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Abstract High‐throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh‐frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single‐pot solid‐phase‐enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96‐well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands‐on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low‐input samples, reproducibly quantifying 500–1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end‐to‐end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost‐effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non‐clinical applications.

There is increasing interest in good agriculture practices that address the issues of sustainability, reduction in inputs such as fertilizers and pesticides while maintaining crop yield and soil fertility. It is important that soil microbial diversity and function are not impaired by altered agricultural practice. In this study, as indicators of soil quality, the bacterial community structure was evaluated from a long-term field trial managed with conventional and low-input fertilization/pesticide regimes. The low-input plots under study received approximately one fifth less N fertilizer than the conventional-input plots, a maximum of half the recommended application rates of fungicides and pesticides and no externally added P source. A non-culturable approach was taken using polymerase chain reaction-denaturing gradient gel electrophoresis analysis of 16S rRNA and alkaline phosphomonoesterase [phosphatase] (ALP) genes in an attempt to relate bacterial community structure to respective field management regimes. To identify the ALP bacteria in these plots, randomly selected ALP clones were sequenced. The results based on Shannon diversity indices and community structure analysis of ALP genes suggest differences in community diversity and structure under conventional and low-input barley sites in most sampling seasons. We conclude that soil fertilization management affects the ALP bacteria in the barley rhizosphere, while the overall changes in bacterial community in these sites are prominently due to seasonal variation compared to crop or input regimes. The randomly selected ALP sequences identified from these sites were mostly from the Alpha and Gamma classes of Proteobacteria. [ABSTRACT FROM AUTHOR]

Countries in Sub-Saharan Africa (SSA) that depend on foreign aid once political independence is gained, continue to be affected by changing aid modalities led by aid communities. It has been claimed that previous irrigation programs in SSA have not improved agricultural production as expected, and that the budget for implementation of further irrigation development has then been decreased. As a result, small-scale operations, which are part of participatory integrated rural development (PIRD), have become mainstream in the implementation of irrigation development in SSA. A small-scale irrigation development (SSID) was considered capable of attracting initial investment, required shorter construction periods, was comparatively easy to design, farmers were able to maintain the system themselves, and it had a lesser environmental impact. In general, to achieve a sustainable irrigation scheme, three systems must be established: a 'water utilization system'; an 'operation and maintenance (O&M) system'; and a 'succession system'. This paper discusses SSID in SSA with regard to a number of important factors, i.e., environmental, economic, and social factors, all of which impact on the sustainability of SSID. The progress of low-input, effective, and sustainable irrigation development (LESID) and the impact of changing aid modalities is followed in three countries, Ghana, Malawi, and Tanzania. In addition, the future effective implementation of SSID by way of LESID in other SSA countries is discussed. A self-supported SSID (as employed in Malawi) is currently considered the most appropriate LESID for least developed countries (LDCs) in SSA. [ABSTRACT FROM AUTHOR]

For low-input crop production, well-characterised varieties increase the possibilities of managing diseases and weeds. This analysis aims at developing a framework for analyzing grain yield using external varietal information about disease resistance, weed competitiveness and yield potential and quantifying the impact of susceptibility grouping and straw length scores (as a measure for weed competitiveness) for predicting spring barley grain yield under variable biotic stress levels. The study comprised 52 spring barley varieties and 17 environments, i.e., combinations of location, growing system and year. Individual varieties and their interactions with environments were analysed by factorial regression of grain yield on external variety information combined with observed environmental disease loads and weed pressure. The external information was based on the official Danish VCU testing. The most parsimonious models explained about 50% of the yield variation among varieties including genotype-environment interactions. Disease resistance characteristics of varieties, weighted with disease loads of powdery mildew, leaf rust and net blotch, respectively, had a highly significant influence on grain yield. The extend to which increased susceptibility resulted in increased yield losses in environments with high disease loads of the respective diseases was predicted. The effect of externally determined straw length scores, weighted with weed pressure, was weaker although significant for weeds with creeping growth habit. Higher grain yield was thus predicted for taller plants under weed pressure. The results are discussed in relation to the model framework, impact of the considered traits and use of information from conventional variety testing in organic cropping systems. [ABSTRACT FROM AUTHOR]