The effect of cover crops on soil quality indicators in a cereal and salad rotation.

PhD in Environment and AgrifoodCover crop (CC)s influence soil function and thus affect crop yield and ecosystem services provided by soil. CCs are a relatively new soil management practice in U.K. agriculture, but are gaining in popularity amongst farmers. However, research on the effect of CCs on soil function in the short term and how to manage CCs effectively in the U.K. is limited. Therefore, field trials investigated the effect of CCs on physical (visual evaluation of soil structure, penetration resistance, bulk density, soil shear strength and soil moisture), chemical (total organic carbon and soil available nitrogen) and biological (earthworm abundance, microbial biomass and diversity) soil quality indicators, as well as crop yield. CCs were established between wheat and forage maize. A companion crop established with the maize remained overwinter after maize harvest until lettuce establishment the following spring. CCs placed between wheat and maize only affected available soil nitrogen with limited significant effects on other soil quality indicators. The addition of a companion crop significantly improved earthworm abundance, microbial community diversity and biomarkers associated with fungi. The companion crop significantly reduced bulk density and soil shear strength at 0.05 and 0.15m, respectively as well as penetrative resistance at 0-0.03m depth. Thus, continued plant presence, achieved through the establishment of cover and companion crops in the rotation allows for the accumulation of positive effects on soil quality and function in a short period of time (20months). Additionally, a survey distributed to U.K. farmers (n = 117) provided an understanding of the use, management and challenges associated with CCs. Respondents reported that the Basic Payment Scheme supporting CC use is not suitable and could be more flexible. Additionally, it took >3 years to realise benefits to soil structure. The knowledge gained from the survey can be used to inform future research and policy so that CCs can be implemented effectively to benefit the ecosystem services provided to the farmer and wider community

Soil water and available nitrogen during cover crop growth

A field trial in Ely, Cambridgeshire was set up to investigate the soil moisture and nitrogen dynamics of a frost sensitive cover crop compared to a control of an over winter stubble. Cover crops were established in late summer following wheat harvest and a summer tillage operation. Soil and aboveground biomass sampling commenced in September 2017 was continued at 2–3 week intervals until May 2018. The results highlight the fast growth of cover crops which rapidly reduced the total oxides of nitrogen present in the soil by late autumn. During winter a gradual increase in total oxides of nitrogen is measured as the cover crop residue is mineralized. The use of the frost sensitive cover crop permitted ease of management and termination, though it is not completely reliable and termination times can vary from year to year

Do cover crops give short term benefits for soil health?

Cover crop use in the UK is increasing with establishment often before spring cereal crops. Therefore trials were implemented to assess two different cover crop mixtures for i) their ability to remediate soil compaction, ii) aid water management and iii) increase earthworm numbers. Two cover crop mixtures; frost sensitive (black oats, oil radish and mustard) and winter hardy (forage rye, oil radish and berseem clover) were compared to control plots. This replicated trial was based at G’s Growers on an organo-mineral soil with a cover crop sown between wheat harvested in August 2016 and maize sown in May 2017. The results suggest that in the short term there are small differences in soil physical characteristics. Notably at a depth of 10–20 cm there is a reduction in soil strength as measured by the penetrologger and shear vane following the frost sensitive cover crop mix. Juvenile earthworm population was significantly greater in the control treatment compared to the frost sensitive cover crop treatment. In May 2017 maize was established across all plots

The use of cover crops in the UK: a survey

A sustainable soil management survey targeting UK arable farmers was distributed via online platforms throughout the winter of 2016–2017. The main focus of the survey was the use and management of cover crops along with tillage practice and aspects of soil health. Following harvest in 2016 two-thirds of participants used a cover crop, with 56% of those using a cover crop having 3 years or less experience. There is evidence that the species selected as a cover crop is linked to soil type whilst the benefits to soil structure is related to the extent of farmer experience. Of the participants using cover crops 81% used herbicide to terminate the cover crop. Participants provided suggestions for improvements to ecological focus area rules (based on the 2016 Basic Payment Scheme) for cover and catch crops with 70% of participants suggesting they are not suitable

Big data and data repurposing – using existing data to answer new questions in vascular dementia research

Introduction: Traditional approaches to clinical research have, as yet, failed to provide effective treatments for vascular dementia (VaD). Novel approaches to collation and synthesis of data may allow for time and cost efficient hypothesis generating and testing. These approaches may have particular utility in helping us understand and treat a complex condition such as VaD. Methods: We present an overview of new uses for existing data to progress VaD research. The overview is the result of consultation with various stakeholders, focused literature review and learning from the group’s experience of successful approaches to data repurposing. In particular, we benefitted from the expert discussion and input of delegates at the 9th International Congress on Vascular Dementia (Ljubljana, 16-18th October 2015). Results: We agreed on key areas that could be of relevance to VaD research: systematic review of existing studies; individual patient level analyses of existing trials and cohorts and linking electronic health record data to other datasets. We illustrated each theme with a case-study of an existing project that has utilised this approach. Conclusions: There are many opportunities for the VaD research community to make better use of existing data. The volume of potentially available data is increasing and the opportunities for using these resources to progress the VaD research agenda are exciting. Of course, these approaches come with inherent limitations and biases, as bigger datasets are not necessarily better datasets and maintaining rigour and critical analysis will be key to optimising data use

The ataxia protein sacsin is a functional co-chaperone that protects against polyglutamine-expanded ataxin-1

An extensive protein–protein interaction network has been identified between proteins implicated in inherited ataxias. The protein sacsin, which is mutated in the early-onset neurodegenerative disease autosomal recessive spastic ataxia of Charlevoix-Saguenay, is a node in this interactome. Here, we have established the neuronal expression of sacsin and functionally characterized domains of the 4579 amino acid protein. Sacsin is most highly expressed in large neurons, particularly within brain motor systems, including cerebellar Purkinje cells. Its subcellular localization in SH-SY5Y neuroblastoma cells was predominantly cytoplasmic with a mitochondrial component. We identified a putative ubiquitin-like (UbL) domain at the N-terminus of sacsin and demonstrated an interaction with the proteasome. Furthermore, sacsin contains a predicted J-domain, the defining feature of DnaJ/Hsp40 proteins. Using a bacterial complementation assay, the sacsin J-domain was demonstrated to be functional. The presence of both UbL and J-domains in sacsin suggests that it may integrate the ubiquitin–proteasome system and Hsp70 function to a specific cellular role. The Hsp70 chaperone machinery is an important component of the cellular response towards aggregation prone mutant proteins that are associated with neurodegenerative diseases. We therefore investigated the effects of siRNA-mediated sacsin knockdown on polyglutamine-expanded ataxin-1. Importantly, SACS siRNA did not affect cell viability with GFP-ataxin-1[30Q], but enhanced the toxicity of GFP-ataxin-1[82Q], suggesting that sacsin is protective against mutant ataxin-1. Thus, sacsin is an ataxia protein and a regulator of the Hsp70 chaperone machinery that is implicated in the processing of other ataxia-linked proteins

Erratum to: Methods for evaluating medical tests and biomarkers

[This corrects the article DOI: 10.1186/s41512-016-0001-y.]

Evidence synthesis to inform model-based cost-effectiveness evaluations of diagnostic tests: a methodological systematic review of health technology assessments

Background: Evaluations of diagnostic tests are challenging because of the indirect nature of their impact on patient outcomes. Model-based health economic evaluations of tests allow different types of evidence from various sources to be incorporated and enable cost-effectiveness estimates to be made beyond the duration of available study data. To parameterize a health-economic model fully, all the ways a test impacts on patient health must be quantified, including but not limited to diagnostic test accuracy. Methods: We assessed all UK NIHR HTA reports published May 2009-July 2015. Reports were included if they evaluated a diagnostic test, included a model-based health economic evaluation and included a systematic review and meta-analysis of test accuracy. From each eligible report we extracted information on the following topics: 1) what evidence aside from test accuracy was searched for and synthesised, 2) which methods were used to synthesise test accuracy evidence and how did the results inform the economic model, 3) how/whether threshold effects were explored, 4) how the potential dependency between multiple tests in a pathway was accounted for, and 5) for evaluations of tests targeted at the primary care setting, how evidence from differing healthcare settings was incorporated. Results: The bivariate or HSROC model was implemented in 20/22 reports that met all inclusion criteria. Test accuracy data for health economic modelling was obtained from meta-analyses completely in four reports, partially in fourteen reports and not at all in four reports. Only 2/7 reports that used a quantitative test gave clear threshold recommendations. All 22 reports explored the effect of uncertainty in accuracy parameters but most of those that used multiple tests did not allow for dependence between test results. 7/22 tests were potentially suitable for primary care but the majority found limited evidence on test accuracy in primary care settings. Conclusions: The uptake of appropriate meta-analysis methods for synthesising evidence on diagnostic test accuracy in UK NIHR HTAs has improved in recent years. Future research should focus on other evidence requirements for cost-effectiveness assessment, threshold effects for quantitative tests and the impact of multiple diagnostic tests

Erratum to: Methods for evaluating medical tests and biomarkers

[This corrects the article DOI: 10.1186/s41512-016-0001-y.]

A UK survey of the use and management of cover crops

There is a growing trend in the use of cover crops in the United Kingdom, and whilst research shows there are many soil and environmental benefits, little is known about the farmer's perspective of cover cropping. A survey was designed and distributed to ask farmers about their use and management of cover crops. The online survey received 117 usable responses between January and March 2017, following distribution through social media in the United Kingdom. The survey highlighted that 66% of respondents used cover crops following harvest in 2016. Respondents observed benefits to soil structure, soil erosion control and water infiltration in addition to reductions in the use of chemical fertilisers, herbicide and fuel use. Of those not using cover crops, 90% would consider their use in the future if additional information on their use and benefits were known in a UK context. Changes to the 2016 Basic Payment Scheme guidelines for cover crops would have been welcomed by 71% of respondents using cover crops