compared to deep tillage was c. £ 60 ha−1 (US$80 ha−1), which compensated for the overall loss in yield. There were no significant differences between the crop yields from the deep and shallow tillage treatments, with shallow tillage offering savings in operational costs of c. £ 30 ha−1 (US$ 40 ha−1). Overall, the controlled traffic farming system, where 30% of the field was trafficked, produced 4% greater crop yields (*P < 0.05), worth £ 39 ha−1 (US$53 ha−1) than standard tyre inflation pressures (STP). The estimated effect of reducing the trafficked area to 15$ 100 ha−1) compared to the STP system. The beneficial effect of low inflation pressure tyres (70 kPa and 80 kPa) on crop yields, for the deep tillage treatment, was significantly greater (*P < 0.05) than those of the standard tyre pressure system (100 kPa to 150 kPa) returning an average 3.9% additional crop yield over the period of the experiment worth £ 39 ha−1 (US$ 53 ha−1)

Complete callosal agenesis, pontocerebellar hypoplasia, and axonal neuropathy due to AMPD2 loss

Objective: To determine the molecular basis of a severe neurologic disorder in a large consanguineous family with complete agenesis of the corpus callosum (ACC), pontocerebellar hypoplasia (PCH), and peripheral axonal neuropathy. Methods: Assessment included clinical evaluation, neuroimaging, and nerve conduction studies (NCSs). Linkage analysis used genotypes from 7 family members, and the exome of 3 affected siblings was sequenced. Molecular analyses used Sanger sequencing to perform segregation studies and cohort analysis and Western blot of patient-derived cells. Results: Affected family members presented with postnatal microcephaly and profound developmental delay, with early death in 3. Neuroimaging, including a fetal MRI at 30 weeks, showed complete ACC and PCH. Clinical evaluation showed areflexia, and NCSs revealed a severe axonal neuropathy in the 2 individuals available for electrophysiologic study. A novel homozygous stopgain mutation in adenosine monophosphate deaminase 2 (AMPD2) was identified within the linkage region on chromosome 1. Molecular analyses confirmed that the mutation segregated with disease and resulted in the loss of AMPD2. Subsequent screening of a cohort of 42 unrelated individuals with related imaging phenotypes did not reveal additional AMPD2 mutations. Conclusions: We describe a family with a novel stopgain mutation in AMPD2. We expand the phenotype recently described as PCH type 9 to include progressive postnatal microcephaly, complete ACC, and peripheral axonal neuropathy. Screening of additional individuals with related imaging phenotypes failed to identify mutations in AMPD2, suggesting that AMPD2 mutations are not a common cause of combined callosal and pontocerebellar defects

Constraining the budget of atmospheric carbonyl sulfide using a 3-D chemical transport model

Carbonyl sulfide (OCS) has emerged as a valuable proxy for photosynthetic uptake of carbon dioxide (CO2) and is known to be important in the formation of aerosols in the stratosphere. However, uncertainties in the global OCS budget remain large. This is mainly due to the following three flux terms: vegetation uptake, soil uptake and oceanic emissions. Bottom-up estimates do not yield a closed budget, which is thought to be due to tropical emissions of OCS that are not accounted for. Here we present a simulation of atmospheric OCS over the period 2004–2018 using the TOMCAT 3-D chemical transport model that is aimed at better constraining some terms in the OCS budget. Vegetative uptake of OCS is estimated by scaling gross primary productivity (GPP) output from the Joint UK Land Environment Simulator (JULES) using the leaf relative uptake (LRU) approach. The remaining surface budget terms are taken from available literature flux inventories and adequately scaled to bring the budget into balance. The model is compared with limb-sounding satellite observations made by the Atmospheric Chemistry Experiment – Fourier Transform Spectrometer (ACE-FTS) and surface flask measurements from 14 National Oceanic and Atmospheric Administration – Earth System Research Laboratory (NOAA-ESRL) sites worldwide. We find that calculating vegetative uptake using the LRU underestimates the surface seasonal cycle amplitude (SCA) in the Northern Hemisphere (NH) mid-latitudes and high latitudes by approximately 37 ppt (35 %). The inclusion of a large tropical source is able to balance the global budget, but further improvement to the SCA and phasing would likely require a flux inversion scheme. Compared to co-located ACE-FTS OCS profiles between 5 and 30 km, TOMCAT remains within 25 ppt (approximately 5 % of mean tropospheric concentration) of the measurements throughout the majority of this region and lies within the standard deviation of these measurements. This provides confidence in the representation of atmospheric loss and surface fluxes of OCS in the model. Atmospheric sinks account for 154 Gg S of the annual budget, which is 10 %–50 % larger than previous studies. Comparing the surface monthly anomalies from the NOAA-ESRL flask data to the model simulations shows a root-mean-square error range of 3.3–25.8 ppt. We estimate the total biosphere uptake to be 951 Gg S, which is in the range of recent inversion studies (893–1053 Gg S), but our terrestrial vegetation flux accounts for 629 Gg S of the annual budget, which is lower than other recent studies (657–756 Gg S). However, to close the budget, we compensate for this with a large annual oceanic emission term of 689 Gg S focused over the tropics, which is much larger than bottom-up estimates (285 Gg S). Hence, we agree with recent findings that missing OCS sources likely originate from the tropical region. This work shows that satellite OCS profiles offer a good constraint on atmospheric sinks of OCS through the troposphere and stratosphere and are therefore useful for helping to improve surface budget terms. This work also shows that the LRU approach is an adequate representation of the OCS vegetative uptake, but this method could be improved by various means, such as using a higher-resolution GPP product or plant-functional-type-dependent LRU. Future work will utilise TOMCAT in a formal inversion scheme to better quantify the OCS budget