FNP Team Project

Mechanistic aspects and spatial effects in cell signalling

within TEAM Programme sponsored by the Foundation for Polish Science, 2009–2013

Concepts and objectives

The leading aim of the project is to identify and study the turning points in molecular pathways of immune response and cancer, in which the single cell fate, understood as a choice between apoptosis, senescence, proliferation, differentiation or cell cycle arrest, is decided. As a model molecular pathways we will consider these related to innate and adaptive immune response and cancer, in which we have expertise. The project will be realized both by means of numerical simulations and theoretical analysis.

TEAM in December 2009.

TEAM project laureates

Postdocs:

Sławomir Błoński
Piotr Szopa (till 31.01.2012)

Ph.D. Students:

Michał Dyzma
Joanna Jaruszewicz
Paweł Kocieniewski

M.Sc. Students:

Marta Bogdał
Dominika Nowicka
Jakub Pękalski (till 31.08.2011)
Paweł Żuk (till 30.09.2011)

Financed topics

Theoretical modeling and experimental analysis of regulatory pathways connected with innate immune response. The candidates are expected to have laboratory experience or/and knowledge in the field of mathematical biology, stochastic processes and differential equations
Evolution and co-evolution of genes (and their regulatory regions) related to IRF3 and NF-κB pathway. Such analysis will be helpful in analysis of crosstalk of IRF3 and NF-κB pathways. The evolutions of genes is related to their biological importance, typically well conserved genes play key roles in the regulatory pathway. Transcription factors IRF3 and NF-κB play central role in innate immune responses. The student will have to learn BLAST (Basic Local Aligment Search Tool) and how to use genome databases and clustering tools.
Mutations of p53 pathways genes in various types of cancer. Various types of cancers are associated with specific mutations of p53, Mdm2, Akt, PTEN and other regulating genes. The students will have to search databases to find the mutations (or deletions) and analyze what is their potential impact on dynamics of p53 regulatory pathways we consider.

Team members

Tomasz Lipniacki – principal investigator (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

Bogdan Kaźmierczak (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

Beata Hat-Plewińska (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

Marek Kochańczyk (Jagiellonian University, Krakow, Poland)

Aleksandra Nowicka (Institute of Theoretical Physics, PAS, Warsaw, Poland) – till 01.10.2011

External collaborators

Mark Alber (Notre Dame University, US)

Allan R. Brasier (University of Texas Medical Branch, Galveston, TX, US)

James R. Faeder (University of Pittsburgh School of Medicine, US)

William S. Hlavacek (Los Alamos National Laboratory, US)

Marek Kimmel (Rice University and MD Anderson Cancer Center, Houston, TX, US)

Vitaly Volpert (Université Claude Bernard - Lyon 1, France)

Michael R.H. White (Liverpool University, UK)