# Seminar

### From Laboratory of Modeling in Biology and Medicine

The seminar "Mathematical models of gene expression and regulatory networks", chaired by prof. Tomasz Lipniacki (IPPT PAN) and prof. Jacek Miękisz (MIM UW), usually takes place in IPPT PAN, room S3 (3rd floor), in Monday afternoons.

##### Upcoming seminars

##### Past seminars

Monika Kurpas

Silesian University of Technology, Gliwice

*Modelowanie układu p53 w odpowiedzi na jedno- i dwuniciowe uszkodzenie DNA**Podwójnoniciowe uszkodzenia DNA wykrywane są przez moduł ATM, a pojedynczoniciowe fragmenty DNA przez moduł ATR. Obydwa szlaki aktywują białko p53 zaangażowane w regulację cyklu komórkowego, naprawę DNA i apoptozę. Pomiędzy szlakami ATM i ATR istnieją zależności. Przykładowo proces resekcji podwójnoniciowych uszkodzeń DNA skutkuje aktywacją modułu ATR. W ramach badań zostały stworzone: model ATM oparty na danych eksperymentalnych, model ATR, wstępny łączony model ATM–ATR uwzględniający proces resekcji podwójnoniciowych uszkodzeń DNA oraz wstępny model ATR połączony z modelem cyklu komórkowego. Otrzymane wyniki znajdują potwierdzenie w literaturze biologicznej.*

Prof. Krzysztof Zabłocki

Nencki Institute, Warsaw

*Jony wapnia w komórce eukariotycznej**Jony wapnia odgrywają kluczową rolę w regulacji przebiegu licznych procesów w komórce. Wszechstronność i uniwersalność Ca ^{2+} jako przekaźnika sygnału wynika z jego właściwości chemicznych i niezwykle precyzyjnej regulacji jego stężenia w różnych przedziałach komórkowych. Zaburzenia tej regulacji są przyczyną poważnych dysfunkcji komórek często prowadzących do ich unicestwienia. Komórki eukariotyczne dysponują szeregiem narzędzi molekularnych pozwalających na kontrolowanie stężenia Ca^{2+}, takich jak systemy transportu i magazynowania tych jonów, a także sensory Ca^{2+} dekodujące sygnał wapniowy. Omówienie tych mechanizmów (ze szczególnym uwzględnieniem roli mitochondriów) będzie przedmiotem mojego wykładu.*

Prof. Jacek Waniewski

IBIB PAN, Warsaw

*Modelowanie procesów transportu w czasie dializy**Przedstawione zostaną proste modele matematyczne opisujące procesy transportu substancji w czasie obu form dializy pacjentów ze schyłkową niewydolnością nerek: hemodializy i dializy otrzewnowej. Zwrócimy uwagę na praktyczne wykorzystanie tych modeli do kontroli parametrów dializy i interpretacji parametrów modeli typu "czarna skrzynka" poprzez parametry fizjologiczne opisujące anatomiczne bariery transportowe.*

Sylwia Pawłowska

IPPT PAN, Warsaw

**Hydrogel nanofilaments for biomedical applications**

The project includes a study of deformable polymer nano-objects dynamics under the influence of mechanical and physical phenomena (such as chaotic thermal movements), performing numerical analysis of complex flow and taking advantage of recently developed tools for analysing highly deformable hydrogel nanofilaments. The ongoing research project involve analysis of the behavior of flexible polymeric nanofilaments, produced by electrospinning technique, in various types of liquids and suspensions. The results can be used for verification of the theoretical models of biological and physical phenomena responsible for the dynamics of the bending of long bio-objects (proteins, DNA) and allow to evaluate the possibility of used flexible nanofilaments as systems for tissue engineering, transport and drug release.

Krzysztof Zembrzycki

IPPT PAN, Warsaw

**Analysis of specific hydrodynamic interactions between particles**

using optical tweezers. A project proposal for NCN Preludium 10

using optical tweezers. A project proposal for NCN Preludium 10

The proposed project will concentrate on the study of interactions between single particles made of polystyrene and glass. The particles will be suspended in water with different concentrations of several types of ions. This study will be conducted using optical tweezers combined with an atomic force microscope and a fluorescence microscope. To fully evaluate the influence of ions, we will not only measure the interaction forces between the particles but also Brownian motion and ballistic motion of single particles confined within the optical trap. The obtained results will be compared with molecular dynamics simulations. The results of this study will help to understand the behavior of nano-objects in complex fluids and also should be useful in calibrations of current numerical models and equipment that rely on the nature of nano-particles in a fluid.

Prof. Michael W.Y. Chan

National Chung Cheng University, Chia Yi (Tajwan)

**Signaling mediated epigenetic silencing of tumor suppressors in ovarian cancer**

Aberrant TGFβ signaling pathway may alter the expression of down-stream
targets and promotes ovarian carcinogenesis. However, the mechanism of
this impairment is not fully understood. By ChIP-chip, we have previously
identified RunX1T1 as a SMAD4 target in an immortalized ovarian surface
epithelial cell line, IOSE. In this study, we demonstrated that
transcription of RunX1T1 was confirmed to be positively regulated by SMAD4
in IOSE cells and epigenetically silenced in a panel of ovarian cancer
cell lines by promoter hypermethylation and histone methylation at H3
lysine 9. SMAD4 depletion increased repressive histone modifications of
RunX1T1 promoter without affecting promoter methylation in IOSE cells.
Epigenetic treatment can restore RunX1T1 expression by reversing its
epigenetic status in MCP3 ovarian cancer cells. When transiently treated
with a demethylating agent, the expression of RunX1T1 was partially
restored in MCP3 cells, but gradual re-silencing through promoter
re-methylation was observed after the treatment. Interestingly, SMAD4
knockdown accelerated this re-silencing process, suggesting that normal
TGFβ signaling is essential for the maintenance of RunX1T1 expression.
Recently, by mathematical modeling, we have demonstrated a TGFβ
inducible miR, miR-193a to be epigenetically controlled by E2F6. Such
epigenetic silencing of miR-193a may induce a bistability of the ovarian
cancer stem marker, c-KIT expression. The mechanism of epigenetic control
in the expression of miR-193a will also be discussed. In conclusion,
dysregulated TGFβ/SMAD4 signaling may lead to epigenetic silencing of a
putative tumor suppressor during ovarian carcinogenesis.

Prof. Jan Karbowski

University of Warsaw

*Optymalizacja połączeń w mózgu**Seminarium będzie poświęcone strukturze mózgu ssaków, w szczególności korze mózgowej (kluczowej dla procesów kognitywnych). W przeszłości wysuwane były sugestie, że struktura mózgu jest w dużej części konsekwencją ewolucyjnej minimalizacji uzwojeń neuronowych (dendryty i aksony), jako że są one kosztowne metabolicznie i biofizycznie. Ostatnio jednak pojawiły się prace, które poddają w wątpliwość tę hipotezę. Na seminarium opowiem o swoim wkładzie w ten problem, i o własnej alternatywnej "zasadzie", na której może być oparta struktura kory mózgowej ssaków. Zasada ta, zwana przeze mnie ekonomiczną maksymalizacją połączeń neuronowych ("spine economy maximization"), wyjaśnia empiryczną hierarchię w strukturze kory oraz posiada potencjał do wyjaśnienia pewnych faktów z wielkoskalowej struktury mózgu. Całość stanowi wstęp do teoretycznych badań na temat ludzkiego konektomu ("human connectome"), co jest jednocześnie ostatnio bardzo ważne i modne w neuronauce. Seminarium będzie oparte w dużej mierze na mojej pracy w PLOS Comput. Biol. (2015).*

Dr. Ryszard Wojnar

IPPT PAN, Warsaw

**Polycrystalline structure of collagen fibrils dense packing**

as the most uniform concentric pattern

as the most uniform concentric pattern

Dr. Izabela Piechocka

Institute of Photonic Sciences, Barcelona

**The role of shear force on blood vessels physiology**

Dr. Carsten Marr

Institute of Computational Biology,

Helmholtz Zentrum München

**Automatic prediction of hematopoietic lineage choice**

in long-term time-lapse microscopy

in long-term time-lapse microscopy

Hematopoietic stem cells are able to self-renew and to give rise to all mature blood cell lineages in an organism via step-wise differentiation. With long-term continuous time-lapse imaging it has become possible to observe these stem cells and their progeny in an unprecedentedly highly resolved manner in vitro. However, limitations in the number and specificity of available molecular markers for hematopoietic lineages hinder a continuous observation of the cellular differentiation kinetics. We thus apply computational methods for the quantification and analysis of single cell states. I will first present a fully automated image processing pipeline that identifies millions of cells in the bright field channel of a time-lapse experiment with an accuracy of over 80%. We combine the single cell segmentation with the temporal information from manually tracked genealogies to study cellular morphodynamics over several cell cycles. Using this information, we train a machine learning method to predict the lineage choice between two competing lineages in the hematopoietic hierarchy. Our method achieves an error rate below 20% up to three divisions before the lineage is detected by standard molecular markers. Our approach thus allows the identification of lineage choice much earlier than current techniques and could be used to identify novel molecular factors that are involved in hematopoietic differentiation.

Prof. Mostafa Adimy

Institut Camille Jordan, Université Claude Bernard Lyon 1

**Age-structured and delay differential–difference**

model of hematopoietic stem cell dynamics

model of hematopoietic stem cell dynamics

We investigate a mathematical model of hematopoietic stem cell dynamics. We take two cell populations into account, quiescent and proliferating one, and we make the difference between dividing cells that enter directly to the quiescent phase and dividing cells that return to the proliferating phase to divide again. The resulting mathematical model is a system of two age-structured partial differential equations. By integrating this system over the age and using the characteristics method, we reduce it to a delay differential–difference system, and we investigate the existence and stability of the steady states. We give sufficient conditions for boundedness and unboundedness properties for the solutions of this system. By constructing a Lyapunov function, the trivial steady state, describing cell's dying out, is proven to be globally asymptotically stable when it is the only equilibrium. The stability analysis of the unique positive steady state, the most biologically meaningful one, and the existence of a Hopf bifurcation allow to determine a stability area, which is related to a delay-dependent characteristic equation. Numerical simulations illustrate our results on the asymptotic behavior of the steady states and show very rich dynamics of this model. This study may be helpful in understanding the uncontrolled proliferation of blood cells in some hematological disorders.

(Joint work with A. Chekroun and T. Touaoula.)

Prof. Je-Chiang Tsai

Dept. of Mathematics, National Chung Cheng University, Chia-Yi, Taiwan

**Curvature dependence of propagating velocity for a simplified calcium model**

It is known that the relation between curvature and wave speed plays a key role in the propagation of two-dimensional waves in an excitable model. For typical excitable models (e.g., the Fitz-Hugh-Nagumo (FHN) model), such a relation is believed to obey the linear eikonal equation, which states that the relation between the normal velocity and the local curvature is approximately linear. In this talk, we show that for a caricature model of intracellular calcium dynamics, although its temporal dynamics can be investigated by analogy with the FHN model, the curvature relation does not obey the linear eikonal equation even in the limiting case. Hence this caricature calcium model may be an unexpected excitable system, whose wave propagation properties cannot be always understood by analogy with the FHN model.

Prof. Carsten Wiuf

Dept. of Mathematical Sciences, University of Copenhagen

**Model reduction in biochemical reaction networks**

In many situations we apply simplified models to complex dynamical systems, either because we are unaware of what the 'correct' model should look like, or because the 'correct' model is too complex to be handled statistically/mathematically. In this talk, I will discuss model reduction for stochastic as well as deterministic biochemical reaction networks. In particular, I will focus on reduction by elimination of intermediate species, which are transient species that typically are consumed at a faster rate than non-intermediates. The focus will be on non-equilibrium dynamics, but if time permits, I will also discuss the system at equilibrium.

Sławomir Białecki

IPPT PAN, Warsaw

*Przestrzenne oscylacje wapniowe w komórce,*

w modelu trójkompartmentowymw modelu trójkompartmentowym

Paweł Nakielski

IPPT PAN, Warsaw

*Systemy uwalniania leków oparte na nanowłóknach*

Tomasz Jetka

IPPT PAN, Warsaw

**Stimulus sensitivity in biochemical networks**

A growing number of studies are revealing that cells can send and receive information by controlling the temporal behaviour of their signalling molecules. Methods, however, that can utilise experimental data in order to understand how the information is processed are largely missing. Specifically, there is a need to study how the information is transferred at the single cells and over time, where the stochastic effects play an important role.

For the last few months we have been developing a framework to extract the sensitivity of cellular outcomes to a biochemical stimulation from stochastic, time-resolved, single cell, experimental data. The method implements an estimation of the Fisher Information from time series using non-parametric concepts of the Principle Component Analysis and kernel density estimation. We test the approach using the model of NF-κB translocation in response to TNF stimulation. Our analysis reveals a sensitivity range of a single cell temporal responses to the TNF stimulation.

This is work in progress therefore we will also discuss the potential of the method in the context of utilising experimental data to better understand the cellular information processing.

Bożena Sikora

IF PAN, Warsaw

**Designing and characterization of biosensors based on colloidal nanoparticles for applications in biology and medicine**

The aim of this work was to design and characterize new materials based on nanoparticles for applications in biology and medicine as biosensors and factors potentially useful in anticancer therapy. Materials obtained and examined in this work are based on nanoparticles with luminescent properties.

We formed ZnO/MgO nanoparticles coated with carboxymethyl-β-cyclodextrin (CMCD). These nanoparticles were used as the donors in Fluorescent Resonance Energy Transfer (FRET) studies. An organic dye, Nile Red was used as the acceptor, which was introduced into the voids of β-cyclodextrin. Nile Red emission shows a clear thermochromic shift, which allows use of ZnO/MgO/CMCD/Nile Red complex as a nanothermometer in an aqueous environment inside living organisms. This complex was for the first time used as a biosensor of environmental changes in HeLa cancer cells.

NaYF_{4} nanoparticles doped with rare earth ions Er^{3+}, Yb^{3+}, Gd^{3+} were prepared, characterized and used. These nanoparticles, after excited with near infrared (IR) radiation, show emission in visible or ultraviolet light by up-conversion. These emission properties can be used in biological imaging of cancer cells and tissues and anticancer therapy by generating reactive oxygen species. NaYF_{4}: Er^{3+}, Yb^{3+}, Gd^{3+} nanoparticles also has strong paramagnetic properties, making them attractive contrast agents for magnetic resonance imaging MRI. Thus formed particles are potentially a good multifunctional material for applications in the biosensing and in anticancer therapy.

Jan Poleszczuk

Faculty of Mathematics, Informatics and Mechanics, University of Warsaw

**Connecting radiation-induced senescence and bystander effect to improve radiation response prediction**

During the seminar I will show a novel attempt to combine two hitherto distinct phenomena – cellular senescence and radiation induced bystander effects. I will show that the cellular senescence and senescence-associated secretory phenotype might be the key players in controlling of the tumor response to ionizing radiation. I will present the experimental data describing the response of human colorectal carcinoma cells (HCT116) with wild (p53^{+/+}) and knockout (p53^{–/–}) *TP53* gene to radiation (2–8 Gy) and signals emitted by irradiated cells. Further, I will explain the data in the terms of customized quantitative mathematical model.

Maciej Czerkies

IPPT PAN, Warsaw

**Analysis of the role of macrophages in shaping inflammatory response of fibroblasts to LPS treatment – basic experimental techniques**

LPS, main component of gram-negative bacterial outer membrane, elicits strong and complexly regulated inflammatory response. Immune cells, like macrophages, have primary role in initiating defensive mechanisms to bacterial infections, transmitting signal to other cells that had or not had yet contact with pathogen. Our studies concern modelling of response of mouse embryonic fibroblasts to LPS treatment, in presence or absence of J774 macrophage cells. This seminar will cover the fundamental experimental techniques used in generating inflammatory gene expression and cytokine production data.

Zbyszek Korwek & Wiktor Prus

IPPT PAN, Warsaw

**Experimental analysis of IRF3 and NF-ĸB signalling in response to LPS and poly(I:C) stimulation**

NF-ĸB and IRF3 are the most important transcription factors activated during bacterial and virial infections. These proteins regulate several hundred genes involved in immune response as well as in proliferation and apoptosis. The NF-ĸB and IRF3 signalling pathways are very complex and highly regulated. In this seminar we will focus on experimental approaches to study the activation of these factors. Using various cell models and techniques we are able to investigate response induced by LPS and poly(I:C), which mimics pathogens infection.

Paweł Kocieniewski

IPPT PAN, Warsaw

**MAPK pathways: structure, functions and regulation in health and disease**

The MAPK cascades belong to the oldest eukaryotic signal transduction pathways. They are characterized by a conserved module consisting of a sequence of three kinases: MAP3K, MAP2K, and MAPK; MAP2K and MAPK require dual phosphorylation to be activated. The MAPK pathways regulate cellular responses to mitotic and stress stimuli. In mammals there are four such pathways: ERK1/2, JNK, p38, and ERK3/4/5. In this seminar I will provide an overview of the structure and regulation of the MAPK cascades, especially in the context of the ERK1/2 pathway, which has been best characterized due to its involvement in the pathogenesis of cancer, RASopathies, and other disorders.

Marek Kochańczyk

IPPT PAN, Warsaw

**Stochastic rule-based modeling of heterogeneous signaling systems on the plasma membrane**

During the ~45 min seminar, I will review the on-lattice kinetic Monte Carlo approach to numerical modeling of kinetics of stochastic spatially extended systems. First, my working implementation of the approach, called SpatKin, will be demonstrated, plus possible further extensions will be discussed. Then, I will present an overview of applications of SpatKin to problems from biophysics (stochastic tranistions on the membrane, diffusion-limited reaction cycles) and cell biology (B cell receptor-proximal signaling, EGF receptor–Ras–MAPK axis signaling).

Paulina Szymańska

Faculty of Mathematics, Informatics and Mechanics, University of Warsaw

**Dependence of effective macroscopic reaction rates on diffusion in phosphorylation–dephosphorylation cycles**

Since the early twentieth century there has been an interest in deriving effective macroscopic reaction rate constants for various chemical schemes. These constants govern the process in a macroscale chemical reactor and are defined using microscopic kinetic rates. We analyzed a phosphorylation–dephosphorylation cycle for which we established, by means of spatial kinetic Monte Carlo simulations (SpatKin), the dependence of effective macroscopic reaction rates on diffusion and enzyme densities. Analytical results are provided for the limiting cases of zero and infinite diffusion and they agree with numerical results obtained for small and large diffusion coefficients. For finite, non-zero diffusion, the effective macroscopic rates depend in a non-trivial way on all microscopic characteristics of the systems: reaction propensities and densities.

Prof. Tomasz Lipniacki

IPPT PAN, Warsaw

**Modeling the NF-ĸB regulatory system**

NF-ĸB is the key transcription factor controlling innate immune responses. I will discuss: 1) the dynamical structure of NF-ĸB model encompassing 3 regulatory feedback loops - two negative and one positive, 2) sources and role of stochasticity, 3) correspondence between single cell and population behavior, confronting experiment with theoretical prediction.

Prof. Mark E.J. Chaplain

University of Dundee, Scotland

**Spatial stochastic modelling of gene regulatory networks**