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Primary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy-cancer comparisons were mapped on protein-protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy-interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer., Scientific and Technological Research Council of Turkey (TÜBİTAK)

In this study, FeSO4 supplementation ranging from 0 to 4.5 mM, and MgSO4 supplementation ranging from 0 to 5.1 mM were investigated to observe the effect on the population dynamics, biochemical composition and fatty acid content of mixed microalgae grown in Anaerobic Liquid Digestate (ALD). Overall, 3.1 mM FeSO4 addition into ALD increased the total protein content 60% and led to highest biomass (1.56 g L−1) and chlorophyll-a amount (18.7 mg L−1) produced. Meanwhile, 0.4 mM MgSO4 addition increased the total carotenoid amount 2.2 folds and slightly increased the biomass amount. According to the microbial community analysis, Diphylleia rotans, Synechocystis PCC-6803 and Chlorella sorokiniana were identified as mostly detected species after confirmation with 4 different markers. The abundance of Chlorella sorokiniana and Synechocystis PCC-6803 increased almost 2 folds both in iron and magnesium addition. On the other hand, the dominancy of Diphylleia rotans was not affected by iron addition while drastically decreased (95%) with magnesium addition. This study helps to understand how the dynamics of symbiotic life changes if macro elements are added to the ALD and reveal that microalgae can adapt to adverse environmental conditions by fostering the diversity with a positive effect on high value product.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A systems-based investigation of the effect of perturbations on metabolic machinery is crucial to elucidate the mechanism behind perturbations. One way to investigate the perturbation-induced changes within the cell metabolism is to focus on pathway-level effects. In this study, three different perturbation types (genetic, environmental and disease-based) are analyzed to compute a list of reporter pathways, metabolic pathways which are significantly affected from a perturbation. The most common omics data type, transcriptome, is used as an input to the bioinformatic analysis. The pathways are scored by two alternative approaches: by averaging the changes in the expression levels of the genes controlling the associated reactions (reaction-centric) and by averaging the changes in the associated metabolites which were scored based on the associated genes (metabolite-centric). The analysis reveals the superiority of the novel metabolite-centric approach over the commonly used reaction-centric approach since it is based on metabolites which better represent the cross-talk among different pathways, enabling a more global and realistic cataloguing of network-wide perturbation effects.