Why dried blood spots are an ideal tool for CYP1A2 phenotyping

Background and Objective: Dried blood spot (DBS) sampling has gained wide interest in bioanalysis during the last decade and has already been successfully applied in pharmacokinetic and phenotyping studies. However, all of the available phenotyping studies used small datasets and did not include a systematic evaluation of DBS-specific parameters. The latter is important since several of these factors still challenge the breakthrough of DBS in routine practice. In this study, caffeine and paraxanthine are determined in capillary DBS, venous DBS, whole blood and plasma for cytochrome P450 (CYP) 1A2 phenotyping. The aim of this study was to explore the usefulness of DBS as a tool for CYP1A2 phenotyping. Methods: A CYP1A2 phenotyping study was conducted in 73 healthy volunteers who received a 150 mg oral dose of caffeine. Six hours post-administration, caffeine and paraxanthine concentrations and paraxanthine:caffeine molar concentration ratios, i.e., the actual CYP1A2 phenotyping indices, were determined in capillary DBS (obtained by non-volumetric application, direct from the fingertip), venous DBS, whole blood, and plasma. Furthermore, the impact of DBS-specific parameters, including hematocrit, volume spotted, and punch location, was evaluated. Results: Concentrations of caffeine and paraxanthine in capillary DBS were, respectively, on average 12.7 and 13.8 % lower than those in venous DBS and 31.5 and 33.1 % lower than those in plasma. While these differences were statistically significant (p = 0.053). This ratio also alleviated the impact of hematocrit and volume spotted. Conclusions: Using the largest DBS-based phenotyping study to date, we have demonstrated that CYP1A2 phenotyping in capillary DBS is a valid and convenient alternative for the classical plasma-based approach. Additionally, we have provided an objective basis as to why DBS are an ideal tool for CYP1A2 phenotyping

Opportunities and limitations of crop phenotyping in southern european countries

ReviewThe Mediterranean climate is characterized by hot dry summers and frequent droughts. Mediterranean crops are frequently subjected to high evapotranspiration demands, soil water deficits, high temperatures, and photo-oxidative stress. These conditions will become more severe due to global warming which poses major challenges to the sustainability of the agricultural sector in Mediterranean countries. Selection of crop varieties adapted to future climatic conditions and more tolerant to extreme climatic events is urgently required. Plant phenotyping is a crucial approach to address these challenges. High-throughput plant phenotyping (HTPP) helps to monitor the performance of improved genotypes and is one of the most effective strategies to improve the sustainability of agricultural production. In spite of the remarkable progress in basic knowledge and technology of plant phenotyping, there are still several practical, financial, and political constraints to implement HTPP approaches in field and controlled conditions across the Mediterranean. The European panorama of phenotyping is heterogeneous and integration of phenotyping data across different scales and translation of “phytotron research” to the field, and from model species to crops, remain major challenges. Moreover, solutions specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses) are in high demand, as the region is vulnerable to climate change and to desertification processes. The specific phenotyping requirements of Mediterranean crops have not yet been fully identified. The high cost of HTPP infrastructures is a major limiting factor, though the limited availability of skilled personnel may also impair its implementation in Mediterranean countries. We propose that the lack of suitable phenotyping infrastructures is hindering the development of new Mediterranean agricultural varieties and will negatively affect future competitiveness of the agricultural sector. We provide an overview of the heterogeneous panorama of phenotyping within Mediterranean countries, describing the state of the art of agricultural production, breeding initiatives, and phenotyping capabilities in five countries: Italy, Greece, Portugal, Spain, and Turkey. We characterize some of the main impediments for development of plant phenotyping in those countries and identify strategies to overcome barriers and maximize the benefits of phenotyping and modeling approaches to Mediterranean agriculture and related sustainabilityinfo:eu-repo/semantics/publishedVersio

Evaluating openEHR for storing computable representations of electronic health record phenotyping algorithms

Electronic Health Records (EHR) are data generated during routine clinical care. EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelerate the pace of precision medicine at scale. A main EHR use-case is creating phenotyping algorithms to define disease status, onset and severity. Currently, no common machine-readable standard exists for defining phenotyping algorithms which often are stored in human-readable formats. As a result, the translation of algorithms to implementation code is challenging and sharing across the scientific community is problematic. In this paper, we evaluate openEHR, a formal EHR data specification, for computable representations of EHR phenotyping algorithms.Comment: 30th IEEE International Symposium on Computer-Based Medical Systems - IEEE CBMS 201

室内植物表型平台及性状鉴定研究进展和展望

Plant phenomics is under rapid development in recent years, a research field that is progressing towards integration, scalability, multi-perceptivity and high-throughput analysis. Through combining remote sensing, Internet of Things (IoT), robotics, computer vision, and artificial intelligence techniques such as machine learning and deep learning, relevant research methodologies, biological applications and theoretical foundation of this research domain have been advancing speedily in recent years. This article first introduces the current trends of plant phenomics and its related progress in China and worldwide. Then, it focuses on discussing the characteristics of indoor phenotyping and phenotypic traits that are suitable for indoor experiments, including yield, quality, and stress related traits such as drought, cold and heat resistance, salt stress, heavy metals, and pests. By connecting key phenotypic traits with important biological questions in yield production, crop quality and Stress-related tolerance, we associated indoor phenotyping hardware with relevant biological applications and their plant model systems, for which a range of indoor phenotyping devices and platforms are listed and categorised according to their throughput, sensor integration, platform size, and applications. Additionally, this article introduces existing data management solutions and analysis software packages that are representative for phenotypic analysis. For example, ISA-Tab and MIAPPE ontology standards for capturing metadata in plant phenotyping experiments, PHIS and CropSight for managing complicated datasets, and Python or MATLAB programming languages for automated image analysis based on libraries such as OpenCV, Scikit-Image, MATLAB Image Processing Toolbox. Finally, due to the importance of extracting meaningful information from big phenotyping datasets, this article pays extra attention to the future development of plant phenomics in China, with suggestions and recommendations for the integration of multi-scale phenotyping data to increase confidence in research outcomes, the cultivation of cross-disciplinary researchers to lead the next-generation plant research, as well as the collaboration between academia and industry to enable world-leading research activities in the near future

Report on adjusting a high throughput screening tool to support water use phenotyping in forages

Drought severely limits forage productivity. The avoidance of water deficit by increasing the capacity for water uptake or by controlling water loss are common responses. A fine interplay exists between the acquisition of water by roots in drying soil and water loss through transpiration. These two components tend to act simultaneously. The following approach and aim is therefore to provide information of shoot development, root development and water use over time of plants growing under greenhouse conditions with soil from target sites. Greenhouse studies is a vital part of phenotyping for drought conditions as allow the recording of responses that would be otherwise impossible under filed conditions