Mechanistic aspects and spatial effects in cell signalling

within TEAM Programme sponsored by Foundation for Polish Science

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 project laureates:

Postdoc: Slawomir Blonski Piotr Szopa, Ph.D. (till 31.01.2012) Ph.D. Students: Michal Dyzma, M.Sc. Joanna Jaruszewicz, M.Sc. Pawel Kocieniewski, M.Sc. Undergraduate Students: Marta Bogdal  Dominika Nowicka Jakub Pekalski (till 31.08.2011) Pawel Zuk (till 30.09.2011)

The following topics are financed:
   
1. 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

2.   Evolution and co-evolution of genes (and their regulatory regions) related to IRF3 and NF-kappaB pathway   
Such analysis will be helpful in analysis of crosstalk of IRF3 and NF-kappaB 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-kappaB 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.

3. 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 Kazmierczak (Institute of Fundamental Technological Research, PAS, Warsaw, Poland)

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

Marek Kochanczyk (Jagiellonian University, Krakow, Poland)

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

External collaborators:

Prof. Mark Alber (Notre Dame University, US),

Prof. Allan R. Brasier (UTMB Galveston, TX, US),

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

Assoc. Prof. William S. Hlavacek (Los Alamos National Laboratories, US),

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

Prof. Vitaly Volpert (Universite Claude Bernard - Lyon 1, France),

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