The 1st CONFERENCE of POST UP · 2014-01-29 · The conference is organized by project POST-UP, CZ.1.07/2.3.00/30.0004 Palacký University, Olomouc The 1st CONFERENCE of POST‐UP

The conference is organized by project POST-UP, CZ.1.07/2.3.00/30.0004

Palacký University, Olomouc

The 1st CONFERENCE of POST‐UP

January 22 – 23, 2014 Olomouc


Palacký University, Olomouc

The 1st CONFERENCE of POST‐UP

January 22 – 23, 2014 Olomouc


Palacký University, Olomouc Křížkovského 8 771 47 Olomouc Czech Republic Copyright © 2013

All rights reserved. No part of this work may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without prior written permission of the Publisher. No responsibility is assumed by the Publisher for any injury and/or damage to persons or property as a matter of product liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Printed in the Czech Republic.


Organizing Committee Chair: prof. RNDr. Jitka Ulrichová, CSc. Members: doc. PhDr. Vlastimil Fiala, CSc. Mgr. František Chmelík, Ph.D. doc. Mgr. Martin Modrianský, Ph.D. prof. RNDr. Tomáš Opatrný, Dr.

prof. Ing. Miroslav Strnad, CSC.,DSc. doc. Mgr. Jiří Špička, Ph.D. doc. Mgr. Kateřina Vitásková, Ph.D.


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Author: Faculty, Department:

Pushpinder Singh, PhD.Faculty of Sciences, Department of Computer Science

Title of Conference Contribution:

Ranking fuzzy numbers and its applications

Ranking of fuzzy numbers play an important role in decision making, optimization,

forecasting, production process etc. A {fuzzy number is an extension of a regular number in

the sense that it does not refer to one single value but rather to a connected set of possible

values, where each possible values has its own weight between 0 and 1. This weight is called

membership function. A fuzzy numbers are thus a special case of convex, normalized fuzzy

set of the real line. Just like Fuzzy logic is an extension of Boolean logic, fuzzy numbers are

an extension of real numbers.

Calculation with fuzzy numbers allows the incorporation of uncertainty on parameter,

properties, geometry, initial conditions. Real numbers can be linearly ordered by, <=, or >=,

however, this type of inequality does not exist in fuzzy numbers. Since fuzzy numbers are

represented by possibility

Distribution, they can overlap with each other and it is difficult to determine clearly whether

one fuzzy number is larger or smaller than the other.

Existing ranking methods can be categorized as follows:

1) Preference relation

(a) Degree of Optimization: Baas and Kwakernaak (1977) and Watson et al.

(1979).

(b) Hamming distance: Kerre (1982), Kolodziejczyk (1986), Nakamura (1986)

and Yager (1980).

(c) a‐Cut: Buckley and Chanas (1989) and Mabuchi (1988).

(d) Comparison function: Delgado, Verdegay, and Villa (1988), Dubois and

Prade (1983) and Tsukamoto et al. (1981).


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(e) Desirability index: Nojavan and Ghazanfari (2006).

2) Fuzzy mean and spread:

(a) Probability distribution:Lee and Li (1988).

3) Fuzzy scoring:

(a) Left/right scores: Chen (1985), Chen and Hwang (1992) and Jain (1977).

(b) Centroid index: Yager (1978) and Cheng (1998

(c) Area measurement: Yager (1980).

4) Linguistic expression:

(a) Intuition: Efstathiou and Tong (1980).

(b) Linguistic approximation: Tong and Bonissone (1984).

Key Words: Fuzzy sets, ranking function, multi criteria decision making problems, risk

analysis.


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Elena Stepanova, Ph.D.Faculty of Science, Department Algebra and Geometry


Robustness of networks, topological properties

Topic of networks robustness is very demanded in several scientific spheres, from biology

and virology to social sciences and computer sciences. Networks are normally considered as

a geometrical object on which distance measure can be defined in various ways. Network

topology has impact on its performance, in particular on ability of a network to resist random

failures.

We study how network structure impacts its tolerance and resistence to random failures or

targeted attacks. It is known that some network measures such as betweeness centrality

were found to be important to look at when studying network robustness. We test some

classical measures that were considered important in static setup of the problem ([1],[2],[3])

under dynamic setup. It turns out that betweenness centrality remains to be important

network measure under dynamic setup when we iterate network failures and recoveries.

Our results agree with previous literature assessing the same problem in a static context.

As future work we plan to study performance of other network measures recently proposed

in the information diffusion literature which are based on random walks on a graph.

[1] R. Albert, H. Jeong, and A. L. Barabasi, Error and attack tolerance of complex networks,

Nature, 406 (2000), pp. 378‐382.

[2] S. Nagaraja and R. Anderson, The topology of covert conflict, Tech.Rep. UCAM‐CL‐TR‐637,

University of Cambridge, Computer Laboratory, July 2005.

[3] H. Kim and R. Anderson, An experimental evaluation of robustness of networks, Systems

Journal, IEEE, 7 (2013), pp. 179‐188.

Key Words: complex networks, scale‐free networks, network resilience, network robustness,

evolutionary game theory, topological properties.


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MgA. Christian T. Herbst, Ph.D.Faculty of Science, Department of Biophysics, Voice Research Lab


Assessment of vocal fold vibration with videokymography and related techniques

Christian T. Herbst is an Austrian voice scientist. He studied voice pedagogy at Mozarteum

University, Salzburg, Austria, and worked for several years as a voice pedagogue. Christian

was a visiting researcher at the Center for Computer Research in Music and Acoustics,

Stanford University, and received his PhD in Biophysics from the University of Olomouc,

Czech Republic. Following a position as head of the Bioacoustics Laboratory, Department of

Cognitive Biology, University Vienna, Christian now works as post‐doctoral researcher at the

Voice Research Lab, Department of Biophysics, Palacký University Olomouc. The general

focus of Christian’s scientific work is on both singing voice physiology, and on the biophysics

of voice production in humans and (other) mammals. He received several international

scientific awards, and has to date published 19 peer‐reviewed papers with a total of ca. 70

impact points.

In humans (and other mammals), voice is produced by flow‐induced self‐sustaining

oscillations of the vocal folds, located in the larynx. Determining the quality of vocal fold

vibration is important in both basic voice science and for medical purposes. In the context of

the POST‐UP project, methods for the assessment of voice production are developed, under

the supervision of Jan Švec, Ph.D. & Ph.D.

Amongst others, the following research projects are pursued:

(a) Design and implementation of a software for analyzing vocal fold vibratory features of

videokymographic recordings [1, 2], in collaboration with the Institute of Information

Theory and Automation, Academy of Sciences of the Czech Republic;

(b) Development of a method for assessing the vertical vocal fold contact depth based on

high‐speed videoendoscopy [3] and electroglottography [4], in collaboration with the


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Dept. of Computer Science, University of Applied Sciences Trier, Germany and the

Department of Cognitive Biology, University of Vienna;

(c) Development of an open‐source software application for acquiring Vocie Handicap

Index [5] data, in collaboration with the Voice and Hearing Centre Prague, Medical

Healthcom Ltd.

References:

[1] J. G. Svec and H. K. Schutte, "Videokymography: high‐speed line scanning of vocal fold

vibration," J. Voice, vol. 10, pp. 201‐205, 1996.

[2] J. G. Svec, et al., "Videokymography in Voice Disorders: What to Look For?," Annals of

Otology, Rhinology & Laryngology, vol. 116, pp. 172‐180, 2007.

[3] J. Lohscheller, et al., "Clinically evaluated procedure for the reconstruction of vocal

fold vibrations from endoscopic digital high‐speed videos," Med Image Anal, vol. 11,

pp. 400‐13, Aug 2007.

[4] R. J. Baken, "Electroglottography," Journal of Voice, vol. 6, pp. 98‐110, 1992.

[5] B. Jacobson, et al., "The voice handicap index (VHI): development and validation,"

J.Speech‐Lang.Path., vol. 6, pp. 66‐70, 1997.

Key Words: Human voice, vocal fold vibration, videokymography, high‐speed video

endoscopy, electroglottography, voice handicap index.


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Mgr. Filip Dyčka, Ph.D.Faculty of Science, Department of Biochemistry


Evaluation of enzyme specificity by mass spectrometry

In proteomic protocols, proteins to be identified are isolated and digested by enzymes in‐

solution or in‐gel. The resulting peptide mixtures are further analyzed by mass spectrometry

(MS). The most often applied enzyme for protein digestion is trypsin for its high specificity,

efficiency and good availability. However, the major drawbacks of trypsin use are rapid

autolysis under basic pH and low thermostability at 37 °C. The aim of the project is to explore

the application of other enzymes for proteomic research. The trypsin autolyzate

pseudotrypsin and enzymes isolated from pronase are used in this study. The isolation of

enzymes is an essential step for further analysis. The ion exchange, size exclusion and affinity

chromatography are used for this purpose. Proteins are digested in‐gel by isolated protease

to evaluate enzyme specificity by MS. Peptides are also separated by reversed‐phased liquid

chromatography prior MS analysis. The specific substrates are used to estimate enzymatic

activity.

The research team of prof. Marek Šebela from Centre of the Region Haná from Department

of Protein Biochemistry and Proteomics participates in the project. The team is focused

mainly on protein analysis by MS. The instruments for separation and purification of samples

are in well equipped laboratories. There are MALDI‐TOF/TOF and ESI‐QTOF instruments for

MS analysis. Characterization of proteins are performed together with quantification and

analysis of posttranslational modifications. Identification of intact cells by MS is achieved.

The applicant Filip Dyčka has his professional experiences in separation methods and in MS

techniques. The main part of his previous work was identification and characterization of

proteins and phosphoproteins regulated by plant hormones cytokinins.

Key Words : enzyme, mass spectrometry, proteomics, pronase, pseudotrypsin, trypsin.


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Nuria De Diego, Ph.D.Faculty of Science, Department of Chemical Biology and Genetics, Center of Region Hana for Biotechnological and Agricultural Research (CRH)


Hormone signalling in plant response

The study of physiology has resolved unknown processes involved in plant development and

crop yield. Among them, the knowledge of the mechanisms implicated in stress response or

biotechnological tools such as tissue culture that allow us the maintenance of plant genetic

has been essential. These processes have been reported to be regulated by molecules known

as growth regulators. Cytokinins, auxins and abscisic acid are some examples of them. They

regulate processes such as plant transpiration by stomata closure or rooting through an

interaction between them. Although they are related to these processes, nowadays more

information is needed about their signalling and action mode in plant. In this regards, Dr.

Karel Dolezal’s research group is working in the identification of their role under different

plant growth conditions and development, being the main aims the improvement of plant

propagation by the testing of more active growth regulators in tissue culture protocols, and

the study of different stress to identify possible signal related to plant tolerance process.

Dr. Nuria De Diego is a plant physiologist with more than 10 years research experience. She

was working in similar topics related to hormone signalling, being the most remarkable her

experience in plant tissue culture and stress response. As result, she has authored/co‐

authored almost 12 publications in International Impact Factor journals, half of them being

classified in the first quartile of their category. The formation she acquired during this past

research phase is been a support to achieve the Dr. Dolezal’s group’s objetives. Actually, they

are working in the study of the signalling role that cytokinins, auxins and abscisic acid have in

the tolerance processes of plant grown under abiotic and biotic stress condition. They are

also involved in the development of micropropagation protocols that allow the conservation


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and multiplication of interesting species, especially trees, whose germoplasm maintenance

and cloning are strong problems to solve.

Key Words (max. 10): physiology, growth regulators, plant, response, stress, tissue culture.


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Nicole Gunter, Ph.D.Faculty of Science, Department of Zoology


Understanding molecular relationships of beetles

With more than 350,000 described species, beetles (Coleoptera) are one of the most species

rich and diverse lineages on the planet. They occupy virtually every non‐marine habitat and

specialisation to different niches has promoted morphological and ecological diversification.

Given their extraordinary diversity and richness, classification in to natural groupings remains

problematic. Molecular phylogenetics has shown promise in piecing together the

evolutionary history and relationships of beetles. Since 2009, I have been specialising in

molecular systematics of beetles, predominately focusing on the Australian fauna. During my

first postdoc at CSIRO, Canberra, my research focused on sequencing as many Australian

beetle genera as we could collect. Four genes were sequenced for over 1,300 genera,

representing over a third of known genera present on the Continent. These data are

currently being combined with data generated in the Bocak laboratory at Palacky University

and in collaboration with the Natural History Museum, London. Molecular phylogenies

produced examine relationships at either family, super‐family or ordinal levels and

investigate systematic relationships and evolutionary history. The research target of this

project aims to produce the most comprehensive beetle phylogenies to date, with taxon

sampling representing even coverage of both Old and New World taxa. Where possible,

divergence dating will examine origins and diversification of families over time. It is hoped

that this research will improve the understanding of why beetles are one of the most diverse

lineages of animals and the key drivers of their evolutionary success.

Key Words: Phylogenetics, systematics, divergence dating, Coleoptera, diversification,

evolution.


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RNDr. Peter Illés, Ph.D.Faculty of Science, Department of Cell Biology and Genetics


Construction of Human Luciferase Gene Reporter Cell Line for Assessment of Thyroid Receptor Activation

Thyroid hormones (THs), triiodothyronine and thyroxine (T3 and T4), regulate gene

expression by binding to high‐affinity thyroid hormone receptors (TRs) and play a crucial role

in growth, development and energy homeostasis. TRs belong to the subfamily of nuclear

receptors that recognize specific response elements (TREs) in promoter regions of TH‐

regulated genes and activate or repress transcription in response to hormone. It is known

that large number of exogenous ligands, including natural and synthetic compounds, drugs

and environmental pollutants, may disrupt thyroid hormone mode of action and thus affect

normal function of endocrine system. Therefore, the development of stable reporter system

for assessment of TR transcriptional activity allowing high‐throughput screening of effects of

various compounds on TR‐dependent regulation of gene expression, would be of great

benefit. In our work we focused on selection of human cell line, meeting the criteria for

successful construction of stably transfected reporter cell line in an effort to consequently

prepare such cell line. Using western blot immunodetection analyses we investigated the

presence of TRs (TR� and TR�) in protein cell lysates of 15 human cell lines. Based on the

results we pre‐selected 5 cell lines with the highest levels of endogenously expressed TRs. In

respect to fact, that only the presence of TRs in cells does not provide the functionality of

mechanism responsible for TR‐dependent regulation of gene expression, we performed

quantitative real time PCR studies in selected cell lines. We observed changes in levels of

mRNA expressions of human Spot 14 gene (TH‐inducible gene) after treatment of cells by

different concentrations of T3 and we selected 2 cell lines with the most prominent induction

of mRNA expression. We also designed and prepared 2 reporter plasmids that were used for

transient transfection of both selected cell lines. Results of luciferase reporter assay


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performed on transiently transfected cells revealed that the most significant induction of

luciferase activity after T3 treatment occurred in human hepatocellular carcinoma cell line

HepG2. Therefore HepG2 cells were transfected repeatedly and selection for monoclonal

populations of stably transfected reporter cell lines is being in progress.

Key Words: Thyroid hormone, thyroid receptor, human cell line, luciferase gene reporter

assay.


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RNDr. Lenka Dzurová, Ph.D.Faculty of Science, Department of Molecular Biology, Center of Region Hana for Biotechnological and Agricultural Research (CRH)


Towards protein crystallization

My study began at the Department of Biochemistry, Faculty of Science, UPJŠ in Kosice,

Slovakia, where I graduated with honors (M.Sc. in Biochemistry). During master study I spent

5 months at the Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth,

Germany under supervision of prof. Dr. Holger Dobbek, where I crystallized Xenobioticum

reductase A from Pseudomonas putida 86. In 2007 I have started PhD study at the

Department of Biophysics, Faculty of Science, UPJŠ in Kosice, Slovakia under the supervision

of prof. RNDr. Pavol Miskovsky, DrSc. The doctoral project was focused on understanding of

physico‐chemical mechanism of anticancer activity of natural photosensitizer Hypericin on

human glioma cell line U‐87 MG. Experimental results were presented on many international

and national congresses. During doctoral study I spent 1 month in the Academic and

University Center Nove Hrady, Czech Republic, 6 months in the laboratory of Dr. Franck

Sureau at Paris VI University, where I have worked with special apparatus for fluorescence

lifetime imaging.

Nowadays I am working at the “postcdoc” position under supervision of prof. RNDr. Ivo

Frébort, CSc., PhD at the Department of Molecular Biology. The project is focused on the

study of biosynthesis, metabolism and function of cytokinins in cyanobacteria.

Understanding of cytokinins action mechanism in cyanobacteria will lead to better

knowledge about the basic functions of these important plant hormones. This research work

takes place at the Center of the Region Hana for Biotechnological and Agricultural Research

(CRH).


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During the project 6 months of professional stay at the University of Pavia, Italy is planned

(group of prof. Andrea Mattevi, solving protein structures of flavoproteins). The aims of my

project include gene cloning, expression, purification and crystallization of proteins. Manage

protein X‐ray diffraction data analysis and protein structure solving is the main challenge of

my work.

This project also comprises educational activities such as teaching of Microbiological

practices, leading of Bc. / M.Sc. students and consultation with students within the team.

Key Words: UPJŠ, hypericin, CRH, cytokinins, crystallization.


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RNDr. Jana Gáliková, Ph.D. Faculty of Science, Department of Inorganic Chemistry , Regional Centre of Advanced Technologies and Materials (RCPTM)


Copper(II) and zinc(II) complexes of biologically relevant 9‐deazahypoxanthine derivatives

9‐Deazahypoxanthine (9dhx) derivatives belong to the group of powerful purine nucleoside

phosphorylase inhibitors used for the treatment of several autoimmune diseases. Based on

several recently published studies, it is evident that coordination compounds may show

higher biological activities as compared to the organic ligands alone. The first step towards

biological studies of such compounds is understanding their structural properties which

could help us design the most active compounds.

In order to study the coordination behaviour of 9dhx, depending on the reaction medium

and molar ratio between the starting compounds, the following Zn(II) and Cu(II) complexes

with diverse coordination motifs and structures have been prepared and thoroughly

characterized, (9dhxH)2[ZnCl4]∙H2O, [Zn(9dhx)Cl2]n, [{Zn(9dhx)(H2O)3}2(µ‐SO4)2],

[Cu(9dhx)2Cl2]n, [Cu(9dhx)2(NO3)2(H2O)2], [{Cu(9dhx)(H2O)3}2(μ‐SO4)2] and [ZnCl2(L)2]∙xSol (L =

6‐alkoxy‐9‐deazapurine derivatives, with Sol = H2O, CH3CN). Moreover, the zinc(II) complexes

were tested for in vitro cytotoxicity against ovarian carcinoma (A2780), prostate carcinoma

(PC3) and prostate adenocarcinoma (LNCaP) human cancer cell lines.

The outlook to the future comprises synthesis and full characterization of new 6‐alkoxy‐9‐

deazapurine complexes with other transition metals i.e. gold(I) while focusing on compounds

which could exhibit significantly high in vitro and in vivo biological activity (e.g. anti‐cancer,

anti‐inflammatory) and at the same time low toxicity to healthy human cells.

Key Words: Zinc(II), Copper(II), Complexes, 9‐Deazahypoxanthine, Cytotoxicity, X‐ray

structure, SQUID experiments.


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Mgr. Andreea‐Maria Iordache, Ph.D. Faculty of Science, Department of Analytical Chemistry, Regional Centre of Advanced Technologies and Materials (RCPTM)


Desorption nanoelectrospray – influence of surface wetting on desorbed ion intensity

Desorption nanoelectrospray (nanoDESI) was developed at Department of Analytical

Chemistry, Palacky University as a miniaturized version of desorption electrospray (1). On

contrary to DESI, nanoDESI uses a spray tip 1‐2 µm I.D. and none assistance of a nebulizing

gas. Although nanoDESI was successfully applied in wine or blood analysis (2,3) many

fundamental questions have to be still addressed. Among others properties of surface with

deposited sample play an important role. We have observed the change of intensity of ions

with wetting of surface. The experiments have been performed using a home‐made ion

source and an ion trap mass spectrometer (LCQ Deca, Thermo Fischer, USA).

Wetting of surface has been controlled by spraying liquid by a nanoDESI tip or using solvent

vapors. In both cases, the increase of intensity in order of magnitude has been observed.

Detail study of mechanism is in progress but so far obtained knowledge facilitates application

of the developed ion source.

NanoDESI‐MS has been used in direct analysis of inks. Profiling of dye components can be

useful e.g. in forensic analysis. After evaluation of influence of experimental parameters

(surface, solvent composition) different dyes (e.g. Basic Blue 7, Basic Violet 3, Basic violet 1,

basic violet 10) were successfully identified in samples deposited on glass or teflon surface.

Nano‐DESI analysis provides a simple and fast way to compare ink specimens and in the same

aspect permits their rapid screening.

1. Ranc, V.; Havlicek, V.; Bednar, P.; Lemr, K.: Desorption electrospray: A modern tool for

organic surface analysis. Chem. Listy 101 (2007) 524‐529.


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2. Ranc, V.; Havlicek, V.; Bednar, P.; Lemr, K.: Nano‐desorption electrospray and kinetic

method in chiral analysis of drugs in whole human blood samples. Eur. J. Mass

Spectrom. 14 (2008) 411‐417.

3. Hartmanova, L.; Ranc, V.; Papouskova, B.; Bednar, P.; Havlicek, V.; Lemr, K.: Fast

profiling of anthocyanins in wine by desorption nano‐electrospray ionization mass

spectrometry. J. Chromatogr. A 1217 (2010) 4223‐4228.

Key Words: Desorption nanoelectrospray, mass spectrometry, desoption/ionization

mechanism.


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Carmen del Cacho, Ph.D.Faculty of Science Department of Analytical Chemistry


Characterization of magnetic nanoparticles by capillary electrophoresis

I am an Analytical Chemist. I joined the Laboratory of Capillary Electrophoresis at the

Department of Analytical Chemistry, Palacký University in Olomouc in January 2013 under

the supervision of Prof. Juraj Ševčík and Dr. Jan Petr. Before coming to the Czech Republic I

worked in Complutense University of Madrid (Spain) and the Institute for Health and

Consumer Protection in Ispra (Italy). I have worked extensively on sample preparation

techniques and separation methods such as high performance liquid chromatography, gas

chromatography or capillary electrophoresis.

Magnetic nanoparticles are recently being used as contrast agents in nuclear medicine (e.g.

NMR) and have been proposed as substitutes of other toxic contrast compounds such as

gadolinium. It is however necessary to evaluate the possible interaction of such

nanoparticles with the body (e.g. proteins) and thus evaluate their potential toxicity.

Capillary electrophoresis seems to be a useful technique for the evaluation of such

interactions.

My work within the Laboratory of Capillary Electrophoresis is therefore oriented towards:

‐ The characterization of the behavior of nanoparticles by capillary electrophoresis

‐ The study of on‐line preconcentration methods of nanoparticles in capillary

electrophoresis

‐ The evaluation of their possible interactions with different proteins / enzymes /

nucleic acids by capillary electrophoresis


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Additionally, during November 2013 I did a foreign stay in Ecole Nationale Superieure de

Chimie de Paris in France, in which I learned the methodology to prepare nanoparticles

suitable for study of their interactions with different cell lines.

Key Words: Analytical chemistry, nanoparticles, capillary electrophoresis.


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Jason A. Perman, Ph.D.Faculty of Science, Department of Physical Chemistry


Pillaring Graphene and Graphene Oxides

Graphene is one of a few 2D single crystalline materials that exhibit very interesting optical,

electronic and mechanical properties. The two former properties are largely under

investigation but the latter is a little trickier as graphene does not behave as well as a small

molecule which can be easily manipulated. The ongoing challenge in which we are

investigating is the ability to control the inter layer space between layers of graphene. The

controlled space can provide useful properties, such as but not limited to sorting and

separation of gases with a high flux, remediation/decontamination of toxic industrial

chemicals (TICs), or the slow release of pesticides among many others. To enable pillaring

two routes can be utilized such as covalent bonds and non‐covalent interactions with

graphene. Here we have chosen both techniques either separately or in tandem to

investigate the porous properties of pillared graphene and graphene oxides. A key challenge

lies with modifying the planar surfaces of graphene or graphene oxide with minimum or no

functionalization of the edges which are known to be more reactive towards many reactions.

Key Words: Graphene, Graphene Oxide, Porous Materials, Pillaring, Remediation,

Decontamination.


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Kasibhatta Kumara Ramanatha Datta, Ph.D. Faculty of Science, Department of Physical Chemistry


Graphene Hybrids

Graphene, the first two‐dimensional crystal enjoying its supremacy, is undoubtedly the most

studied material in interdisciplinary science and technology since the last decade. The

extraordinary properties of this sp2 bonded carbon hexagonal two‐dimensional crystal

include high surface area, transparency, electrical conductivity, carrier mobility, surface

reactivity, strength, flexibility, etc., makes it an emerging and forefront candidate for diverse

applications.1 We are interested in bringing out the novel properties graphene and its

derivatives, i.e. graphene oxide and halogenated graphenes, either via chemical

functionalization or by anchoring functional nanomaterials onto graphene. My experience on

nanostructured carbon materials, inorganic nanoparticles, graphene hybrids along with the

center‘s (RCPTM) expertise and experience on graphene, halogenated graphenes and carbon

nanodots2‐4 with strong theoretical support will help in developing new functional

nanostructures based on graphene and its derivatives.

Assembly of positively charged quaternary carbon dots (QCD) over negatively charged

graphene oxide (GO) was achieved by non‐covalent approach. These hybrids are highly

fluorescent and energy transfer occurs from QCD’s to GO. The fluorescence of the hybrids

can be tuned by suitable modification of GO, i.e. by changing the surface chemistry of GO.

Further the cytotoxicity of GO‐QCD hybrids are evaluated against Mouse fibroblasts NIH3T3

cells.5 Also during the talk iron oxide nanoparticles embedded graphene oxide,

functionalized halogenated graphene derivatives and some of the current results will be

briefly highlighted.


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References:

1. A Roadmap for Graphene

K. S. Novoselov, V. I. Fal'ko, L. Colombo, P. R. Gellert, M. G. Schwab, K. Kim, Nature

2012, 490, 192‐200.

2. Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives

F. Karlický, K. K. R. Datta, M. Otyepka, R. Zbořil, ACS Nano, 2013, 7, 6434–6464.

3. Halogenated Graphenes: Emerging Family of Two‐dimensional Materials

K. K. R. Datta, R. Zbořil, Book Chapter, Wiley (submitted)

4. Surfactant‐Derived Amphiphilic Carbon Dots with Tunable Photoluminescence

O. Kozák, K. K. R. Datta, M. Greplová, V. Ranc, J. Kašlík, R. Zbořil, J. Phys. Chem.

C, 2013, 117, 24991–24996

5. Two Dimensional Graphene Oxide‐Carbon Dot Fluorescent Nanoarchitectures

K. K. R. Datta, O. Kozák, H. Markéta, A. B. Bourlinos, K. Safarova, R. Zbořil, M. Otyepka

(manuscript under preparation)

Key Words: Graphene oxide, Carbon dots, Iron oxide, zerovalent iron, fluroscence, cell

labelling, hybrids, halogenated graphene.


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Mgr. Radina Kralchevska, PhDFaculty of science, Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials (RCPTM)


Application of hight valent iron materials for water treatment

My work as a junior researcher in RCPTM and Palacky University in Olomouc started

immediately after PhD graduation at the University of Sofia, Bulgaria. My previous scientific

experience is based on application of photocatalytic and oxidation technologies for water

treament, especially using TiO2 pure and modified materials for degradation of organic water

pollutants such as pesticides, industrial dyes, estrogens. Modification of TiO2 nanomaterials

during synthesis aimed to improve different characteristics of the samples.

My research activity at RCPTM, in group of doc. Libor Machala is focused on the possible

applications of high valent iron materials for water treatment.

Currently I am working on two scientific projects. The first one is devoted to exploration of

optimal experimental conditions, i.e. pH and doses of ferrate(VI) in order to remove

phosphates from water by sorption. The leader of this project is Dr. Robert Prucek. In future

we are planning to continue with simultaneous removal of both As‐contaminants and

phosphates in water.

The second project is based on water treatment of environmental samples, especially ground

water using oxidation and coagulation capacity of ferrate(V) or ferrate(VI) materials. The

leader of the project is doc. Libor Machala and my supervisor is Dr. Jan Filip. Partner in this

project is the University of Liberec, so next year a short visit is planed there.

The two research topics that I already mentioned are a priority for me at the moment,

however later on I am also planning to continue my investigation, focused on applying

various oxidation technologies for degradation of free and complex cyanides.

Key Words: Ferrate (VI), water treatment, phosphates, environmental samples.


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Ing. Vadim Evseev, Ph.D.Faculty of Science, Department of Optics


The Development of Spectropolarimeter for Characterization of Polarizing Elements in a Wide Spectral Range

The work is mainly focused in the field of spectropolarimetry, in particular, on further

development and application of the dual rotating‐retarder spectropolarimeter which has

been developed by Dr. J. Kapitán in collaboration with Mgr. R. Čelechovský at the Department

of Optics. The spectropolarimeter is designed for comprehensive characterization of various

polarizing elements such as waveplates and polarizers in a wide spectral range, which is one

of major research targets of the current project. As a starting point, a new algorithm is

developed by the postdoctoral fellow for the spectropolarimeter error compensation and

data analysis. In contrast to methods published in the literature, the developed algorithm

offers much flexibility in accounting for values of various operation parameters and sources

of errors hence providing opportunity for comprehensive optimization analysis of the

spectropolarimeter and its configuration, which is another research target. Along with the

work on the spectrpolarimeter, the research team is focused on the development of the

experimental setup for the measurement of Raman scattering and Raman optical activity

spectra of various biochemical compounds. The experimental setup includes polarizing

elements as main parts, and in that respect, the characterization of polarizing elements by

the spectropolarimeter in a wade spectral range, being a stand‐alone target, makes it helpful

also for this part of the current project which is focused on the Raman instrumentation.

Formulated above professional specialization and research targets of the postdoctoral fellow

in the current project is a logical extension of his previous experience which has been mainly

focused on infrared spectroscopy and its industrial applications, in particular, on the

development of an experimental setup for measurement of gas spectra in the infrared range

on industrial scale, such as a power plant or an internal combustion engine, the development


27

of software for modeling of gas spectra, and on the development of a linear control system

for an angular vibration table used for calibration of various micromechanical inertial

guidance elements, such as micromechanical accelerometers and gyroscopes.

Key Words: polarimetry, waveplate, retarder, polarizer, Raman scattering, Raman optical

activity, infrared spectroscopy.


28


Mgr. Michal Sedlák, PhD.Faculty of Science, Department of Optics


Characterization and discrimination among quantum optics devices

My current research activities at the Palacky University are based on the cooperation with Doc.

Jaromír Fiurášek, whose is my mentor within the PostUP project. We propose experiments and

methods of their characterization for quantum optics laboratory situated in our department of optics.

These experiments are closely related to the field of quantum information processing, where is my

main expertize.

We have already proposed an efficiently measurable lower bound on quantum process fidelity of N‐

qubit controlled‐Z gates. A distinct advantage of our approach is that only fidelities with product

states need to be measured while keeping the total number of measurements much smaller than

what is necessary for full quantum process tomography. As an application, we use this method to

experimentally estimate quantum process fidelity F of a three‐qubit linear optical quantum Toffoli

gate.

The second project that I’m involved in concerns discrimination of quantum measurements. Here I

participate not only by proposing the experiment, but also by modelling the expected sources of

noise and processing of the actual experimental data. As a „pure theorist“ I got a chance to see the

experiment slowly growing on the optical table and to understand the typical sources of errors and

problems that one has to face. Via discussions with experimentalists we managed to propose a model

of the experiment that quite faithfully captured the capabilities of our experiment and guided the

experimentalist in their final measurements.

Key Words: quantum optics, quantum information, estimation, discrimination.


29


Mgr. Alexander Shurupov, Ph.D.Faculty of Science, Department of Optics


Experimental research in quantum information processing based on quantum optics

I have joined experimental group in the department of Optics. Our experimental laboratory is

focused on scientific research in the field of non‐classical light sources (for example, sources

of entangled photon pairs), detection of single photons and the use of non‐classical states of

light for encoding, transmitting and processing information. While there are several ongoing

experiments, my main task up to now was experimental realization of new highly efficient

source of correlated photon pairs. It is based on so called Sagnac‐type loop interferometer,

when a non‐linear crystal is pumped by laser beam from both directions. With proper

adjusting of focus condition for the pump beam and collection optics it is possible to achieve

either very high spectral brightness single photons or high efficiency of that source which is

expressed as ration of pairs count to single photon count. Main advantages of such source

are its stability (the optical loop have to be stabilized only to the order of coherent length of

the laser pump), high visibility of the entangled photon pairs and possibility to make linear

dimensions very compact.

As this work is only started, by the time of this talk we have purchased most of the necessary

elements – periodically polled non‐linear crystal, custom made polarization beam‐splitters,

and polarization retarders. The temperature controller and control schemes, crystal oven and

holder are being developed and constructed.

The second part of ongoing work is development of custom software for ultra‐fast time

tagging module, which will be used in the latter part of the project. This activity is performed

in close collaboration with the original device manufacturer from Austrian Institute of

Technology.

Key Words: Non‐linear optics, quantum optics, single photon source.


30


Kimin Park, Ph.D. Faculty of Science, Department of Optics


Arbitrary quantum operations induced by single photons

For various purposes of science it is crucial to be able to precisely manipulate a system at

will. This ability is the key both to experimental tests of fundamental principles and to the

actual development of quantum technology. The ultimate goal in this direction is the

implementation of arbitrary transformations and generation of arbitrary quantum states the

quantum systems. One feasible way of approaching this daunting task lies in disassembling

general operations into a common elementary building block. For two‐level (qubit) quantum

systems, such building blocks are the single qubit rotations and the two‐qubit controlled NOT

operation. In a similar vein, the basic building blocks for continuous variable harmonic

oscillator systems are the operations imposing quadratic and cubic potentials. The quadratic

potential inducing Gaussian operations can be considered readily available. A general

method of achieving any form of quadratic potential uses squeezed states of light which

interact with the oscillator and are subsequently measured by optical homodyne detection.

In this talk I present a complementary approach which relies on the continuous variable

position operator, the sole variable of potential for harmonic oscillator. Our method may

allow the simulation of the dynamics in an arbitrary nonlinear potential on a quantum

oscillator by a sequential application of conditional X‐gates. As a key resource, we use single

photon guns, which were recently extensively developed for broad class of applications. We

theoretically propose a conceptual structure of the elementary X‐gate and feasible

realizations of the X‐gate using basic coupling of light to the various quantum oscillators. We

analyze the performance and feasibility of this methodology with regard to realistic

experimental situations and emphasize the generation of the cubic nonlinearity and efficient

state preparation of non‐Gaussian states.


31


Mgr. Martina Benešová, Ph.D.Philosophical Faculty, Department of General Linguistics


The Menzerath‐Altmann law under the magnifying glass

In my paper I try to map the research and experiments which I participate in. The field of my

interest is quantitative linguistics, recently and currently in particular testing linguistic

samples using the Menzerath‐Altmann law (MAL).

Firstly, there is a certain methodology of a quantitative linguistic experiment which is to be

followed. Starting asking the right question in a right way, i.e. enunciating a hypothesis, it

consists of certain stages. Each stages needs discussing and understanding the reason for its

being a part of the experiment.

Secondly, the verbal formulation of MAL stated first by Paul Menzerath has been interpreted

mathematically in several different ways. Their usage, meaning, differences has to be tested

and cleared. Also the meaning of the MAL parameters has to be stated in some hypotheses

and further tested.

Thirdly, for the linguistic sample to be quantifies and the outcomes to be processed, the

sample has first to be segmented using appropriate and suitable linguistic units in

accordance with the valid and accepted linguistic laws. The pitfalls of such segmentations

need to be pointed out.

A vital stage of any experiment is testing its qualities employing statistical methods. For using

a particular statistical method we have to understand its limitations and requirements for the

data being tested by them.

Last but not least, suspected fractality of language and texts is tested. A link between some

qualities of fractal objects and MAL has been noticed by e.g. Luděk Hřebíček and developed

further by Jan Andres. Tested language and text fractality has become an important part of

the above sketched research.


32

The mentioned questions have provoked some hypotheses which have been and are going to

be tested on several text samples of different styles, languages, length and other features to

ensure the research plausibility.

Key Words: Quantitative linguistics, the Menzerath‐Altmann law, text fractality, stages of

experiment, text segmentation, testing the experiment validity.


33


Mgr. Lukáš Motyčka, Ph.D.Philosophical Faculty, Department of German Studies


The research of German Moravian literature at Palacký University Olomouc

The paper will briefly present to the participants of the conference the Research Centre for

German Moravian Literature/ Arbeitsstelle für deutschmährische Literatur, an institution

well‐known and recognised in the European context, which has been focusing on the

research of German literature from the Moravian area since 1998. The presenter, a

postdoctoral assistant and the organisation manager of this institution, will introduce the

activities and future goals of the Centre.

The essential point of the paper will be the contextualisation of the academic research of the

Centre with trends in humanities or cultural studies. The presentation will focus on the

involvement of the Centre, its members and the manager in various projects. Since its

establishment, the Centre has shown a great deal of popularising and scientific activity. The

members have participated and are still involved in many projects. The role of the

organisation manager mainly comprises the coordination of the activities of the members

and the initiation of new cooperation. Another point will be the organisation structure of the

institution and the resulting responsibilities of the organisation manager, including the

engagement of students from the bachelor and master study programmes in the activities of

the Centre. Furthermore, he is responsible for pedagogical and consulting work.

Key Words: German Moravian Literatur; German Literature; Olomouc; Moravia; Palacký

University; Research Centre for German Moravian Literature, reginal literature.


34


Mgr. Mirna Šolić, Dr.Faculty of Philosophy, Czech Language and Literature


Postdoctoral Research Project „The Narrative Construction of Space:“ Targets and Objectives

My postdoctoral project “The Narrative Construction of Space” seeks to examine how space

is constructed in a variety of narrative texts and media. My participation in this project draws

directly on my previous research expertise from the University of Toronto (Ph.D. awarded in

2008) and the University of Glasgow (where I am currently in residence), which could be

roughly defined as travel writing, cultural identity and literature, intermediality, and gender

and literature, themes which I approach using narratology as the principal theoretical tool.

My contribution to the project is the monograph on the narratological constitution of space

in Karel Čapek’s travel writings (to be published by the University of Toronto Press) as well as

two studies which examine the 20th century Czech travel writing. While the monograph

focuses on the experimental nature of Čapek’s travel writing opus and discusses it within the

20th European travel writing canon, the two studies investigate construction of space in

postwar Czech travel writing literature. The first study investigates the Czech travel writing of

the 1950s and the 1960s, whereas the second analyses the representation of travel in

contemporary Czech literature and new media.

Alongside the postdoctoral research project I participate in two research teams. The first,

already well‐established students‐led project “The Space in Literature,” is centred around

team‐work on a publication which seeks to offer a possible methodology for the

narratological examination of space. In the second research project, in conjunction with the

colleagues from the UP and elsewhere (with Professor Dagmar Mocná and Dr Jana Vrajová as

the core members), my role is to analyse the position of contemporary travel writing within

the popular Czech cultural and literary discourse.


35

I also offer research‐based teaching which is closely tied to the examination of space in

different genres and literary periods: the poetics of Czech travel writing, Karel Čapek’s work,

the gendered space in women’s writing and the representation of Prague in Czech literature.

Key Words: Postdoctoral project, space in literature, narratology, Karel Čapek, travel writing,

Czech literature, popular literature and culture.


36


PhDr. Martina Číhalová, Ph.D.Philosophical faculty, Department of Philosophy


Natural Language Analysis via TIL

The main aim of my research is the logical analysis of natural language. The background

theory is Transparent Intensional Logic (TIL) with its procedural (as opposed to denotational

semantics). This presentation introduces TIL in brief and its application on natural language

analysis. From the formal point of view, TIL is a hyperintensional, partial typed lambda

calculus. For its great expressive power, TIL is well suited for a fine‐grained logical analysis of

natural language. TIL rich procedural semantics makes it possible to state explicitly all the

semantically salient features of natural language expressions. Namely it is able for instance to

distinguish explicitly analytical and empirical concepts and the three kinds of context in

which the same meaning of an expression may occur. These context levels are the following:

the extensional level of truth‐functional connectives, the intensional level of modalities and

finally the hyper‐intensional level of attitudes. The importance of the correct context‐

recognition for the natural language analysis is illustrated by means of the examples.

Furthermore, this presentation also introduces research team I cooperated with and the brief

introduction of the publications I have presented at international conferences.

Key Words: hyperintensional, intensional, extensional context, construction, Transparent

Intensional Logic.


37


PhDr. Daniel Dostál, Ph.D. Philosophical faculty, Department of Psychology


Autistic traits and scientific interests: a general review

There is a substantial rising interest in the autism research in recent decades among

psychologists. The empathizing–systemizing theory formulated by Simon Baron‐Cohen is one

of the novel authoritative theories concerning this topic. Is assumes that there is a

continuum of autistic traits rather than two discrete categories and that it can be observed

and measured even in non‐clinical population. The paper summarizes the current knowledge

and the results of our studies on autistic traits in scientific workers and university students of

various specializations. It confirms the existence of the general pattern that certain

personality traits associated with autism (social aloofness, lower social intelligence,

introversion) are most intense among representatives of the exact disciplines (e.g. math,

technology, physics).

Key Words: autism, psychology of science, systemization.


38


Mgr. Eva Lebedová, Ph.D.Philosophical Faculty, Department of Politics and European Studies


Voter polarization in the Czech Republic

The process of election campaigning which is in contemporary democracies characteristic

with the use of political marketing is considered as a period of sharpening ideological

conflicts and rising negativity among the political parties. For that reason I want to analyse

and measure in this paper, whether election campaigning together with political marketing

can increase ideological differences among the parties and what impact a marketing

campaign can have on the polarization of voters. I will focus on answering several research

questions: Can we detect an increase in voter polarization in connection with the advent of

marketing campaign in 2006 in the Czech Republic? How does the voter polarization change

over the time (1993–2012)? Do the campaign activities of the party elites and media

exposure contribute to the increasing voter polarization during the pre‐election period?

Key Words: Voter polarization, election campaigning, L‐R scale, ideological divisions, Czech

Republic.


39


Mgr. Petr Lyko, Ph.D. Philosophical faculty, Department of musicology


The research of musical culture in Krnov in the 1st half of the 20th century

The object of the research is the phenomenon of musical culture in Krnov in the 1st half of

the 20th century. The chosen object of the research comprises, in its primary level, all the

products of German and Czech musical culture and musical life (i e institutional background,

music clubs, music ensambles, associations, choirs, composers and their work, performers,

contemporary reception, criticism, music education etc.). It also offers a comprehensive

thematic field for a detailed processing of basic resources and performing of basic research.

However, at the same time it represents a sufficiently extensive field of research for

achieving synthesizing findings of the higher territorial, respectively national units and

suggested interdisciplinary approach.

One of the primary aims of the project ‐ in addition to the basic musical topographic research

‐ is to evaluate the phenomena associated with the German and Czech musical culture in the

broad, general cultural and historical context.

The project will also deal with the terminology and substance of the entities "German/Czech

(musical) Culture/Music" etc.

The basic methods will be the work with resources, analysis and comparison of the resources

found and synthesis of partial findings into comprehensive theses

Key Words: Krnov, musical culture, musical life, musical institutions, music clubs.


40


Brenda Peters, EdD., MEd., BEd(Hons). Faculty of Education Institute of Special Education Studies


The development of inclusive educational practices: Partnership and collaboration across educational communities

Research interest. The development of inclusive educational practices: Partnership and

collaboration across educational communities.

I was a teacher for children with Special Educational Needs (SEN) who experienced the

paradigm shift in educational provision in the UK and HK e.g., from integration to inclusive

education. As a post‐graduate researcher I investigated the whole school approach adopted

by regular primary schools in Hong Kong in 2008 as part of a team. These two valuable

experiences have contributed to my research focus for the post doc.

Project 1

Enhancing the development of Inclusive practices in the community: An investigation of

partnerships between University and schools. Trends noted in international literature

concern the promotion of partnerships and sharing responsibility for developing inclusive

practices within educational communities. Anecdotal evidence suggests partnership work for

inclusive practices is highly desirable in the Czech Republic, however, current partnerships

might be established on an ad hoc basis. Furthermore, collaboration between educational

professionals to develop inclusive educationl practices may be difficult because of cultural

historical influences and currents concepts of special educational provision.

Goals. The project examines collaborative activities between educational communities with a

view to enhancing inclusive educational practices.

Project 2: School principals’ attitudes towards students with Special Educational Needs. Co‐

investigator Professor Milon Potmesil. Outcomes ‐ Manuscript submitted for publication co

authored by Milon Potmesil and Chris Forlin, HKIEd. Conference presentations at ICERI

conference 2013 Seville, Spain & HKICEPS Hong Kong.


41

Project 3: Value priorities in adolescents with hearing impairment‐ PI: J Kossewska, Poland.

Co‐I Milon Potmesil, Brenda Peters and Petra Potmesilova. Manuscript accepted &

Conference Krakow, Poland, December 2013.

Project 4: Promoting Peer Interaction of Deaf and Hard‐of‐Hearing Children in Inclusive

Education manuscript submitted for publication; authored by Xie Yuhan, co‐authored by

Professor Milon Potmesil and myself.

Key Words: Inclusion, Stakeholders attitudes & pupils with SEN, Inclusive practices,

Communities, Networks.


42


JUDr. Olga Pouperová, , Ph.D.Faculty of Law, Department of Administrative Law and Administrative Science


An ideal organizational arrangement of a broadcasting regulatory authority

Organizational arrangement of a broadcasting regulatory authority represents one of

significant aspects over the quality of media regulation as it predicates whether regulation

will be executed independently of political influence and whether media will be able to fully

perform their social function. Freedom of expression or freedom of mass media (and

explicitly or implicitly the independence of broadcasting regulatory authorities) is laid down

in numerous documents (recommendatory as well as binding ones). The same as in the

Czech Republic, in some other European countries those independent broadcasting

regulatory authorities were first established in the 90‐ies. Their establishment brought about

the need to find ways to secure their independence. The resulting scheme was determined

by political and legal system of the given country, the level of legal and political culture of the

given society and then perhaps optimistic social atmosphere. In response to the financial

crisis and the tendencies towards the downsizing of public administration in the Czech

Republic, the last few years brought about proposals on the re‐arrangement of the

Broadcasting Council into which politicians again tend to project the tempting opportunity to

keep some influence over the staffing of the Council. The issue of how to organize the

broadcasting regulatory authority so as to ensure its independence thus becomes topical

again. The objective of my paper is to identify and systematize the existing approaches

applied with the aim of safeguarding independence of broadcasting regulatory authorities

and use the analysed approaches and their key elements as the basis for determining an

ideal organizational arrangement of a broadcasting regulatory authority which would suit the

Czech legal system and, to an optimum extent possible, meet the criterion of independence.


43

Key Words: Broadcasting, Council for Radio and Television Broadcasting freedom of

expression, freedom of mass media, independent regulatory agency.


44


JUDr. Ondřej Šmíd, Ph.D.Faculty of Law, Department of Civil and Labour Law


Evaluation of the current activities of a post‐doctor in the period from 12/2012 – 12/2013

The author will in the contribution pay attention to his current activities as a post‐doctor at

the Department of Civil and Labour Law of Palacky University in Olomouc. He will mainly

focus on presenting his scientific outputs (monographs, commentaries, textbooks, articles)

and involvement in research teams both at the Law Faculty of Palacky University and other

institutions, as well. He will further present other activities in which he is also engaged

(organization of scientific conferences, teaching, leadership of theses, participation in

national and international conferences and symposia).

Key Words: Research, maintenance, divorce, family law.


45


Mgr. Jitka Široká Ph.D.Faculty of Medicine and Dentistry, Laboratory for Inherited Metabolic Disorders and Metabolomic Group


Development of methods for metabolite assessment in biological samples for diagnosis of diseases and metabolic disorders

The aim of metabolomic approach is the identification, quantification and interpretation of

metabolic changes in biological system. It represents a comprehensive view to the

pathobiochemical processes in the living organism and facilitates automated diagnosis of

metabolic disorders.

The first step of metabolomic assays is the metabolite extraction from the biological samples

(plasma, urine, cell extracts etc.), followed by analysis by convenient analytical technique ‐ in

our case tandem mass spectrometry (TMS; QTRAP 5500, AB SCIEX, USA) with flow injection

analysis (FIA‐MS) or coupled to high performance liquid chromatography (HPLC‐MS)

(Ultimate 3000 RS, Dionex, USA). The data acquired are evaluated statistically by principal

component analysis (PCA) and discriminant function analysis (DFA).

The metabolomic method developed in our laboratory permits determination about 400

analytes in total. Since July 2013 the methodology was applied on plasma and leukocyte

extract from leukemic patient from University Hospital in Hradec Králové, from non‐clinical

samples on plasma of mice treated by different diet from Institute of physiology AV CR and

Netherland. Also various unusual biological matrices like aqueous humour, spleen and bone

marrow extracts were investigated by this methodology. Recently there is a concern of

various HPLC columns testing.

Key Words: metabolomics, liquid chromatography, mass spectrometry, biological samples.


46


Mgr. Barbora Lišková, Ph.D.Faculty of Medicine and Dentistry, Department of Pharmacology


Study of cytochrome P450 at the Department of Pharmacology

Department of Pharmacology is a cooperating institute of University Hospital and Medical

Faculty of Palacky University Olomouc. It was established in March 1946. Prof. MUDr. H.

Zemanková‐Kunzová, who came to Olomouc from Masaryk University, Brno, was first head of

this department.

This department is dealing with teaching, research and preventative medical care in the field

of experimental and clinical pharmacology. Among others, the main aim of our department is

studying interactions of cytochrome P450 and potentials drugs under leadership of Professor

Pavel Anzenbacher.

The P450 enzymes are versatile drug‐oxidizing systems in drug response, drug toxicity and

drug interactions. The term cytochrome P450 (CYP) is reported as large group (superfamily)

of enzymes containing in its molecule heme. These enzymes are part of the most important

system phase I biotransformation of endo‐(e.g., steroids, bile acids, fatty acids,

prostaglandins, leukotrienes, biogenic amines) but also exogenous substances.

For study of expression and enzymatic activity of cytochrome P450 are used methods of

analytical chemistry (UV/VIS spectroscopy, HPLC) and molecular biology (RT‐PCR). Real‐time

PCR is quantitative PCR method used for the determination of number of PCR templates such

as DNA or cDNA in a PCR reaction. There are two types of real‐time PCR: probe‐based and

intercalator‐based. Both methods require a special thermocycler equipped with a sensitive

camera that monitors the fluorescence in each well of plate at frequent intervals during the

PCR reaction.

Key Words: Department of Pharmacology, cytochrome P450, Real‐time PCR.


47


Mgr. Ermin Schadich, Ph.D.Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine


Identification of novel drugs against tropical infectious diseases and cancer

The project aims to identify the novel drug candidates with in vitro and in vivo activities

required for therpaeutical measures against tropical infectious disease and cancer. In the

first part of study, the two stable human reporter cell lines for identification of modulators of

cellular signal transduction pathways associated with pathogenesis of cancer were

developed and validated trough co‐operation with other team members. They are cAMP

response element binding protein (CREB)‐human embryonic kidney cells HEK293 and

antioxidant response element (ARE)‐human hepatocellular carcinoma HepG2 reporter cell

line. Their signals were highly specific and sensitive both in bioassays with known effective

drugs and novel pathway modulators. These results open the avenues for use of these cells

in identification of novel pathway modulators in high‐throughput studies. Currently, the

devloped reporter cell line for identifcation of compounds with effects on poptotic pahway is

tested for signal production and further work on this part of the project depends on it. The

part of project on dvelopment of anti‐parastic drugs is designated for testing of the novel

compounds against an intracellular parasites asscoaietd with infectious disease in tropical

countries. They will be tested for their activity both by studies in vitro and in vivo disease

models with infected mice during preclincial phase of drug development. After their

completions, further clincial phases of drug development with selected candidates will be

carried out through colaborative work with the instututions from tropical countries that are

affected by disease.

Key Words: Modulators, kinase, cancer, tropical, parsites, intracelluar, reporter and cells.


48


Pharm.Dr. Lucie Stejskalová, Ph.D.Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Department of Pharmacology and Toxicology


ADME methods and other methods for studying the drug distribution in organism

In the position of postdoc, I have become the member of the scientific group Pharmacology

and Toxicology of the Institute of Molecular and Translational Medicine, Faculty of Medicine

and Dentistry, Palacky University in Olomouc with the focus of ADME/Tox methods. ADME is

actually an abbreviation used in pharmacology for Absorption, Distribution, Metabolism and

Excretion. All these processes are part of the pharmacokinetics and investigate the fate of

drugs in the body. ADME/Tox methods are actually used to study the optimal

pharmacokinetic properties of drugs in preclinical drug development (also used partially

during the first phase of clinical trials). Study of the optimal pharmacokinetics of drugs is

important as well as the biological (pharmacodynamic) effect of the drugs.

In our scientific group we want to initiate a number of ADME methods (plasma stability

assay, microsomal stability assay, plasma protein binding, permeability detection of

substances through the intestinal wall), which can be used to test new promising

substances/drugs.

Other part of interest should be also expression of Aryl hydrocarbon receptor (AHR) in colon

carcinoma cell lines, and its effect on expression of target genes (CYP1A1, CYP1A2…), which

are regulated through this receptor.

Experience with the study of AHR receptor, its aryl hydrocarbon receptor nuclear translocator

and their effect on biotransformation enzymes using qRT‐PCR, Westernblotting and EROD

activity assay was gained during postgraduate studies, where we focused on AHR expression

in primary cultures of human trophoblast and choriocarcinoma cell lines.

Key Words: ADME, Aryl hydrocarbon receptor, carcinoma cell line, cytochrome P450.


49


RNDr. Marika Havlíková, Ph.D.Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Department of Medical Chemistry and Biochemistry


Organotypic cultures of HepG2 cells for in vitro toxicity studies

Liver plays many essentials roles in maintaining normal physiology. It is also a vulnerable

target of many drugs or other chemicals because the liver is involved in complex metabolism.

It is well known, that the HepG2 cell line from human hepatocellular carcinoma retains some

functions of the human liver. It can also be used for preparing spheroids. It was shown, that

HepG2 cells grown as multi‐cellular spheroids represent a more complex system than the

convetional cell monolayers.

In this study, we used a commercially available 96 well plate system for generation of 3D

spheroids using hanging drop method. We investigated the HepG2 spheroid formation over

time including growth in size. Moreover, we investigated effect of palmatine on the 3D

HepG2 spheroids.

The protoberberine alkaloid palmatine is one of the main bioactive components of

preparations from medicinal plants such as Coptis chinensis and Corydalis yanhusuo. Herbal

products containing palmatine and other protoberberine alkaloids are mainly used in

traditional medicine in China, Korea and India for thein antimicrobial, antiinflammatory,

antidiabetic, hepatoprotective and analgesic effects. Palmatine has been found to inhibic the

activity of several human CYP enzymes, however, the effect of palmatine on the expression of

drug metabolizing enzymes has not been studied in detail. In this study we investigate how

palmatine affects the expression of CYP1A enzymes in human hepatoma HepG2 cells grown

as spheroids compared with monolayer.

Key Words: 3D HepG2 spheroids, hanging drop method, protoberberine alkaloid, palmatine,

CYP1A enzyme.


50


Mgr. Ján Gurský, Ph.D.Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine


Inhibition of DNA Damage Response Signaling in Cancer Therapy

The Laboratory of Genome Integrity (Institute of Molecular and Translational Medicine) is

focused on elucidating the regulation of DNA Damage Response (DDR) network and

identification of possible targets for cancer therapy.

DNA Damage Response involves mechanisms that prevent and repair DNA damage,

coordinate activation of cell cycle checkpoints and DNA repair with a number of cellular

processes. One of two DDR branches, ATR/Chk1, is rapidly activated upon replication stress,

and helps cells to cope with this excessive replication stress. Checkpoint signaling through

ATR/Chk1 and the complementary ATM/Chk2 module, that responds primarily to DNA

double‐strand breaks, was shown to trigger cellular senescence of rapidly proliferating pre‐

cancerous cells thereby providing barrier against tumor progression. On the other hand, in

more advanced tumors that have already escaped the initial DDR barrier and continue to

experience enhanced replication stress, the ATR‐ Chk1 may help the tumor to cope with it

and thrive despite the enhanced genotoxic stress.

Activation of MLL‐ENL fusion oncogene in our mouse model (Takacova S. et al., Cancer Cell.

2012 Apr 17;21(4):517‐31) initiates multistep pathogenesis of leukemia, leading to long

latency mixed‐lineage leukemia (MLL) development. Using this mouse model, MLL‐ENL

mediated malignant transformation was critically limited by DDR barrier, as experimental

attenuation of the barrier with caffeine, a dual ATM/ATR inhibitor, accelerated acute

leukemia development.

In our current project the MLL‐ENL mice are treated with ATR and Chk1 inhibitors at different

stages of leukemogenesis. Our first goal is to dissect the particular role of ATR/Chk1 in the

mediation of DDR‐activated anticancer barrier at early stage of leukemia development.


51

Second goal is to address whether inhibition of ATR/Chk1 pathway could be possibly toxic to

highly replicative tumor cells at later stages of cancerogenesis, focusing on ATR/Chk1

pathway as a target for cancer therapy.

Key Words: DNA damage response, replication stress, cancer, mixed‐lineage leukemia, ATR

and Chk1 inhibitors.


52


MUDr. Josef Srovnal, Ph.D.Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine


New genomic technologies in prediction of therapeutic response in leukemic patients

Background: The aim of this project is to identify factors predicting response or resistance to

glucocorticoid therapy in patients with childhood acute lymphoblastic leukemia (ALL) using

advanced molecular‐biological methods. Glucocorticoid therapy is widely used for ALL.

However, there are no clear predictive factors of therapy response and a percentage of

patients do not benefit from it.

Methods and patients: At first, DNA microarray analysis using the GeneChip Human Exon 1.0

ST Array (Affymetrix) was performed. The data were analyzed using “R” software and the

Bioconductor package. Bone marrow samples before glucocorticoid therapy were collected

in 31 ALL patients. In the next step, Next‐Generation Sequencing (NGS) methods will be used

based on Illumina platform. We will focus on transcriptomic sequencing and identification of

different gene splicing variants.

Preliminary results: In total, 124 GeneChip Human Exon 1.0 ST Arrays were performed in 31

ALL patients. In supervised clustering analysis we found 62 differentially expressed genes

identifying patients with good or poor prednisolone response. We found different exon

expression in the PBX1 gene (pre‐B‐cell leukemia homebox 1; NM_002585). The PBX1 gene

has more than 30x times higher expression in resistant patients.

Conclusion: Identification of patients who are likely to benefit from the treatment will

contribute to the individualization of therapy, reduction of side effects and the rational use of

resources. In this study, we identified gene expression profiles allowing prediction of

glucocorticoid therapy results in ALL patients. We plan to find specific splicing gene variants

using NGS.


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Research Team: I graduated from general medicine in I. Medical Faculty of Charles University

in Prague at 2003. Then, I finished my PhD study in Laboratory of Experimental Medicine in

Olomouc in 2010 with thesis “Minimal residual disease in solid cancer”.

Now, my postdoc position in Institute of Molecular and Translational Medicine is focused on

finding of new predictive factors using modern genomic approaches.

Key Words (max. 10): Acute lymphoblastic leukemia, DNA microarray, Next‐Generation

Sequencing, predictive factors.


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Lakshman Varanasi, Ph.D.Faculty of Medicine and Dentistry, Laboratory of Experiment Medicine (IMTM)


Development of Serum biomarkers of Colorectal Cancer

The larger goal of my work is to identify and develop protein and glycoprotein biomarkers of

colorectal cancer from xenograft mice serum.Colorectal cancer is one of the most prevalent

cancers in the Czech Republic. Such markers are expected to enable the early diagnosis of

patients afflicted with this disease and thereby vastly improve the prognosis for those

patients.

The immediate focus of my research is to develop a methodology for biomarker discovery.

This includes the development, optimisation and standardization of protocols for sample

processing, assay and data analysis. We are simultaneously exploring ways of scaling up

these protocols to increase throughput. The project is being overseen by Marian Hajduch,

MUDr, Ph.D, and Petr Dzubak, MUDr, PhD. Other team members include doctoral students

Dusan Holub (Mass Spectrometry) and Miroslav Hruska (Computational data analysis).

The overall project progress is satisfactory. We estimate that the process development will be

over by January and that it will be ready for deployment by early February. The spin‐off

benefit from the work done so far is the development of a software suite (Dymka) for

comprehensive mass‐spectrometry data analysis.

I also have the opportunity to mentor an undergraduate student during my tenure here and

to try to encourage his inclination for science.

My doctoral training is has been in biochemistry and was conducted at the University of

Mississippi Medical Center (UMMC), USA (Advisor, Jon Hosler, Ph.D) . My prior research

experience has centered on gene‐expression analysis in the context of breast cancer, also at

UMMC (Advisor, Luis Martinez, Ph.D.).

Key Words: Discovery, serum, biomarkers, colorectal cancer, Dymka.


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Mgr. Svatopluk Binder, Ph.D.Faculty of Medicine and Dentistry, Department of Medical Biophysics


Photodynamic therapy: alternative approach to tumour treatment

Within the research project „ Encourage the creation of excellent research teams and

intersectoral mobility at Palacký University in Olomouc“ I will deal with the study of the

effects of photosensitive substances used for photodynamic therapy. My postdoctoral

fellowship was carried out in the workplace of prof. Mauricio da Silva Baptista at the

Department of Biochemistry, Faculty of Science, University of Sao Paulo in Sao Paulo, Brazil.

His research team is engaged in several research fields, among others photodynamic therapy.

Other areas are bioactives mechanisms of action in skin and hair model systems and surface

plasmon resonance and membrane biosensors“ Photodynamic therapy (PDT) is considered

to be a promising and clinically used alternative method of a tumour treatment which

involves administration of a tumour‐localizing photosensitizer followed by activation of light

of a specific wavelength. The PDT results in a cascade of photochemical and photobiological

processes causing irreversible photodamage to tumour tissues. Photodynamic therapy

causes either cell apoptosis or necrosis that leads to DNA damage. Irradiation of the

photosensitizers results in a photochemical reaction which converts O2 to cytotoxic singlet

oxygen1O2 and other forms of reactive oxygen species (ROS). Effects of photosensitizer will

be investigated in vitro on non‐tumour and tumour cell lines. As the light source LEDs will be

used. For determining the effectiveness of the photosensitizer fluorescent and

spectrophotometric analytic methods will be employed. The aim of the research is to find the

mechanism of cell death induction after photodynamic therapy and to determine effective

concentrations in conjunction with doses of irradiation.

Key Words: photodynamic therapy, oxidative damage, cell death, tumour cells, Sao Paulo.


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Mgr. Ferdinand Salonna, Ph.D.Faculty of Physical Culture, Center for Kinanthropology Research


Adolescents walking and physical activity in varying home and school environment

Physically inactive lifestyles are becoming more prevalent worldwide, as are the chronic

diseases they cause. To change behavior on a population‐wide basis, it is important to

understand the underlying forces responsible for current patterns and trends. Among the

many possible factors that are being studied, physical environment variables are particularly

promising. There is substantial evidence linking the design of communities and access to

recreational facilities with active transportation and recreation. There is high prevalence of

unhealthful diet and physical activity patterns in adolescents. Studies of adults have

demonstrated consistent associations of community design (“walkability”) and recreational

environments with physical activity, and a few studies suggest neighborhood food

environment is related to eating patterns. Such data in young people are limited. Ecological

models posit that health behaviors are influenced by individual, social/cultural, policy, and

environmental variables. Data on all levels of influences are needed to guide multi‐level

interventions, but most studies have been limited to individual and social/cultural variables.

The present project aims to evaluate the ability of a multi‐level model to explain variation in

physical activity, sedentary behavior in adolescents, with an emphasis on neighborhood

environments. Project will be implemented by Center for Kinanthropology Research at

Faculty of Physical Culture Palacký University, within the frame of IPEN (The International

Physical Activity and the Environment Network). The following measures willbe used IPAQ

(International Physical Activity Questionnaire), ANEWS (Neighborhood Environment

Walkability Survey – Abbreviated), GIS (Geographic Information Systems), akcelerometry.

Key Words: physical aktivity, walkability, adolescents, physical environment variables, IPAQ,

ANEWS, GIS, akcelerometry.


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Mgr. Zuzana Kováčiková, Ph.D.Faculty of Physical Culture, Department of Natural Sciences in Kinanthropology


The balance assessment under various conditions in amputees

I finished my PhD. on Faculty of Physical Education and Sport in Bratislava, Slovakia. During

this period led by Prof. Zemková, PhD., I worked on many projects focused at assessing

balance, force and reaction in parkinsonʼs, PE studets, older adults , young individuals and

obese. The name of my PhD. thesis was: Changes in reaction‐speed abilities after various

forms of agility training. The aim of the study was to detect the changes in the parameters of

disjunctive reaction‐speed abilities after 8 week agility training under simulated competitive

and non‐competitive conditions.

Now, I work on Faculty of Physical Culture, Palacky University. I joined to the team of Prof.

Janura, Ph.D., on department of natural sciences in kinanthropology. The area of my present

research is the balance assessment under various conditions in amputees. Assessment of

balance is carried out by force platforms (Kistler Instrumente AG, Winterthur, Swiss) and by

dynamic computer posturography (NeuroCom). Patients undergoing tests of postural

stability: bipedal stance with eyes open and closed, one leg stance on amputated and non‐

amputated lower limb, jump, gait and EquiTest. Without this, patients undergoing battery of

functional tests consisting of : Functional Reach Test, Lateral Reach Test, Timed Up and Go,

Timed Up and Go with cognitive task, Four Square Step Test. With my colleague Mgr.

Kateřinou Neumannovou, Ph.D., the research area focuses on the balance analysis in children

with bronchial asthma compared to healthy children and balance analysis before and after

spa treatment, respectively.

Key Words: balance, transtibial amputations, children with asthma bronchiale.


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Mgr. Kateřina Neumannová, Ph.D.Faculty of Physical Culture, Department of Natural Sciences in Kinanthropology


Walking, balance and increased risk of falls related to COPD

My professional focus is on complex care of patients with breathing disorders. I am a

member of the Department of Natural Sciences in Kinanthropology, where I have been

extending my previous research which was focused on the effect of pulmonary rehabilitation

treatment in patients with breathing difficulties (eg. chronic obstructive pulmonary disease ‐

COPD, bronchial asthma disease, interstitial lung diseases) on ventilatory function, exercise

capacity and on health related quality of life.

The main aim of our study is to describe gait pattern and dynamic and static stability in COPD

patients and investigate the effect of incremental shuttle walking test on stability and gait

parameters in COPD patients. We know that COPD is characteristic disease for ageing

population and for that reason there could be not only breathing disorders during physical

activities (especially during walking) caused by the disease but also there could be balance

problems which could lead to other reasons of walking difficulties and higher risk of falls.

We will randomise 40 COPD patients for our study from the Czech National Research

Database of COPD: Registry of the Czech Pneumological Society and the Czech Medical

Association.

Our main inclusion criteria will be: stable phase of COPD (III or IV stage, bronchitic or

emphysematic phenotype), age over 50 years old, physically independent, stable condition

(without any exacerbation within 4 weeks prior to study), absence of other conditions that

could impair the evaluation (e.g. orthopaedic or neurological problems, which can influence

walking, contraindication for exercise testing due to other illnesses).

Our planned analysis will be focused on assessing acute effects of incremental intensity

effort on gait pattern and on static and dynamic stability in COPD patients and on comparing


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gait pattern, static and dynamic stability in COPD patients with bronchitic and emphysematic

phenotype.

This research will be done in cooperation between Department of Natural Sciences in

Kinathropology and Pulmonary Department in Olomouc, Hradec Kralove, Brno and Prague

Motol.

Key Words: Chronic obstructive pulmonary disease, gait pattern, postural stability,

incremental shuttle walking test.


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Mgr. Adrián Agricola, Ph.D.Faculty of Physical Culture, Department of Natural Sciences in Kinanthropology


Visual and kinesthetic perception in the control of gait pattern in children

Developmental coordination disorder (DCD) is a heterogeneous syndrome, which may be

associated with perceptual deficits and deficits in planning and programming in the control

of movement or motion. Therefore, it is important for intervention the diagnosis of different

types of DCD. The aim of our research is to explore the different kind of DCD children,

applying a diagnostic view by using walking exercises based on a variety of sensory inputs

and external conditions.

AIM: The main aim of the study is to detect differences in the gait pattern of children with

typical development and those with developmental coordination disorder. We assume that,

with this experiment, manipulating visual and kinesthetic information in performing various

types of walking tasks could help us to find the level and type of sensorimotor deficits in

school‐age children.

METHOD

Participants: In this study will take part children from 6 to 10 years old (n=80). 50% of the

subject from each group (TD and DCD children) and all of them will be matched in age and

gender.

Instruments: The Optojump equipment will be used to analyze the gait pattern and obtain

the data required (quantitative data). A qualitative checklist will be used to analyze

qualitative data related to the head movement, arm, trunk or legs. This checklist should be

validated in advance by teachers, physiotherapist and other professionals related with the

motor development. The camcorder will be used to record the movements of the above

mentioned body parts.

Procedure: All participants will be tested by Optojump, that provides comprehensive data

about walking of tested subjects (speed, stride length, etc.). The participants will be recorded


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by camcorder during the experiment. Based on this video will be made a motion analysis of

individual body parts of each testing subject (head, shoulders, trunk, legs). These findings will

be register in the checklist (Qualitative observations checklist). This checklist was made

based of information from scientific literature about proper posture in normal subjects (TD)

and subjects with DCD. The findings of qualitative research will be compared with the results

from Optojump (quantitative research).

Key Words: Visual perception, Motor difficulties, Motor planning, Gait patterns, Qualitative

observations.

Documents

The 1st CONFERENCE of POST UP · 2014-01-29 · The conference is organized by project POST-UP, CZ.1.07/2.3.00/30.0004 Palacký University, Olomouc The 1st CONFERENCE of POST‐UP