Seminaria Zakładu Biosystemów i Miękkiej Materii

kolor czcionki + kolor tła = plan do 7 dni.

2019-06-28
 plan 
14:00, Sala: S3 im. W. Fiszdona, piętro III
prof. Tony Ladd
University of Florida

Transverse migration of polyelectrolytes in microfluidic channels: Concentrating and purifying DNA?

I will describe recent microfluidics experiments using DNA as a model polyelectrolyte. The DNA is introduced into the channel by a pressure driven flow, and simultaneously subjected to an axial electric field. Epifluorescent and confocal microscopy have been used to show that, under opposing fields, the DNA migrates to the walls of the microfluidic channel. An interesting consequence is that DNA then rapidly accumulates near the channel inlet, suggesting a possible means to both concentrate and purify DNA. Unlike a number of electrokinetic-based separations, the trapping of the DNA does not depend on complex flows orfields. Rather, it exploits (we think) a little studied aspect of polyelectrolytes; namely that an electric field can generate a long-range (1/r 3 ) flow around the molecule. When combined with symmetry breaking, induced (for example) by a shear flow, this leads to novel length-dependent motions of the polymer. In this talk I will summarize the results of our experiments, present the outline of a theory to describe the migration, and suggest possible biotechnology applications.
Tony Ladd, Mert Arca, Ryan Montes and Jason Butler, Unversity of Florida.

2019-06-26
 plan 
12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Marcin Lewandowski
IPPT PAN

MedTech 2020 – how “digital disruption” can impact healthcare

The continuously rising cost of healthcare and an ageing society threaten even the strongest economies. Today, developed countries spend 9% to 12% (USA 17%) of their GDP on this sector.
Medtech is a broad spectrum of product and technologies for medical and healthcare applications, including prevention, diagnosis, monitoring, therapy, and care. We will look at its complex landscape and how "digital disruption" can impact the future of the medical ecosystem and improve the quality of our lives. We will also discuss the increasing role played by digital health and how it could be used in data-driven decision making, shifting the care paradigm from reactive to proactive.
In addition, I will also present my team and our commitment to medical technologies developed at the Institute. Hopefully, a fruitful discussion on current bio-research that might impact the future of Medtech products will conclude my seminar.

2019-06-19
 plan 
12:30, Sala: Aula im. Wacława Olszaka, piętro II
prof. Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
University of Kansas

MULTIPLE PATHWAYS OF HELIX FOLDING FROM KINETIC COARSE GRAINED MODELS

Long-term molecular dynamics simulations and a coarse-grained kinetic analysis were carried out to describe the mechanism of formation of an alpha-helical structure. A 12 microsecond molecular dynamics simulation of a 21-residue helix-forming model peptide was generated in explicit solvent, yielding structural and dynamic properties in good agreement with available experimental data. Clustering and optimal dimensionality reduction were applied to produce low-dimensional coarse-grained models of the underlying kinetic network in terms of 2-5 metastable states. In accord with the generally accepted understanding of the multiple conformations and high entropy of the unfolded ensemble of states, the “coil” metastable set contains the largest number of structures. Interestingly, the helix metastable state was also found to be structurally heterogeneous, consisting of the completely helical form and several partly folded conformers which interconvert at a time scale faster that global folding. The intermediate states contain the fewest structures, have lowest populations and have the shortest lifetimes. As the number of considered metastable states increases, more intermediates and more folding paths appear in the coarse-grained models. One of these intermediates corresponds to the transition state for folding, which involves an “off-center” helical region over residues 11-16. The kinetic network model is consistent with a statistical picture of folding following a simple reaction coordinate counting the helical population of individual residues.

2019-05-29 12:30, Sala: S3 im. W. Fiszdona, piętro III
Yasamin Ziai
IPPT PAN

Synthesis and characterization of biocompatible, pH sensitive chitosan-PEG nanoparticles for drug delivery of curcumin used for breast cancer

As the mainstay in the treatment of various cancers, chemotherapy plays a vital role, but still faces many challenges, such as poor tumor selectivity and multidrug resistance. Targeted drug delivery using nanotechnology has provided new strategies which have minimum damage to healthy tissues and maximum release of the drug. Coupling a specific stimuli-triggered drug release mechanism with these delivery systems such as Nanocarriers is one of the most prevalent approaches for improving therapeutic outcomes. Among the various stimuli, pH triggered delivery is regarded as the most general strategy, targeting the acidic extracellular microenvironment and intracellular organelles of solid tumors.
The purpose of my master thesis was to synthesize nanoparticles based on biocompatible chitosan, for drug delivery of curcumin to tissues damaged by breast cancer using pH-triggered delivery. For this purpose, hydrophilicity of chitosan chains were first modified by adding carboxymethyl substitution. In the next step, folate groups were selected to increase tumor targeting in the body as well as enhancing the polymers ability in the process of self-assembly of the nanoparticles, and were grafted into the main chains. One of the characteristics of cancerous tissues is the acidity of pH, which can be used as a stimulant for targeted drug delivery. To create pH-sensitive acetal bonds on carboxymethyl chitosan folate chains, in the first step, amino groups of these chains were protected using phethalic anhydride and then methoxy-polyethylene glycol containing aldehyde groups at one end of their chains (mPEG-Aldehyde) were bonded to carboxymethyl-free hydroxyl groups, and at the final step the phethalic anhydride groups were de-attached using sodium hydrobutyrate (NaBH4). At each stage, the synthesis and structure of the obtained polymers were verified using the FT-IR and H-NMR tests. In the last step of this study, drug containing nanoparticles were made and these nanoparticles, were examined by DLS, SEM and then, using the UV-Vis, the amount of drug loaded in these nanocomposites was obtained and finally, drug release profile is obtained. The system was tested in two pH conditions (e.g. 7.4 and 4.8). The results of this test indicate an increase in the release rate of the drug in the acidic environment.

2019-05-22 14:00, Sala: S5 im. L. Filipczyńskiego, piętro V
Dr. Maciej Lisicki
Insitute of Theoretical Physics, Faculty of Physics
University of Warsaw

Pumping and swimming: two faces of phoretic flows

Janus particles with the ability to move phoretically in self-generated chemical concentration gradients are model systems for active matter. On the other hand, chemically active surfaces can lead to microscale flow generation, becoming an effective pumping mechanism in inertia-less small-scale flows. In this talk, after a broad review of the physics and biology of microswimmers, I will review briefly both phenomena relating to the same concept of phoretic flow generation. Asymmetry needed for the flow to be initiated can be induced by geometry or by chemical patterning. I will show examples of both ways and some applications in biomimetic systems of fully three-dimensional phoretic swimmers.

2019-04-17 12:30, Sala: S3 im. W. Fiszdona, piętro III
Paweł Nakielski, PhD
IPPT PAN

Electrospun nanofibers for haemorrhage arrest (SONATA) and intervertebral disc regeneration (LIDER)

During the seminar I will show preliminary results of Sonata project entitled Investigation of blood clotting mechanism in the contact with nanofibers. During the second part I will show research plans for the project entitled Injectable scaffolds for tissue engineering that was recently financed in the LIDER programme.

2019-04-10 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Margaritis Voliotis
University of Exeter

Understanding how the brain controls reproduction: the neural mechanisms behind the pulsatile secretion of reproductive hormones

Fertility critically depends on the gonadotropin-releasing hormone (GnRH) pulse generator, a neural construct comprised of hypothalamic neurons co-expressing three key neuropeptides: kisspeptin, neurokoinin-B and dynorphin. Using mathematical modeling and in-vivo optogenetics we investigate how this neural construct initiates and sustains the appropriate ultradian frequency essential for reproduction. Our model predicts how pulsatile dynamics emerge from non-linear positive and negative feedback interactions mediated through neurokinin-B and dynorphin signaling and stresses the crucial role of basal network activity in regulating pulsatile dynamics. We verify model predictions and show experimentally that robust pulsatile release of luteinizing hormone, a proxy for GnRH, emerges abruptly as we excite the neuronal network using continuous low frequency optogenetic stimulation. Further increase of optogenetic stimulation markedly increases pulse frequency and eventually leads to pulse termination. Our results shed light on the long-elusive GnRH pulse generator offering new horizons for reproductive health and wellbeing.

2019-02-27 12:30, Sala: S3 im. W. Fiszdona, piętro III
Monika Dolega
Institute for Advance Biosciences, Grenoble, France
Group of C. Guilluy, Mechanotransduction and Nuclear Functions

Propagation of Mechanical Stress Thorugh Multicellular Structures

Recent works provided evidence for a long-distance mechanosensing, demonstrating that cells within epithelial sheets are capable to adjust to local changes for example in substrates rigidity at the tissue scale level by altered cell-cell and cell-ECM signalling. We have proposed first quantitative approach to measure tissue stress within 3D cellular aggregates (Dolega et al, Nature Comm 2017). In our model, we study effects of controlled osmotic stress on spheroid growth and invasion. To understand how spheroids respond to such external compression, and how the exerted pressure is transferred from the outside to the inside of the spheroid, we incorporoate elastic Polyacrylamide (PAA) microbeads within intercellular volume to serve as internal sensors of compression. Spatial distribution of incorporated microbeads within CT26 cancerous spheroids allowed obtaining a pressure profile along the radius upon externally applied compressive stress. Our experiments revealed that upon compression the pressure is spatially not homogenous and has a direct impact on the biological response of cells.

2019-01-30 12:30, Sala: S3 im. W. Fiszdona, piętro III
Magdalena Bogdańska
MIMUW

Mathematical models of low grade gliomas and their response to chemotherapy

In this talk I present the results of my PhD thesis devoted to study of mathematical models describing the evolution and the response to treatments of low-grade gliomas. Low-grade gliomas are brain tumours usually growing slowly but causing death due to their progression to more malignant counterparts. We constructed macroscopic models of low-grade gliomas' growth in such a way that they were accurate enough to reflect available clinical observations and simple enough so that they could be analysed analytically. We studied the proposed models both analytically and numerically. We also showed that the solutions of the developed mathematical models fit well to the dynamics of low-grade gliomas of individual patients. On the basis of our validated models, we addressed some problems of clinical practice. Finally, we derived analytical estimates which could be potentially useful in assessing tumours aggressiveness and selecting the best therapies.

2019-01-16 12:30, Sala: S3 im. W. Fiszdona, piętro III
Maciej Dobrzynski
University of Bern

Spatio-temporal oncogenic signaling in a breast cancer epithelial community

We measure ERK/AKT dynamics in single MCF10A mammary epithelial cell. We observe that pulses of ERK/AKT activation in quiescent cells are propagated across epithelium during epithelial extrusion with a highly choreographed spatio-temporal dynamics. Spectral properties of pulses and pulse propagation are significantly altered by KRAS and PIK3CA mutations, as well as by drug interventions. We apply pulsed growth factor stimulations using microfluidic devices to dissect the coupling between MAPK/ERK and PIK3CA/AKT networks, and to understand factors that shape pulse dynamics.

2018-12-12 12:30, Sala: S3 im. W. Fiszdona, piętro III
Dr Petr Juřík
University of Chemistry and Technology, Prague

Self-organized metal structures formed on polymer substrates

Self-organization of the structures is visible both in daily life and cutting edge research, where scientific teams are occupied by searching for parameters suitable for emergence of functional structures. These methods allow preparation of materials with properties, which would be hardly obtainable by classical methods and which allow simple scaling of the process, which predetermines them for simple proliferation and mass production. In this presentation I will focus mainly on formation of self-organized structures on the surfaces of two polymer substrates: poly-L-lactic acid and polyethersulfone.

On the samples of poly-L-lactic acid with thin metal layer permanent wrinkle-like structures are formed after heat treatment. Shape, size, conductivity and other properties of such structures are easily influenced by the change of type and thickness of sputtered metal. Comparison of acquired data with literature shows that inner stress in polymer foil plays critical role for formation of the wrinkle-like structure, without which permanent wrinkle-like structure does not emerge. This stress is also responsible for directionality of this structure. Furthermore effect of the type of the metal on the size of the wrinkle-like structure was examined. Applicability of prepared nanostructures was demonstrated on NIH 3T3 cells` cultivation, where significant improvement of the properties of the nanostructured samples in comparison to unmodified poly-L-lactic acid was observed and in some properties even surpassed tissue polystyrene.

Samples of the polyethersulfone with thin metal layer formed globular structures on the surface after heat treatment, which showed effects of the localized surface plasmon resonance visible in form of peak in the UV-Vis spectra. The explanation of emergence of these structures is coalescence of metal layer followed by formation of metal clusters separated by polymer substrate. These properties are applicable in sensor construction.

2018-11-22 12:30, Sala: S3 im. W. Fiszdona, piętro III
Rachel Rigby
MRC Weatherall Institute of Molecular Medicine
University of Oxford

Characterisation of the heterogeneity of human type I IFNs

2018-10-17 12:30, Sala: S3 im. W. Fiszdona, piętro III
prof. Andrzej Nowicki
IPPT PAN

The value of flow mediated dilation in prediction of vascular disorders

There is growing interest in the application of non-invasive clinical tools allowing to assess the endothelial function, preceding atherosclerosis. A comparison of 7-12 MHz and 20 MHz scanners for flow mediated dilation (FMD) and shear rate (SR) measurements in radial artery is reported. The experiments in vitro using closely spaced food plastic foils proved over three times better resolution of the high frequency 20 MHz scanner (<0.1 mm) over the 7-12 MHz one. Also the sensitivity of the external single transducer 20 MHz pulse Doppler proved to be over 20 dB better (in terms of SNR) than the pulse Doppler incorporated into linear 7-12 MHz linear array. These results justified designing of a high-frequency scanning system consisting of a 20 MHz linear array transducer combined with 20 MHz pulsed Doppler probe to validate its usefulness in estimation of the degree of radial artery FMD and SR after 5 minutes of reactive hyperaemia.

In the pilot studies, 12 healthy volunteers (38–71 yr old) and 14 patients (36–77 yr old) with chronic coronary artery disease (CAD) were included. The diagnosis of chronic CAD was based on the presence of symptoms of stable angina or a positive myocardial ischemia stress test. The Imaging/Doppler system was modified by adding the single element 20 MHz pulse Doppler with a sample volume size being equal 0.3 mm axially and 0.8 mm laterally, to the linear array transducer, providing to high precision FMD and SR measurements. The normalization of FMD to shear rate is done by dividing the peak FMD by the accumulated value of shear rate area under the curve.

Statistically significant differences between the two groups were confirmed by a Wilcoxon-Mann-Whitney test for both FMD and FMD/SR (p-values < 0.01). AUCs of ROC curves for FMD and FMD/SR were greater than 0.9. The results confirm the usefulness of the proposed measurements of radial artery FMD and SR in differentiation of normal subjects from those with chronic coronary artery disease.

2018-10-08 14:00, Sala: S3 im. W. Fiszdona, piętro III
Francesca Petronella
Institute for Chemical Physical Processes, Italian National Council of Research

Smart nanomaterials: a new route towards novel environmental and biological applications

Nanostructured materials exhibit outstanding size/shape dependent properties that make them extremely promising in several application fields. Fundamental features that include (but are not limited to) their optical response, thermodynamic behaviour, plasmonic, magnetic and catalytic properties can be modulated by varying nanocrystal size and shape, without altering their chemical composition.1 Furthermore, synthesis routes as well as characterization techniques have rapidly evolved thus enabling to rationally design, synthesize process and organise nanomaterials. In this perspective, they can be regarded as building blocks that allow to achieve structures with compelling complexity; hence providing nanostructured materials properly addressable to target applications.2 The present contribution aims at sharing the experience, gained by the Bari Division of CNR-IPCF, on the development of synthetic strategies for preparation of colloidal nanocrystal based materials (metal, semiconductors and oxides), and tailoring their physical and chemical properties towards photocatalytic3, optoelectronic,4 environmental,5 (bio)sensing and biomedical applications.6 The ultimate goal is to organize the prepared nano-objects in mesoscopical structures to be integrated in advanced functional materials and devices.

1. Alivisatos, A. P., Perspectives on the Physical Chemistry of Semiconductor Nanocrystals. The Journal of Physical Chemistry 1996, 100 (31), 13226-13239.
2. Curri, M. L.; Comparelli, R.; Striccoli, M.; Agostiano, A., Emerging methods for fabricating functional structures by patterning and assembling engineered nanocrystals. Physical Chemistry Chemical Physics 2010, 12 (37), 11197-11207.
3. Petronella, F.; Truppi, A.; Ingrosso, C.; Placido, T.; Striccoli, M.; Curri, M. L.; Agostiano, A.; Comparelli, R., Nanocomposite materials for photocatalytic degradation of pollutants. Catalysis Today 2017, 281 (Part 1), 85-100.
4. Ingrosso, C.; Bianco, G. V.; Pifferi, V.; Guffanti, P.; Petronella, F.; Comparelli, R.; Agostiano, A.; Striccoli, M.; Palchetti, I.; Falciola, L.; Curri, M. L.; Bruno, G., Enhanced photoactivity and conductivity in transparent TiO2 nanocrystals/graphene hybrid anodes. Journal of Materials Chemistry A 2017, 5 (19).
5. Petronella, F.; Pagliarulo, A.; Striccoli, M.; Calia, A.; Lettieri, M.; Colangiuli, D.; Curri, M.; Comparelli, R., Colloidal Nanocrystalline Semiconductor Materials as Photocatalysts for Environmental Protection of Architectural Stone. Crystals 2017, 7 (1), 30.
6. Depalo, N.; Iacobazzi, R. M.; Valente, G.; Arduino, I.; Villa, S.; Canepa, F.; Laquintana, V.; Fanizza, E.; Striccoli, M.; Cutrignelli, A.; Lopedota, A.; Porcelli, L.; Azzariti, A.; Franco, M.; Curri, M. L.; Denora, N., Sorafenib delivery nanoplatform based on superparamagnetic iron oxide nanoparticles magnetically targets hepatocellular carcinoma. Nano Research 2017, 10 (7), 2431-2448.

2018-09-19 11:00, Sala: S3 im. W. Fiszdona, piętro III
Paramita Chatterjee
IPPT PAN

Mathematical analysis of a new model of bone pattern formation

The study of vertebrate limb development is an important example of organogenesis connected with limb bud growth and shaping as well as on its skeleton formation. This process has been modeled by many authors. We tried to explain some mathematical properties of a relatively new model of this phenomenon designed by T. Glimm et al. in a paper from 2014. The most widely used mathematical scenario of pattern formation in biology, among them the formation of chonrogenetic pattern, is the Turing bifurcation. In our publication from 2016, we use this method to study the bacterial patterns driven by chemotaxis and patterns on the sphere, which can correspond to some other biological phenomena.

2018-08-08 12:30, Sala: S3 im. W. Fiszdona, piętro III
Paramita Chatterjee
IPPT PAN

Analysis of a model of avian limb formation

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018

Mathematical analysis of a system of mixed parabolic-hyperbolic equations proposed in (Glimm, Newman, 2014). The model was designed to describe the process of bone formation pattern during chicken embryo morphogenesis. In our study, we propose some simplifications making the model more convenient to analyze, in particular reducing it to a standard system of reaction-diffusion equations.

2018-07-10 12:30, Sala: S3 im. W. Fiszdona, piętro III
Abhyudai Singh, Associate Professor
University of Delaware, Newark, DE

Systems Biology in Single Cells: A Tale of Two Viruses

In the noisy cellular environment, expression of genes has been shown to be stochastic across organisms ranging from prokaryotic to human cells. Stochastic expression manifests as cell-to-cell variability in the levels of RNAs/proteins, in spite of the fact that cells are genetically identical and are exposed to the same environment. Development of computationally tractable frameworks for modeling stochastic fluctuations in gene product levels is essential to understand how noise at the cellular level affects biological function and phenotype. I will introduce state-of-the-art computational tools for stochastic modeling, analysis and inferences of biomolecular circuits. Mathematical methods will be combined with experiments to study infection dynamics of two viral systems in single cells. First, I will show how stochastic expression of proteins results in intercellular lysis time and viral burst size variations in the bacterial virus, lambda phage. Next, I will describe our efforts in stochastic analysis of the Human Immunodeficiency Virus (HIV) genetic circuitry. Our results show that HIV encodes a noisy promoter and stochastic expression of key viral regulatory proteins can drive HIV into latency, a drug-resistant state of the virus.

2018-06-27 11:30, Sala: S3 im. W. Fiszdona, piętro III
Karol Nienałtowski
IPPT PAN

Bayesian approach ​to reconstruction of​ time series from snapshot data

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018

Fluorescent live imaging (FLI) has become a powerful technique ​in ​studies at the single-cell level. One of ​its key advantages ​​is the ability to ​measure ​quantities of interest, e.g. protein levels, ​over time in the same cell. ​Most often however reliable quantitative measurements require time-consuming and costly preparation of cells, e.g. stable transfection with a fluorescent protein. An alternative approach is the high-throughput immunocytofluorescence (ICF) microscopy that uses fluorescent antibodies to detect molecules of interests. Unfortunately, ​the latter method is limited to fixed (dead) cells, what leads to the loss of information ​regarding correlation​s​ ​over time​. Therefore, the question arises​, ​whether the missing information could be augmented using a tailored statistical technique.
Here, we propose a Bayesian approach to reconstruct time-series of the heterogeneous behaviour of single cells​ from snapshot data.​ ​Time-series are described as a Gaussian process (GP) with the mean and variance ​of ICF data and the correlations between time-points ​are augmented with a prior.​ ​The covariance matrix of ​the ​GP ​is modeled ​using the inverse-Wishart distribution with a prior described by kernel covariance functions. ​The possibility to reconstruct time-series is useful in studies of various dynamic processes in single cells. Here, the method allowed us for more accurate estimation of information transfer in the JAK-STAT pathway.

2018-06-27 12:00, Sala: S3 im. W. Fiszdona, piętro III
Damian Zaremba
IPPT PAN

Modular microfluidic geometries for passive manipulations on droplets

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018

Microfluidics is still a new and rapidly growing field of science and has the potential to influence subject areas from chemical synthesis and biological analysis to optics and information technology. Droplet-based microfluidic is the branch of this field, where we use two immiscible fluids. The first liquid is used to produce droplets. Most often it is water and its mixtures. The second liquid is most often fluorinated oil (FC-40, HFE-7500) or hexadecane. This liquid is used to push droplets through complex microfluidics channels.
Two-phase flows have a lot of interesting physical phenomena and these phenomena can be used to complex manipulations on droplets in microfluidics. Changing the geometry of microfluidic structures, e.g. by adding a slit or an obstacle, significantly changes the behavior of flowing drops in the channels. I'll present the comprehensive study of the geometry of microfluidic components which can manipulate on droplets and next I'll show the new approach to the construction of microfluidic devices using these geometries.

2018-06-27 12:30, Sala: S3 im. W. Fiszdona, piętro III
Chris Trombley
IPPT PAN

Charged Particles Sedimenting Under Gravity In A Viscous Fluid

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018
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