No abstract

The so-called "hub proteins" are those proteins in a protein-protein interaction network system that have remarkably higher interaction relations (or degrees) than the others. Therefore, the information of hub proteins can provide very useful insights for selecting or prioritizing targets during drug development. In this paper, by combining the multi-agent-based method with the graphical spectrum analysis and immune-genetic algorithm, a novel simulator for identifying the hub proteins from membrane protein interaction networks is proposed. As a demonstration of using the simulator, two hub membrane proteins, YPL227C and YIL147C, were identified from a complicated network system consisting of 1500 membrane proteins. Meanwhile, along with the two identified hub proteins, their molecular functions, biological processes, and cellular components were also revealed. It is anticipated that the hub-protein-simulator may become a very useful tool for system biology and drug development, particularly in deciphering unknown protein functions, determining protein complexes, and in identifying the key targets from a complicated disease system.

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

P53, a vital anticancer gene, controls the cell cycle arrest and cell apoptosis by regulating the downstream genes and their complicated signal pathways. To simulate the investigation of the cellular response under continuous Ion Radiation (IR), a predictive model of P53 gene regulatory networks is proposed at single cell level. The model can be used to simulate the dynamic processes of the double-strand breaks (DSBs) generating and their repair, ataxia telangiectasia mutated (ATM) and ARF activation, as well as the oscillations in the P53-MDM2 feedback loop under continuous effect of acute IR. Especially, the model can predict the plausible outcomes of cellular responding DNA damage under different conditions.

A field experiment was conducted at the Horticultural Research Center in Chanhassen, Minn. to help refine recommendations for use of calcium (Ca) sprays to reduce the incidence of bitter pit in `Honeycrisp' apple. Specific objectives were to: evaluate the amount of translocation from leaves to fruit using strontium (Sr) as a tracer for potential Ca movement, determine whether there are differences in translocation in early vs. later phases of fruit development, and evaluate the effect of an experimental adjuvant on spray efficacy. Seven treatments tested included the following: 1) Control (no Sr applied), 2) Sr without adjuvant, fruit covered during spray application, full season, 3) Sr without adjuvant, fruit uncovered during spray application, full season, 4) Sr + adjuvant, fruit covered during spray application, full season, 5) Sr + adjuvant, fruit uncovered during spray application, 6) Sr + adjuvant, fruit covered during spray application, late season, 7) Sr + adjuvant, fruit uncovered during spray application, late season. Results from this study strongly suggest that Sr is a suitable tracer for foliar applied Ca. Up to 18% of the Sr applied to leaves was translocated to fruit. Eight full season spray applications more than doubled the concentration and content of fruit Sr compared to four late season sprays. The experimental adjuvant was found to double Sr absorption by and translocation to fruit compared to not using an adjuvant. Implications for foliar application of Ca to apple trees will be discussed.