Background: A classical problem in metabolic design is to maximize the production of a desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is addressed as a linear optimization problem over the flux cone. The prior construction of the flux cone is computationally expensive and no polynomial-time algori...

Metabolic systems are governed by a compromise between metabolic benefit and enzyme cost.This hypothesis and its consequences can be studied by kinetic models in which enzyme profiles arechosen by optimality principles. In enzyme-optimal states, active enzymes must provide benefits: ahigher enzyme level must provide a metabolic benefit to justify the additional enzyme cost. This...

As an aromatic and colorful plant of substantive taste, saffron (Crocus sativus L.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. Regarding the critical role of microRNAs in secondary metabolic synthesis and the limited number of identified miRNAs in C. sativus, on the other hand, one may see the point how the characte...

The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unli...

Metabolism is executed by an efficient, interconnected and ancient biochemical system, the metabolic network. Its evolutionary origins are, however, barely understood. We here discuss that because of niche adaptation, selection acting on network structure distinguishes modern species early life forms. Yet, its basic remained conserved over more than three billion years diverging evolution. spec...

cancer treatment is still of the greatest challenges that health care providers and patients are facing. one of the unsolved problems in cancer treatment is cells’ reaction to metabolic stress caused by harsh nutritional conditions around tumor. in order to be able to treat this disease properly, it is important to understand the true nature of the disease. in fact, the cells inside the central...

Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic s...

Autocatalytic Sets are reaction networks theorised as at the basis of life. Their main feature is ability spontaneously emerging and self-reproducing. The Reflexively Food-generated theory provides a formal definition in terms graphs with peculiar topological properties. This formalisation has been proved to be powerful tool for study chemical underlying life, it was able identify autocatalytic...

In living cells we can observe a variety of complex network systems such as metabolic network. Studying their sensitivity is one of the main approaches for understanding the dynamics of these biological systems. The study of the sensitivity is done by increasing/decreasing, or knocking out separately, each enzyme mediating a reaction in the system and then observing the responses in the concent...

The knowledge about control and dynamics of biological systems is often limited or incomplete but, especially for cell metabolism, network structures are often well-characterized. A major challenge in systems biology, therefore, concerns the reverse-engineering of cellular control structures from the available knowledge on the controlled systems’ structures. Here, we propose a method to analyze...