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Zastosowanie sieci petriego do modelowania procesów biologicznych

100%

Błażewicz J., Formanowicz D., Formanowicz P.

Kosmos

2009

vol. 58

issue 1-2

79-88

Rapid growth of the amount of available biological data made it clear that an analysis of complex biological processes can be made only with the support of mathematics and computer sciences. It is especially important nowadays when the systems biology approach is becoming more and more widely used in biological science. This new way of investigation of biological phenomena allows, at least in principle, to observe complex relationships between different parts of the analyzed system. These interactions may be crucial for the system's nature and behavior, so observing them may lead to important biological discoveries. Probably the most important part of this process consists in building of a formal model of the biological process. One of the promising methods of such an analysis is based on the theory of Petri nets. Models expressed in the language of this theory are very precise on the one hand, and on the other, they are intuitive, which makes their analysis easier in comparison, for example, to models based on ordinary differential equations. In this paper, a brief introduction to the theory of Petri nets is given and its applications for modeling of some exemplary biological processes are shortly discussed. Moreover, some extensions of the classical Petri nets and their biological applications are also presented.

Modelowanie udziału żelaza w powstawaniu miażdżycy - podejście systemowe

100%

Formanowicz D., Radom M., Formanowicz P.

Kosmos

2014

vol. 63

issue 3

331-344

Hipotezę zakładającą, że wyższe stężenie żelaza w surowicy odgrywa ważną rolę w rozwoju chorób układu sercowo-naczyniowego zaproponował w 1981 r. J.L. Sullivan. Dziś, wyniki coraz liczniejszych badań potwierdzają istotne znaczenie żelaza w rozwoju miażdżycy. Zasadniczą rolę przypisuje się katalizowanej przez jony tego pierwiastka reakcji Fentona, w następstwie której powstaje silnie toksyczny rodnik hydroksylowy, biorący udział w peroksydacji lipidów. W następstwie wspomnianego procesu powstają zmienione cząsteczki lipidowe, które w sposób nieograniczony wyłapywane są przez komórki jednojądrzaste i stają się komórkami piankowatymi, a potem ciałkami apoptotycznymi tworzącymi blaszkę miażdżycową. W pracy tej przedstawiono systemowe podejście do badania prezentowanego zagadnienia. W tym celu został zbudowany model dotyczący udziału żelaza w powstawaniu miażdżycy oparty na sieciach Petriego. Analiza tego modelu pozwoliła na wyciągnięcie wniosków, iż bez reakcji Fentona, którą katalizuje żelazo, blaszka miażdżycowa nie może powstać.

The hypothesis that higher serum iron concentration plays an important role in the development of diseases of the cardiovascular system has been proposed in 1981 by J.L. Sullivan. Nowadays, more and more research results confirm importance of iron in the development of atherosclerosis. The essential role plays Fenton reaction catalyzed by ions of this chemical element, which produces highly toxic hydroxyl radical involved in lipids peroxidation. As a result of this process, modified lipid molecules are produced and phagocytosed in unlimited way by mononuclear cells to become foam cells and then apoptotic bodies that form atherosclerotic plaque. In this paper, a systemic approach to the study of these issue is presented. For this purpose, a model based on Petri nets of the iron participation in the development of atherosclerosis has been built. The analysis of this model allowed us to draw the conclusion that without the Fenton reaction, which is catalyzed by iron, atherosclerotic plaque cannot actually arise.

Assembling the SARS-CoV genome - new method based on graph theoretical approach.

64%

Błażewicz J., Figlerowicz M., Formanowicz P., Kasprzak M., Nowierski B., Styszyński R., Szajkowski Ł., Widera P., Wiktorczyk M.

vol. 51

issue 4

983-993

Nowadays, scientists may learn a lot about the organisms studied just by analyzing their genetic material. This requires the development of methods of reading genomes with high accuracy. It has become clear that the knowledge of the changes occuring within a viral genome is indispensable for effective fighting of the pathogen. A good example is SARS-CoV, which was a cause of death of many people and frightened the entire world with its fast and hard to prevent propagation. Rapid development of sequencing methods, like shotgun sequencing or sequencing by hybridization (SBH), gives scientists a good tool for reading genomes. However, since sequencing methods can read fragments of up to 1000 bp only, methods for sequence assembling are required in order to read whole genomes. In this paper a new assembling method, based on graph theoretical approach, is presented. The method was tested on SARS-CoV and the results were compared to the outcome of other widely known methods.

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2 Kosmos

1 Acta Biochimica Polonica

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1 2009

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3 Formanowicz P.

2 Błażewicz J.

2 Formanowicz D.

1 Figlerowicz M.

1 Kasprzak M.

1 Nowierski B.

1 Radom M.

1 Styszyński R.

1 Szajkowski Ł.

1 Widera P.

1 Wiktorczyk M.

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Zastosowanie sieci petriego do modelowania procesów biologicznych

Modelowanie udziału żelaza w powstawaniu miażdżycy - podejście systemowe

Assembling the SARS-CoV genome - new method based on graph theoretical approach.