Andrzej Mizera, PhD |
Doctoral thesis
2011-11-24 | Methods for Construction and Analysis of Computational Models in Systems Biology Applications to the Modelling of the Heat Shock Response and the Self-Assembly of Intermediate Filaments
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Recent publications
1. | Czeizler Eu.♦, Mizera A., Czeizler El.♦, Back R-J.♦, Eriksson J.E.♦, Petre I.♦, Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin, IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, ISSN: 1545-5963, Vol.9, No.3, pp.885-898, 2012 | ||||||||||||||||
2. | Mizera A., Gambin B., Modelling of ultrasound therapeutic heating and numerical study of the dynamics of the induced heat shock response, COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION, ISSN: 1007-5704, DOI: 10.1016/j.cnsns.2010.04.056, Vol.16, No.5, pp.2342-2349, 2011 Abstract: In this presentation we consider hyperthermia, a procedure of raising the temperature above 43 C, as a treatment modality. To this purpose, a numerical model of in vivo soft tissue ultrasound heating is proposed by extending a previously presented in vitro model. Based on the numerical simulations, a heating scheme satisfying some constraints related to potential clinical applications is established, and the resulting temperature time-course profile is composed with the temperature-dependent protein denaturation formula of a recently published mathematical model for the eukaryotic heat shock response. The obtained simulation results of the combined models are discussed in view of potential application of ultrasound soft tissue heating in clinical treatment. Keywords:Hyperthermia, Heat Shock Response dynamics, Ultrasound therapeutic treatment, mathematical modelling Affiliations:
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3. | Mizera A., Gambin B., Stochastic modeling of the eukaryotic heat shock response, JOURNAL OF THEORETICAL BIOLOGY, ISSN: 0022-5193, DOI: 10.1016/j.jtbi.2010.04.029, Vol.265, No.3, pp.455-466, 2010 Abstract: The heat shock response (HSR) is a highly evolutionarily conserved defence mechanism allowing the cell to promptly react to elevated temperature conditions and other forms of stress. It has been subject to intense research for at least two main reasons. First, it is considered a promising candidate for deciphering the engineering principles underlying regulatory networks. Second, heat shock proteins (main actors of the HSR) play crucial role in many fundamental cellular processes. Therefore, profound understanding of the heat shock response would have far-reaching ramifications for the cell biology. Stochastic model, Computer simulations, Markov chain, Gillespie algorithm, Stationary distribution Affiliations:
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4. | Gambin B., Kujawska T., Kruglenko E., Mizera A., Nowicki A., Temperature fields induced by low power focused ultrasound during gene therapy. Numerical predictions and experimental results, ARCHIVES OF ACOUSTICS, ISSN: 0137-5075, Vol.34, No.4, pp.445-460, 2009 Abstract: The aim of this work is twofold. Firstly, to verify a theoretical model which is capable of predicting temperature fields appearing in soft tissues during their ultrasound treatment. Secondly, to analyze some aspects of the dynamics of Heat Shock Response induced by the heating process in the context of therapeutic treatment. The theoretical investigations and quantitive analysis of temperature increments at any field point versus time of heating process, depending on the heat source power, spatial distribution and duration as well as on the tissue thermal properties, has been carried out by Finite Element Method (FEM). The validation of the numerical model has been performed by comparison of the calculation results with the experimental data obtained by measuring in vitro of the 3D temperature increments induced in samples of the turkey and veal liver by the circular focused transducer with the diameter of 15 mm, focal length of 25 mm and resonance frequency of 2 MHz. Various ultrasonic regimes were considered. They were controlled by adjusting ultrasound power and exposure time. The heat shock proteins (HSP) and misfolded proteins (MFP) levels during the proposed cyclic sonification are presented. Keywords:heat-responsive gene therapy, temperature field, low-power focused ultrasound, soft tissues, ultrasonic regime control, heat sources distribution, heat shock proteins Affiliations:
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5. | Dojer N.♦, Gambin A.♦, Mizera A., Wilczyński B.♦, Tiuryn J.♦, Applying dynamic Bayesian networks to perturbed gene expression data, BMC BIOINFORMATICS, ISSN: 1471-2105, DOI: 10.1186/1471-2105-7-249, Vol.7, No.249, pp.1-11, 2006 Abstract: Background
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Conference papers
1. | Kruglenko E., Mizera A., Gambin B., Tymkiewicz R., Zienkiewicz B., Litniewski J., Nagrzewanie ultradźwiękami tkanek miękkich in vitro i własności akustyczne wytworzonych wzorców tkanek miękkich, 59th Open Seminar on Acoustics, 2012-09-10/09-14, Boszkowo (PL), pp.129-132, 2012 Abstract: W pracy przedstawiono wstępne wyniki pomiaru pola temperatury wewnątrz tkanki in vitro w czasie procesu nagrzewania wiązką ultradźwiękową o słabej mocy oraz pomiaru właściwości akustycznych wzorców tkanek miękkich. Wzorce te zbudowano w celu dalszych badań nad powiązaniem wzrostu temperatury z właściwościami akustycznymi, gdyż próbki tkankowe in vitro okazały się niepowtarzalne i nietrwałe. Na wykonanych 3 wzorcach tkankowych dokonano pomiaru sygnału przejścia i wyznaczono prędkość propagacji impulsu, współczynnik tłumienia oraz zbadano statystykę rozproszenia. Przedyskutowano wpływ liczby elementów rozpraszających na te wielkości. Keywords:wzorce tkanek, sygnał ultradźwiękowy, prędkość dźwięku, tłumienie, statystyka rozproszenia Affiliations:
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