Soil microbiomes drive critical functions in agro-ecosystems, including soil fertility, crop productivity and stress tolerance. Previous work demonstrates that agricultural practices influence the link between soil structure and microbiome functionality. System-level agricultural management practices can induce structural alterations, thereby changing the microbial processes at the micro-scale. These changes have large-scale consequences, such as soil erosion, reduced soil fertility and increased greenhouse gas emissions. Currently, the major soil health indicators are categorised into three groups: physical, chemical, and biological. Soil assessments focus on soil nutrients, agronomic requirements, and management recommendations. Yet soil microbiology is an important component of the soil health discussion.
With the recent developments in microbiome research, the established quantification of soil health, dominated by chemical and physical indicators, needs to dramatically evolve to include the importance of ecosystem services provided by soil microbial function as well as microbial biodiversity in this system. Together biotic and abiotic soil factors need to be integrated to inform soil-health indices which support the overarching sustainability goals. Several initiatives have already been reported, indicating a shift towards such multidimensional approaches. For instance, Neal et al. (2020) explored the interplay between soil carbon levels, soil physical properties, and the functional status of the microbiome to develop a paradigm for assessing soil health. Additionally, the Large-Scale Rotation Experiments (LSRE) provide an established experimental platform at Rothamsted which includes a matrix of agronomic approaches, initially proposed by Jowett et al. (2020), offering a nuanced approach to assess soil health indicators. Furthermore, Prout et al. (2022) devised a soil health indicator specific to the UK based on the SOC/clay ratio. To accelerate the development and adoption of these novel dimensions and concepts, a collaborative effort has been established among three leading entities: Eagle Genomics, renowned for their expertise in network graph and AI-augmented big data analytics and bioinformatics; Rothamsted Research, recognised for their proficiency in soil science and microbiome research; and CABI, experienced in the cryopreservation of environmental samples.
This unique consortium aims to combine soil chemical, textural and microbiological measurements with cutting-edge analytical network science analyses. By leveraging these advanced techniques, the consortium aims to develop a new, distinctive holistic barometer, serving as an instrument to assess soil health and provide recommendations for improvement through innovative agronomic approaches. The collaborative nature of this endeavour enhances the potential for significant progress in understanding and managing soil health, ultimately contributing to sustainable agricultural practices and environmental stewardship.
"We are doing research to improve the health of people who get a kind of chronic liver disease called Non-alcoholic fatty liver disease (NAFLD). Patients who develop NAFLD may go on to develop more serious form of liver disease called non-alcoholic steatohepatitis (NASH), which can result in liver fibrosis and liver cancer. Ultimately these patients may need a liver transplant. It is very difficult to diagnose this disease as the vast majority of liver disease is found when the disease is at later stages because it does not cause symptoms before this point. The only reliable diagnostic method is biopsy where liver tissue is obtained by inserting a needle into the patient, and the tissue is then assessed under a microscope. Liver biopsy has serious limitations: it can be painful and there is a risk of serious complications. Despite this disease becoming more common, there are no approved drugs as a treatment for NASH and there is no way to determine which patients will develop the more serious form of the disease. In medicine and research, a huge amount of data is now available. This data is often scattered in many different locations. Even within the NHS, it exists is in many different forms and locations. Data can be in the form of information about genes and genetics, medical records, information from tests or prescription data or imaging data from scans or x-rays. If we want to include information from researchers or from drug companies working on this disease, it becomes even more complicated. Our project will bring all these different forms of data together in one place which should make the task of being able to diagnose and treat this disease much easier.
We have assembled a multi-disciplinary team consisting of clinicians, data scientists, pathologists, computer scientists and drug companies to work together to determine what information they would need in order to be able to find new treatments for this disease, what we need to do to be able to tell if treatments are working, how we can diagnose this disease. When treatments become available, we should be also to determine which patients will go on to develop the more serious form of the disease."
The global life science industry spends billions of dollars annually on research innovation. This activity generates huge volumes of data e.g. clinical, omics with the potential to generate powerful innovation insights to drive business decisions, but dicovering and understanding data assets can account for up to 80 percent of the cost of an eResearch study. Eagle proposes a data enrichment and curation platform that automates this critical but currently manual process through sophisticated valuation and prioritisation algorithms that weigh data value against the curation effort scientific, operational, economic, business. Eagles Platform will increase the effectiveness and efficiency of modern eResearch.
Mathew Woodwark, Director of Bioinformatics, MedImmune, says This conversation between the scientist and the data sets is the next wave of innovation that we need deployed to our RandD teams, so we can quickly and systematically find and validate new compounds in this Precision Medicine era. Eagle is very much focused on solving this problem and we fully support their product plans.
In February 2016, Frost and Sullivan recognized Eagle for its vision and expertise in describing data value to the scientist and driving learning in the system towards true data driven drug discovery. This industry leadership will also lead to much needed transformation in the journey to personalized medicine.
In this project the performance of a bioinformatics tool kit will be evaluated within an oil seed rape breeding programme. We will test the tool kit on large data sets to identify molecular genetic markers associated with oil content. The project will help Eagle Genomics to access new markets in crop breeding.
High-throughput technologies, such as microarrays or Next Generation Sequencing (NGS), are revolutionising life science research. These technologies are already having an impact on plant and animal breeding, research into crop protection and more importantly in human health. The cost of generating these data is falling, but the ongoing cost of supplying locally the substantial compute and associated resources required for their analysis remains high. As an efficient and scalable alternative to local provision, this proposal will develop infrastructure that will harness the power of cloud computing and UK e-research expertise in scientific workflows to provide an on-line analytics service, in the first instance, for DNA analysis. It is an innovative use of existing commercial Amazon EC2 cloud computing technologies to deliver computationally intensive analyses without the financial overhead of local computational infrastructure. It is also innovative in the analysis pipelines it will offer, providing new, leading-edge scientific methods. We will operate an analysis on-demand service via a web portal. Customers will be charged for their compute time on the cloud and for the maintenance of the service. Bespoke solutions for individual clients can be developed and deployed in consultation.