Homegarden commercialization: extent, household characteristics, and effect on food security and food sovereignty in Rural Indonesia

Homegardens have long been recognized for contributing to household food security, nutritional status, and ecological sustainability in especially poor, rural areas in low-income countries. However, as markets and policies drive the commercialization of food and farming systems, and of rural livelihoods in general, it becomes increasingly difficult for small-holder farmers to maintain homegarden plots. Rather than autonomous spaces to grow food for self-consumption, farmers are transforming the land around their dwellings into an income-generating space by planting commercial crops for sale in urban and processing markets. The objective of this study was to examine homegarden commercialization in the Upper Citarum Watershed of West Java, Indonesia, and its effects on food security and food sovereignty. We employed a mixed-method approach to survey 81 village households involved in agricultural production. For quantitative analysis, we calculated a “homegarden commercialization index,” and developed indicator frameworks to examine relationships between commercialization, household food security, and food-related decision-making. Accompanied by insights from qualitative interviews, our results show that homegardens are highly commercialized, which contributes to the spread of monocultural production in the region. We argue that homegardens should be included and supported in food, agricultural, health, environmental, and rural development policy, in Indonesia and generally

Quantitative comparison of genomic-wide protein domain distributions

Investigations into the origins and evolution of regulatory mechanisms require quantitative estimates of the abundance and co-occurrence of functional protein domains among distantly related genomes. Currently available databases, such as the SUPERFAMILY, are not designed for quantitative comparisons since they are built upon transcript and protein annotations provided by the various different genome annotation projects. Large biases are introduced by the differences in genome annotation protocols, which strongly depend on the availability of transcript information and well-annotated closely related organisms. Here we show that the combination of de novo gene predictors and subsequent HMM-based annotation of SCOP domains in the predicted peptides leads to consistent estimates with acceptable accuracy that in particular can be utilized for systematic studies of the evolution of protein domain occurrences and co-occurrences. As an application, we considered four major cla sses of DNA binding domains: zink-finger, leucine-zipper, winged-helix, and HMG-box. We found that different types of DNA binding domains systematically avoid each other throughout the evolution of Eukarya. In contrast, DNA binding domains belonging to the same superfamily readily co-occur in the same protein