Seminaria Zakładu Biosystemów i Miękkiej Materii

kolor czcionki + kolor tła = plan do 7 dni.

12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Marcin Lewandowski

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.

2019-09-18 12:30, Sala: S3 im. W. Fiszdona, piętro III
Massimiliano Lanzi
Department of Industrial Chemistry “Toso Montanari”
University of Bologna, Italy

New functional polythiophene materials: fine-tuning of photovoltaic or chiro-optical properties

The last research activity of our group at Dipartimento di Chimica Industriale “Toso Montanari”-University of Bologna, Italy, concerned the synthesis, characterization and study of the optical and photoactive properties of new organic semiconducting materials based on polythiophenes.
There is a remarkable level of interest in the development of π-conjugated polymers (ICPs) which have been employed, thanks to their promising optical and electronic properties, in numerous applications including photovoltaic cells, light emitting diodes and thin-film transistors. Although high power conversion efficiency can be reached using poly(3-alkylthiophenes) (P3ATs) as electron-donating materials in polymeric solar cells of Bulk-Heterojunction type (BHJ), their relatively large band gap limits the solar spectrum fraction that can be effectively harvested. A common approach to the preparation of narrow band gap polymers consists in the design and synthesis of conjugated architectures where an extended π electronic conjugation is achieved by the alternation of electron-donor and acceptor units along the polymer backbone.
New 4,7-bis(3-alkylthiophen-2-yl)benzo(2,1,3)thiadiazole monomers, functionalized with different alkyl chains, have been synthesized through a palladium-catalyzed Suzuki cross-coupling reactions and then polymerized by oxidative coupling using FeCl3. As the side chain functionalization influences the optical and electrical properties of building blocks and related polymeric derivatives, we have therefore also investigated the effect of the insertion of an oxygen atom into different positions in side chains of similar length. Moreover the synthesis of symmetrical trimers with HH (head-to-head) regiochemistry has allowed to obtain completely regioregular polymers despite the use of a non-regio-specific polymerization method.
The newly synthesized polymers have been characterized by common analytical techniques and thus tested as active media in air-processed Bulk-Heterojunction devices, alone and blended with PC61BM (1:1 w/w) as additional acceptor material.
After the interesting results achieved with these main-chain donor-acceptor polymers, the research project was oriented to the development and study of similar systems but having the acceptor units in the side chain, known as double cable materials.
Starting from soluble, regiorandom and regioregular homopolymeric precursors new alkylthiophenic copolymers, bearing the C60-fullerene group at the end of a hexylic side chain at position 3 of the thiophene ring, have been prepared with a simple and straightforward post-polymerization functionalization procedure based on Grignard coupling. The materials were synthesized with different content of fullerene, in order to study the effect on the final performance of the photoactive layer.
Homo- and copolymers were fully characterized and tested as active media in organic solar devices, respectively blended with PC61BM (1:1 w/w) as the acceptor material and as double-cable materials.
The research activity has also been devoted to investigate the behavior of polythiophenes with chiral side chain, that are fascinating materials capable to assume helix supramolecular structures, exhibiting optical activity in the aggregated state.
In this context, since head-to-tail regioregularity has demonstrated to produce a strong influence on the self-assembly of the macromolecular chains in the solid state, an investigation about the influence of regioregularity on the chiral behaviour of optically active polythiophenes was carried out. The polymers were obtained by regiospecific organometallic coupling (GRIM method) or non-regiospecific oxidative coupling with FeCl3, starting respectively from chiral mono- or bithiophenic monomers. These procedures allow to obtain the corresponding polymeric derivatives with well defined head-to-tail (HT) or head-to-head/tail-to-tail (HH-TT) regioregularity. Moreover, the effect of the presence of a different heteroatom (oxygen or sulfur), connecting the alkyl chiral side chains to the thiophene ring, was studied.
The optical activity of polymers was evaluated by circular dichroism (CD), upon aggregation of the macromolecules by gradual addition of a poor solvent to their chloroform solutions.

Massimiliano Lanzi, Elisabetta Salatelli, Luca Zuppiroli, Martina Marinelli
Conjugated polymers group
Department of Industrial Chemistry “Toso Montanari”
Viale Risorgimento, 4
40136 Bologna Italy

2019-09-05 12:00, Sala: S3 im. W. Fiszdona, piętro III
Aishwarya Dhar, Ph.D. student
Department of Physics, University of Rome Tor Vergata and INFN Sezione di Tor Vergata, Rome, Italy

Aβ peptides and β-sheet breakers. A coarse grained molecular dynamics approach using GoMartini

The problem of protein misfolding is at the origin of a class of pathologies called protein conformational disorders (PCD) to which all neuro-degenerative diseases belong. PCD’s are characterized by the misfolding of proteins that grow in aggregates of fibrillar shape. Among them, Alzheimer Disease (AD) is one of the most studied for its high impact on the modern society. The plaques present in the brain of AD patients show deposition of fibril made of amyloid β (Aβ) peptides [1]. The process that leads to misfolding, aggregation and amyloid plaques formation is not yet fully elucidated. It seems, however, that the “trigger” of the process is an abnormal switch of the peptide secondary structure leading to β-sheet formation.
Several factors are known to affect Aβ aggregation processes. An important role seems to be played by metal ions that have been observed to be quite abundant in fibrils [2-4]. Recently, the observation that short synthetic peptides, called β-sheet breaker (BSB's), are able to directly interact with Aβ, precluding (or disfavouring) amyloid polymerisation. This finding has stimulated a lot of work in the direction of trying to understand the molecular mechanism by which BSB's are able to slow down or even prevent Aβ aggregation and fibrillation [5].
In this presentation we show how one can get a good understanding of the role that BSBs play in the aggregation process of Aβ peptides by means of coarse-grained molecular dynamics simulations based on the Martini force-field. Since the secondary structure switching is a crucial event for the successive aggregation process, we have extended the standard Martini approach to incorporate GO-Martini algorithm [6] that allows to properly model structural switches and study the secondary structure dynamical evolution of Aβ peptides in the presence of BSBs.

1. LC Serpell, BBA, 1502(1):16-30, 2000
2. E De Santis et al., JPCB, 119, 15813-15820, 2015
3. S Morante, GC Rossi, Advance Alz Res,2:100-147, 2014
4. F Stellato et al., Biophys Chem, 229, 110-114, 2017
5. V Minicozzi et al., JBC, 289, 11242-11252, 2014
6. AB Poma et al., J Chem Theory Comput, 13(3):1366-1374, 2017

2019-08-28 10:00, Sala: Aula im. Wacława Olszaka, piętro II
Princeton University, USA

Some multiphase flow problems:
(i) Moderate Reynolds number flows at T-junctions and
(ii) low-Reynolds-number diffusiophoretic flows

I will discuss two distinct multi-phase flow problems that we have worked on in recent years. First, I will illustrate dynamics of bubble and particle flows in bifurcating geometries when the Reynolds number is O(100-1000) and show an unexpected trapping phenomenon. Second I will describe our studies of chemically driven particle motions, which involves the subject of diffusiophoresis.

2019-07-31 12:00, Sala: S3 im. W. Fiszdona, piętro III
Roberto Fiorelli, PhD
Barrow Neurological Institute - Phoenix, AZ (USA)

Advancing 3D Immunohistochemistry

To address the inefficiency of passive diffusion for antibody penetration in thick tissue samples, which limits clearing-technique applications, we developed a versatile and simple device to perform antibody incubation under increased barometric pressure. Pressurized immunohistochemistry (pIHC) greatly improves the uniformity, intensity, and depth of fluorescent immunostaining in thick human and mouse brain samples cleared with the CUBIC or PACT techniques. Furthermore, pIHC substantially decreased the time required for classic staining of thin sections.

2019-07-11 12:00, Sala: S3 im. W. Fiszdona, piętro III
Dr. Hideki Kobayashi
Department of Chemistry, University of Cambridge, UK

The self-consistent multiscale simulation of complex fluids

We present a method that uses self-consistent simulation of coarse grained and fine-grained models, in order to analyse properties of physical systems. The method uses the coarse-grained model to obtain a first estimate of the quantity of interest, before computing a correction by analysing properties of the fine system. We plan to illustrate the method by applying it to the Asakura-Oosawa (AO) model of colloid-polymer mixtures. We show that the liquid-vapour critical point in that system is affected by three-body interactions which are neglected in the corresponding coarse-grained model. It is also presented the analyse the size of this effect and the nature of the three-body and higher interactions.

2019-06-28 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.

2019-06-24 11:30, Sala: S3 im. W. Fiszdona, piętro III
Karol Nienałtowski

Quantitative methods for analysing cellular signalling

Seminarium w ramach przeglądu wyników doktorantów w 2018/2019

Mathematical methods of information theory appear to provide a useful language to describe how stimuli are encoded in activities of signaling effectors. Exploring the information-theoretic perspective, however, remains conceptually, experimentally and computationally challenging. Specifically, existing computational tools enable efficient analysis of relatively simple systems, usually with one input and output only. Moreover, their robust and readily applicable implementations are missing. During seminar, I will describe a novel algorithm, SLEMI - statistical learning based estimation of mutual information, to analyze signaling systems with high-dimensional outputs and a large number of input values.

2019-06-24 12:00, Sala: S3 im. W. Fiszdona, piętro III
Damian Zaremba

Badanie oddziaływań hydrodynamicznych kropel w wybranych układach mikroprzepływowych

Seminarium w ramach przeglądu wyników doktorantów w 2018/2019

Mikroprzepływy to wciąż nowa i szybko rozwijająca się dziedzina nauki, która może wpływać na obszary badań, od syntezy chemicznej i analizy biologicznej po optykę i technologię informacyjną. Mikroprzepływy dwu-fazowe to gałąź tej dziedziny, w której używamy dwóch niemieszających się płynów. Pierwsza ciecz jest używana do produkcji kropelek, druga ciecz służy natomiast do transportu tych kropelek przez skomplikowaną sieć kanałów. Celem badań jest poznanie mechanizmów rządzących ruchem kropel w złożonych strukturach mikroprzepływowych oraz opracowanie nowych struktur mikroprzepływowych, które umożliwiają skomplikowaną manipulację kropel wewnątrz układu mikroprzepływowego bez użycia elementów aktywnych takich jak zawory, cewki, elektrody itd. Prowadzone badania mają również potencjał aplikacyjny do zastosowań biomedycznych min. generowania kropel o dowolnych stężeniach np. antybiotyku lub do hodowli bakterii oraz komórek eukariotycznych.

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


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

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

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

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

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