2nd_call_CZECH_teams

Partners from the CZECH REPUBLIC for the 2nd call





2nd call topic organisation contact Interests/contributions/related

document



Advanced genomics and its applications for health



Fundamental knowledge and basic tools for functional genomics in all organisms

Gene expression and proteomics

LSH-2003-1.1.1-1 Lab. of DNA-Molecular Complexes, Jiri Fajkus fajkus@ibp.cz,  telomerase activity (humans,

Global in situ gene Inst. of Biophysics, ASCR, Dpt. of Kralovopolska 135, 61265 Brno, plants)

expression analysis in Functional Genomics and Proteomics, Czech Republic.

rodent models and

 biomedicine of telomeres

human tissues

Masaryk University phone: 420-541517199,  molecular diagnostic

http://www.ibp.cz/labs/LDMC/ FAX: 420-541211293 (neuromuscular disorders)

10_insitu_gene_expresion_Fajkus

LSH-2003-1.1.1-1 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  human fibrinolytic system

Global in situ gene Pilsen, Charles University marie.korabecna@lfp.cuni.cz (regulation of plasminogens tPA

expression analysis in Karlovarska 48, 30166 Pilsen, and uPA)

rodent models and

human tissues

Czech Republic  ISH, human tissues,

tel.: 00420 377593 262, Imunohistochemistry, RT PCR

4_second_call_Korabecna



Structural genomics

LSH-2003-1.1.2-1 Department of Biochemistry and Tomáš Ruml  M-PMV (retroviral

Comparative structural Microbiology ICT Prague Tomas.Ruml@vscht.cz integration,capsid assembly

biology of viral http://biomikro.vscht.cz/indexen.html, Institute of Chemical Technology, and maturation)

replication

Department of Protein Biochemistry of Technicka 5  inhibitors (assembly,

ASCR http://www.uochb.cas.cz/ and 166 28, Prague 6, integration)

Center for Integrated Genomics Czech Republic. 26_viralrepl_genetherapy_Ruml

http://cig.img.cas.cz/ phone: +420 224 353 022

LSH-2003-1.1.2-1 Department of Molecular Genetics Jaroslav Matoušek  viroid-caused pathogenesis,

Comparative structural http://www.umbr.cas.cz/804_www/ind jmat@umbr.cas.cz propagation, antisensing,

biology of viral ex.htm Institute of Plant Molecular Biology variability

replication

Institute of Plant Molecular Biology of Branisovska 31,  PSTVd, hop viroids

Academy of Sciences of the Czech 370 05 Ceske Budejovice,  Functional genomics of hop

Republic Czech Republic  Antisensing and gene silencing

phone:+420 38 53 10 357,  Virus variability research

fax: +420 38 53 10 356

LSH-2003-1.1.2-2 Laboratory of Molecular Cytogenetics Doc. Ing. Jaroslav Doleţel, DrSc.  wheat

Structure and Cytometry, Inst. of Experimental Sokolovská 6  functional genomics

determination of large Botany, ASCR , 77200 Olomouc, Czech Republic

protein complexes

18_genomics_wheat_Dolezel

www.ueb.cas.cz/olomouc1 Tel.: 585 228 521

Fax: 585 228 523

Email: dolezel@ueb.cas.cz



Comparative genomics and population genetics

LSH-2003-1.1.3-1 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  fetal DNA in maternal plasma

Developing new Pilsen, Charles University marie.korabecna@lfp.cuni.cz  Y chromosome analysis (RT

molecular tools and Karlovarska 48, 30166 Pilsen,

approaches for high

PCR)

throughput molecular

Czech Republic 4_second_call_Korabecna

phenotyping of human tel.: 00420 377593 262,

populations

LSH-2003-1.1.3-2 Protein Engineering Group, Masaryk Jiri Damborsky jiri@chemi.muni.cz  mycobacteria pathogenesis

Standardisation and University  testing, validation technologies

integration of genomic

and phenotypic

5_second_call_damborsky

information to

characterise bacterial

diversity with relevance

to human health



Bioinformatics

LSH-2003-1.1.4-1 Laboratory of DNA Biophysics and JAROSLAV KYPR  unusual doublehelixes of DNA

Bioinformatics grid for Genome Bioinformatics, Institute of (Head of Laboratory)  DNA crystal structures

European genomics

research Biophysics, Academy of Sciences of Phone: (420) 541517198  Long range structure of

the Czech Republic Fax: (420) 541240497 genomes

http://salsero.ibp.cz/, E-mail: kypr@ibp.cz 23_bioinformatics_Kypr

LSH-2003-1.1.4-2 Protein Engineering Group, Masaryk Jiri Damborsky jiri@chemi.muni.cz  modelling of biochemical

Development of an University reactions (TRITON software)

integrated software

platform to tackle

 large amount of data

genomic (sequential, structural, kinetics,

sequence-structure-fun biochemical)

ction relationships  haloalkane dehalogenases

5_second_call_damborsky



Multidisciplinary functional genomics approaches to basic biological processes

LSH-2003-1.1.5-2 Laboratory of Molecular Pathology UP, Mgr. Nicol Vavrusova  peroxisome

Functional genomics Department of Pathology, Palacký vavrusova@seznam.cz proliferator-activated receptors

approaches to the University http://lmp.upol.cz/ Hnevotinska 3 ˇ(PPARs)

study of peroxisomes

in health and disease

Olomouc  glial cancerogenesis, cell cycle,

CZ-775 15 appoptosis

Phone: +420 585 632 451  cell kinetics, gene expression,

Fax: +420 585 632 966 gene transfer, biotechnology

3_second_call_peroxisomes

LSH-2003-1.1.5-5 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  fetal DNA in maternal plasma

DNA damage and Pilsen, Charles University marie.korabecna@lfp.cuni.cz  Y chromosome analysis (RT

repair mechanisms in Karlovarska 48, 30166 Pilsen,

health and disease

PCR)

Czech Republic 4_second_call_Korabecna

tel.: 00420 377593 262,



Application of knowledge and technologies in the field of genomics and biotechnology for health

Rational and accelerated development of new, safer, more effective drugs including pharmacogenomics approaches

Inst. Of Pharmacology, 1st Faculty of Ass. Prof. Dr. František Perlík,  genetic predispositions for

Medicine, Charles University DrSc. interindividual changes in

Albertov 4, Na Bojisti 1 pharmacokinetics

Prague 2, 120 00

Czech Republic: fperl@lf1.cuni.cz  therapeutic efficacy and safety

Phone: +420 224968146  enzyme activity, transporters

 univ. hospital (1000 beds)

7_pharmacoepidemiology-combm

ajdis_Perlik

Charles University, Faculty of Medicine Professor Jiřina Martínková, M.D.,  basic and clinical pharmacology

in Hradec Kralove, Dpt. of Ph.D. martinkova@lfhk.cuni.cz  CYP450 drug metabolism

pharmacology Head on Department of  biomarkers of inflammantory

http://www.lfhk.cuni.cz/farmakol/ Pharmacology processes

 therapy in oncology

 therapy of psoriasis with

LDMTX

16_basic_clinic_pharmacology_m

artinkova

Department of Pharmaceutics, Faculty Miloslava Rabišková,  technology of dosage forms and

of Pharmacy, University of Veterinary rabiskovam@vfu.cz matrix tablets

and Pharmaceutical Sciences Palackého 1-3  polymeric excipients

61242 Brno, Czech Republic 17_drugs_Rabiskova

LSH-2003-1.2.1-1 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  fetal DNA in maternal plasma

Medicines for children Pilsen, Charles University marie.korabecna@lfp.cuni.cz  Y chromosome analysis (RT

Karlovarska 48, 30166 Pilsen, PCR)

Czech Republic 4_second_call_Korabecna

tel.: 00420 377593 262,

LSH-2003-1.2.1-2 Institute of Chemical Technology in Blanka Kralova, E-mail:  Molecular modelling (proteine

Computer assisted Prague, Dpt. of Biochemistry and karasovp@vscht.cz structure, molecular dymanics,

modelling for drug Microbiology Technicka 3 protein-ligand docking)

discovery and testing

http://biomikro.vscht.cz/groups/lab211/ Prague 6, 166 28  Virtual screening, fold

index.html Czech Republic recognition, continuum

Phone: +420224353077 electrostatics calculations,

Fax: +420224355167 free-energy of binding

 Linux, SGI IRIX

1_computer_ass_drugs-Kralova

LSH-2003-1.2.1-2 Protein Engineering Group, Masaryk Jiri Damborsky jiri@chemi.muni.cz  development and validation of

Computer assisted University methods

modelling for drug

discovery and testing

 modelling and prediction of drug

metabolism within a living cells

5_second_call_damborsky



Development of new diagnostics

National Reference Laboratory for Hana Zákoucká  treponema pallidum

Diagnostics of Syfilis, Department of U Nemocnice 2, 128 08 Prague 2,  RT PCR

Dermatology, 1.st Faculty of Medicine, Czech Republic 12_SyfilisRTPCR_Stork

Charles University Phone: 224 920 610

Fax: 224 923 759

E-mail: kozni@lf1.cuni.cz



Charles University, Faculty of Alice Laznickova  receptor-specific peptides

Pharmacy in Hradec Kralove Heyrovskeho 1203  radioactivity labelling

500 05 Hradec Kralove 24_pharmacology_Laznickova

tel: 495 067 478

fax: 495 518 002

E-mail: laznicko@faf.cuni.cz

LSH-2003-1.2.2-1 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  fetal DNA in maternal plasma

Development of Pilsen, Charles University marie.korabecna@lfp.cuni.cz  Y chromosome analysis (RT

genetic tests allowing Karlovarska 48, 30166 Pilsen,

for harmonisation,

PCR)

validation and

Czech Republic 4_second_call_Korabecna

standardisation tel.: 00420 377593 262,

LSH-2003-1.2.2-2 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  human fibrinolytic system

In vivo molecular Pilsen, Charles University marie.korabecna@lfp.cuni.cz (regulation of plasminogens tPA

imaging: identification Karlovarska 48, 30166 Pilsen, and uPA)

of new markers for

diagnostic purposes

Czech Republic  ISH, human tissues,

tel.: 00420 377593 262, Imunohistochemistry, RT PCR

4_second_call_Korabecna

Development of new in vitro and in silico tests to replace animal experimentation

Department of Pharmaceutics, Faculty Miloslava Rabišková,  technology of dosage forms and

of Pharmacy, University of Veterinary rabiskovam@vfu.cz matrix tablets

and Pharmaceutical Sciences Palackého 1-3  polymeric excipients

61242 Brno, Czech Republic 17_drugs_Rabiskova



Development and testing of new preventive and therapeutic tools, such as somatic gene and cell therapies (in particular

stem cell therapies, for example those on neurological and neuromuscular disorders) and immunotherapies

Department of Molecular Embryology, Dr. Petr Dvorak  fibroblast growth factor

Institute of Experimental Medicine, Phone: +425 45133298 signalling

ASCR Fax: + 425 45133298  cell cycle regulators

http://uemweb.biomed.cas.cz/dvorak/d E mail: dvorakp@mendelu.cz  oocyte development

vorak.html  human and Mouse ES cells

(derivation, propagation,

differentiation)

 syntetic hydrogel supports

(propagation, differentiation of

ES cells)

14_embrstemcells_Dvorak

LSH-2003-1.2.4-1 Department of Biochemistry and Tomáš Ruml  retroviral capsid assembly and

Improved gene delivery Microbiology ICT Prague Tomas.Ruml@vscht.cz maturation

systems for the therapy http://biomikro.vscht.cz/indexen.html, Institute of Chemical Technology, 26_viralrepl_genetherapy_Ruml

of severe acquired

diseases

Department of Protein Biochemistry of Technicka 5

ASCR http://www.uochb.cas.cz/ and 166 28, Prague 6,

Center for Integrated Genomics Czech Republic.

http://cig.img.cas.cz/ phone: +420 224 353 022

LSH-2003-1.2.4-3 Department of Molecular Embryology, Dr. Petr Dvorak  fibroblast growth factor

Design of rational Institute of Experimental Medicine, Phone: +425 45133298 signalling

protocols for safety,

quality and

ASCR Fax: + 425 45133298  cell cycle regulators

standardisation of stem

http://uemweb.biomed.cas.cz/dvorak/d E mail: dvorakp@mendelu.cz  oocyte development

vorak.html

1

cells and  human and Mouse ES cells

establishment of a (derivation, propagation,

European registry of

stem cells differentiation)

 syntetic hydrogel supports

(propagation, differentiation of

ES cells)

14_embrstemcells_Dvorak

LSH-2003-1.2.4-5 Department of Infectious Diseases , Jana Táborská  clinical studies

New improved Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

vaccines based on University Dr. E. Beneše 13 ska

genomic and proteomic

information

Plzeň 305 99, Czech Republic

Phone: +420 377402263



LSH-2003-1.2.4-5 Laboratory of Molecular Biology of Peter Sebo, PhD.,  membrane penetration

New improved Bacterial Pathogens, Cell and sebo@biomed.cas.cz  bacterial protein toxins

vaccines based on

genomic and proteomic

Molecular Microbiology Division, Videnska 1083  immunogens and vectors for

information

Czech Academy of Sciences, Institute 142 20 Prague 4, Czech Republic delivery of foreign antigens

of Microbiology phone: (+420) 241 062 762  immune responses against

http://sun2.biomed.cas.cz/mbu/Lab12 fax: (+420) 241 062 152 infectious agents and tumors

5/index.html 22_genomicsproteomics_Sebo

LSH-2003-1.2.4-6 Department of Infectious Diseases , Jana Táborská  clinical studies

Dendritic cells for novel Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

immunotherapies University Dr. E. Beneše 13 ska

Plzeň 305 99, Czech Republic

Phone: +420 377402263



LSH-2003-1.2.4-6 Laboratory of Molecular Biology of Peter Sebo, PhD.,  membrane penetration

Dendritic cells for novel Bacterial Pathogens, Cell and sebo@biomed.cas.cz  bacterial protein toxins

immunotherapies Molecular Microbiology Division, Videnska 1083  immunogens and vectors for

Czech Academy of Sciences, Institute 142 20 Prague 4, Czech Republic delivery of foreign antigens

1

Id 9

of Microbiology phone: (+420) 241 062 762  immune responses against

http://sun2.biomed.cas.cz/mbu/Lab12 fax: (+420) 241 062 152 infectious agents and tumors

5/index.html 22_genomicsproteomics_Sebo



Innovative research in post-genomics, which has high potential for application

LSH-2003- 1.2.5-1 Laboratory of Predictive Oncology from Miroslav Svoboda,  oncology

RNA as a human the Masaryk Memorial Cancer svoboda@mou.cz 19_RNA_terapeutictool_Svoboda

therapeutic tool Institute, Zluty kopec 7

656 53 Brno, Czech Republic

LSH-2003-1.2.5-2 Laboratory of Molecular Biology of Peter Sebo, PhD.,  membrane penetration

Post-genomic Bacterial Pathogens, Cell and sebo@biomed.cas.cz  bacterial protein toxins

approaches to the

study of human

Molecular Microbiology Division, Videnska 1083  immunogens and vectors for

pathogens

Czech Academy of Sciences, Institute 142 20 Prague 4, Czech Republic delivery of foreign antigens

of Microbiology phone: (+420) 241 062 762  immune responses against

http://sun2.biomed.cas.cz/mbu/Lab12 fax: (+420) 241 062 152 infectious agents and tumors

5/index.html 22_genomicsproteomics_Sebo

LSH-2003-1.2.5-2 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  fungal pathogens (Candida,

Post-genomic Pilsen, Charles University marie.korabecna@lfp.cuni.cz non-Candida species)

approaches to the

study of human

Karlovarska 48, 30166 Pilsen,  diagnostic application

pathogens

Czech Republic 4_second_call_Korabecna

tel.: 00420 377593 262,

LSH-2003- 1.2.5-3 Dpt. of Imunology, Institute for Clinical Assoc. Prof. Ilja Striz, MD, PhD  innate immunity in rejection

Induction of transplant and Experimental Medicine Vídeňská 1958/9, mechanisms

tolerance using

post-genomic

140 21 Prague 4, Czech Republic  cytokine gene polymorphisms

approaches

ilja.striz@medicon.cz in organ transplantation

 sequence based HLA typing

 HLA and diseases

2_transplant_Hlozanek

LSH-2003- 1.2.5-4 Laboratory of Molecular Biology of Peter Sebo, PhD.,  membrane penetration

New bioassays and Bacterial Pathogens, Cell and sebo@biomed.cas.cz  bacterial protein toxins

biosensors using

post-genomic

Molecular Microbiology Division, Videnska 1083  immunogens and vectors for

Czech Academy of Sciences, Institute 142 20 Prague 4, Czech Republic

approaches for of Microbiology phone: (+420) 241 062 762 delivery of foreign antigens

detection of harmful http://sun2.biomed.cas.cz/mbu/Lab12 fax: (+420) 241 062 152  immune responses against

microbes

5/index.html infectious agents and tumors

22_genomicsproteomics_Sebo

LSH-2003- 1.2.5-4 Protein Engineering Group, Masaryk Jiri Damborsky jiri@chemi.muni.cz  biosensors development

New bioassays and University  dehalogenating enzymes

biosensors using

post-genomic

5_second_call_damborsky

approaches for

detection of harmful

microbes

LSH-2003- 1.2.5-7 Inst. of Microbiology, ASCR Dr. Sylvie Pazoutova  hypocreales (Claviceps,

Exploitation of fungal http://www.biomed.cas.cz/~pazouto/p Videnska 1083 Geosmithia, Phialophora,

genomics and azouto.htm 142 20 Prague 4, Czech Republic Ophiostoma)

application of

filamentous fungal

phone: (+4202) 9644 2332  genetic variability (molecular

biotechnology for the fax: (+4202) 9644 2347 markers)

benefits of human mail: pazouto@biomed.cas.cz  moleculat taxonomy

health

 secondary metabolites

8_fungi_Pazoutova



Combating major diseases

Inst. Of Pharmacology, 1st Faculty of Ass. Prof. Dr. František Perlík,  genetic predispositions for

Medicine, Charles University DrSc. interindividual changes in

Albertov 4, Na Bojisti 1 pharmacokinetics

Prague 2, 120 00  therapeutic efficacy and safety

Czech Republic: fperl@lf1.cuni.cz  enzyme activity, transporters

Phone: +420 224968146  univ. hospital (1000 beds)

7_pharmacoepidemiology-combm

ajdis_Perlik

Application-orientated genomic approaches to medical knowledge and technologies

General

LSH-2003-2.1.0-1 Department of Experimental Kuneš Jaroslav (head of Dpt.)  NO synthase

Eicosanoids and nitric

oxide: mediators of Hypertension, Institute of Physiology , kunes@biomed.cas.cz  salt hypertension

cardiovascular,

cerebral and neoplastic

Academy of Sciences of the Czech Videnska 1083  NO/O2 dysbalance

diseases

Republic 14220 Prague 4, Czech Republic  antioxydant therapy

http://www.biomed.cas.cz/fgu/ Phone:+420-296442420  peroxynitrities

 Dahl rats

25_PROJECT_Kunes

LSH-2003-2.1.0-1 Department of Infectious Diseases , Jana Táborská  clinical studies

Eicosanoids and nitric Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

oxide: mediators of University Dr. E. Beneše 13 ska

cardiovascular,

cerebral and neoplastic

Plzeň 305 99, Czech Republic

diseases Phone: +420 377402263

LSH-2003-2.1.0-2 Department of Infectious Diseases , Jana Táborská  clinical studies

Coordination of clinical Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

trials in Europe University Dr. E. Beneše 13 ska

Plzeň 305 99, Czech Republic

Phone: +420 377402263





Combating, cardiovascular disease, diabetes and rare diseases

Department of Preventive Medicine, Prof.Vladimir Janout, MD.PhD.  epidemiological studies

Faculty of Medicine, Palacky University Hnevotinska 3, 77515 OLOMOUC  cancer,

Czech Republic 21_Xlinkedsyndrome_Janout

Phone: 00420-68-5632651

Fax: 00420-68-5632668

E-mail: janout@tunw.upol.cz

Department of Pharmaceutics, Faculty Miloslava Rabišková,  technology of dosage forms and

of Pharmacy, University of Veterinary rabiskovam@vfu.cz matrix tablets

and Pharmaceutical Sciences Palackého 1-3  polymeric excipients

61242 Brno, Czech Republic 17_drugs_Rabiskova

LSH-2003-2.1.1-8 I. Internal Clinic, 3rd Faculty of Jiri Horak  hereditial hemochromatozis

Combating disorders of Medicine, Charles University in Prague horak@fnkv.cz

inborn errors of

metabolism Srobarova 50, 10034 Praha 10

Czech Republic

Phone: 00420-267162315

Fax: 00420-267162658



Combating resistance to antibiotics and other drugs

LSH-2003-2.1.2-1 Department of Infectious Diseases , Jana Táborská  clinical studies

Functional genomics of Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

antibiotics-producing University Dr. E. Beneše 13 ska

organisms

Plzeň 305 99, Czech Republic

Phone: +420 377402263



LSH-2003-2.1.2-2 Department of Infectious Diseases , Jana Táborská  clinical studies

New molecular targets Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

for the development of University Dr. E. Beneše 13 ska

drugs against

pathogens causing

Plzeň 305 99, Czech Republic

severe resistance Phone: +420 377402263

problems

LSH-2003-2.1.2-3 Department of Infectious Diseases , Jana Táborská  clinical studies

Novel approaches to Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

address antimicrobial University Dr. E. Beneše 13 ska

resistance through

non-antimicrobial

Plzeň 305 99, Czech Republic

based therapies Phone: +420 377402263





Studying the brain and combating diseases of the nervous systém

LSH-2003-2.1.3-2 Department of Infectious Diseases , Jana Táborská  clinical studies

Neuronal networks, Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

learning and memory: University Dr. E. Beneše 13 ska

from genes to

behaviour

Plzeň 305 99, Czech Republic

Phone: +420 377402263

LSH-2003-2.1.3-3 Department of Infectious Diseases , Jana Táborská  clinical studies

Molecular mechanisms Faculty of Medicine in Plzen, Charles taborska@fnplzen.cz 11_LFPlzen_clinicalstudies_Tabor

of neuronal University Dr. E. Beneše 13 ska

degeneration

Plzeň 305 99, Czech Republic

Phone: +420 377402263



LSH-2003-2.1.3-4 Department of Molecular Embryology, Dr. Petr Dvorak  fibroblast growth factor

Stem cells and nervous Institute of Experimental Medicine, Phone: +425 45133298 signalling

systém ASCR Fax: + 425 45133298  cell cycle regulators

http://uemweb.biomed.cas.cz/dvorak/d E mail: dvorakp@mendelu.cz  oocyte development

vorak.html  human and Mouse ES cells

(derivation, propagation,

differentiation)

 syntetic hydrogel supports

(propagation, differentiation of

ES cells)

14_embrstemcells_Dvorak



Studying human development and the ageing process

LSH-2003-2.1.4-2 Dpt. of Biology, Faculty of Medicine in RNDr.Marie Korabecna,  human fibrinolytic system

Molecular mechanisms Pilsen, Charles University marie.korabecna@lfp.cuni.cz (regulation of plasminogens tPA

of embryo implantation Karlovarska 48, 30166 Pilsen, and uPA)

Czech Republic  ISH, human tissues,

tel.: 00420 377593 262, Imunohistochemistry, RT PCR

4_second_call_Korabecna

LSH-2003-2.1.4-3 Dpt. of Biophysics and Physical Ďoubal Stanislav,  aging, theories of ageing,

Coordinating EuropeanChemistry, Faculty of Pharmacy in HK, doubal@faf.cuni.cz biological age

research in ageing and

longevity

Charles University Heyrovského 1205  verification, markers of ageing

500 05 Hradec Králové, 9_gerontology-Ďoubal

Czech Republic

LSH-2003-2.1.4-4 Dpt. of Biophysics and Physical Ďoubal Stanislav,  aging, theories of ageing,

European research on Chemistry, Faculty of Pharmacy in HK, doubal@faf.cuni.cz biological age

ageing Charles University Heyrovského 1205  verification, markers of ageing

500 05 Hradec Králové, 9_gerontology-Ďoubal

Czech Republic





Across the area

Department of Molecular Genetics Jaroslav Matoušek  viroid-caused pathogenesis,

http://www.umbr.cas.cz/804_www/ind jmat@umbr.cas.cz propagation, antisensing,

ex.htm Institute of Plant Molecular Biology variability

Institute of Plant Molecular Biology of Branisovska 31,  PSTVd, hop viroids

Academy of Sciences of the Czech 370 05 Ceske Budejovice,  Functional genomics of hop

Republic Czech Republic  Antisensing and gene silencing

phone:+420 38 53 10 357,  Virus variability research

fax: +420 38 53 10 356

Dpt. of Imunology, Institute for Clinical Assoc. Prof. Ilja Striz, MD, PhD 

innate immunity in rejection

and Experimental Medicine Vídeňská 1958/9, mechanisms

 cytokine gene polymorphisms

140 21 Prague 4, Czech Republic

ilja.striz@medicon.cz in organ transplantation

 sequence based HLA typing

 HLA and diseases

2_transplant_Hlozanek

Inst. Of Pharmacology, 1st Faculty of Ass. Prof. Dr. František Perlík,  genetic predispositions for

Medicine, Charles University DrSc. interindividual changes in

Albertov 4, Na Bojisti 1 pharmacokinetics

Prague 2, 120 00  therapeutic efficacy and safety

Czech Republic: fperl@lf1.cuni.cz  enzyme activity, transporters

Phone: +420 224968146  univ. hospital (1000 beds)

7_pharmacoepidemiology-combm

ajdis_Perlik

Department of Molecular Embryology, Dr. Petr Dvorak  fibroblast growth factor

Institute of Experimental Medicine, Phone: +425 45133298 signalling

ASCR Fax: + 425 45133298

http://uemweb.biomed.cas.cz/dvorak/d E mail: dvorakp@mendelu.cz  cell cycle regulators

vorak.html  oocyte development

 human and Mouse ES cells

(derivation, propagation,

differentiation)

 syntetic hydrogel supports

(propagation, differentiation of

ES cells)

14_embrstemcells_Dvorak

Charles University, Faculty of Medicine Professor Jiřina Martínková, M.D.,  basic and clinical pharmacology

in Hradec Kralove, Dpt. of Ph.D. martinkova@lfhk.cuni.cz  CYP450 drug metabolism

pharmacology Head on Department of  biomarkers of inflammantory

http://www.lfhk.cuni.cz/farmakol/ Pharmacology processes

 therapy in oncology

 therapy of psoriasis with

LDMTX

16_basic_clinic_pharmacology_m

artinkova

Department of Preventive Medicine, Prof.Vladimir Janout, MD.PhD.  epidemiological studies

Faculty of Medicine, Palacky University Hnevotinska 3, 77515 OLOMOUC  cancer,

Czech Republic 21_Xlinkedsyndrome_Janout

Phone: 00420-68-5632651

Fax: 00420-68-5632668

E-mail: janout@tunw.upol.cz





Cancer

Oncology Dpt. The General Faculty Martina Zimovjanová, M.D.  chemoresistance prediction by

Hospital, 1st Faculty of Medicine, zimov@seznam.cz MTT assay

Charles University Oncology Department  viability of tumor cells

The General Faculty Hospital 6_prediction_chemosenzitivity_Zi

Prague 2, Czech Republic

movjanova



Dpt. of Oncology, 1st Faculty of Filip Janku, janku.filip@vfn.cz  mammaglobin

Medicine, Charles University U Nemocnice 2  cytokeratin19

Prague 2 128 08  detection of minimal residual

Czech Republic disease in early breast cancer

Phone: +420 224962219 , patients

+420 224917830 20_Detection_mammaglobin_cyto

Fax: +420 224921716 keratin_Janku



ASCR, Inst. of Plant Molecular Biology, Doc. RNDr. Jindrich Briza, CSc.  HPV16 virus

Dpt. of Gene Manipulations, Branisovska 31  HPV 16 associated cancer

http://www.umbr.cas.cz/807_www/ind 370 05 Ceske Budejovice, Czech therapy

ex.htm Republic  vaccines based on plant

Tel.: 387 775 515 antigens

Fax: 385 310 356 15_HPV16_cancer_Briza

e-mail: briza@umbr.cas.cz

1_computer_ass_drugs-Kralova



We would like to offer a co-operation in the topic



Computer assisted modelling for drug discovery and testing – NETWORK OF EXCELLENCE



What we may offer to you:

1) Our laboratory is experienced in a number of molecular modelling techniques, including protein structure prediction by

homology modelling, molecular dynamics simulation and protein-ligand docking. We have particular experience with basic quantum

chemistry methods (ab initio and semiempirical calculation of properties of isolated small molecules and noncovalent interactions),

application of protein-ligand docking to virtual screening, fold recognition, continuum electrostatics calculations, prediction of

free-energy of binding (application of empirical scoring functions, free energy perturbation) and other techniques that could be applied

in structure-based drug design. We have experience with using following molecular modelling programs and packages: Modeller,

Amber, Gromacs, Gamess US, Mopac7, Autodock, Dock, Grid20, Sybyl, Insight and basic visualisation and other software in Linux or

SGI IRIX environment. We are experienced in using of Linux-based clusters.

2) We have long-time experience in various methods: molecular biology (expression of recombinant proteins, mutagenesis),

enzymology (we deal especially with glycosidases and transfer of glycerol groups), chromatography (HPLC, FPLC), and other

isolation and purification techniques.



Contact person:

Blanka Kralova, E-mail: karasovp@vscht.cz

Department of Biochemistry and Microbiology, ICT Prague : http://biomikro.vscht.cz/groups/lab211/index.html

Technicka 3

166 28, Prague 6

Czech Republic

Phone: +420224353077

Fax: +420224355167

2_transplant_Hlozanek



Department of Immunology of Institute for Clinical and Experimental Medicine (IKEM) would like to find a partners for the FP6 project

at the area:



 The role of innate immunity in rejection mechanisms (evaluation of cytokine levels in clinical samples, tissue culture models of

macrophage/epithelial interactions with respect to cytokine networking, adhesion molecules)

 Cytokine gene polymorphisms in organ transplantation (our lab participates in the 13th workshop of International

Histocopatibility Working Group, gene polymorphisms evaluated by PCR-SSP)

 Sequence based HLA typing (currently working on a grant dealing with „null allels“)

 HLA and diseases (the association between HLA haplotypes on the high resolution level and predisposition to diabetes,

cardiovascular diseases,... etc.)



The Institute represents one of the the biggest organ transplant centers in the Central Europe, the number of patients with kidney,

heart, kidney, and pancreas transplantations is sufficient for reasonable clinical studies, the laboratories are fully equipped, HLA lab is

accredited by the European Federation of Immunogenetics.

Contact:

Assoc. Prof. Ilja Striz, MD, PhD

Department of Immunology

Institute for Clinical and Experimental Medicine (IKEM)

Vídeňská 1958/9, 140 21 Prague 4, Czech Republic

ilja.striz@medicon.cz



Selected publications in the last 5 years:



1. I.Stříţ, T.Mio, Y.Adachi, V.Baţil, S.I.Rennard. The CD14 molecule participates in regulation of IL-8 and IL-6 release by bronchial epithelial cells. Immunol.

Lett. 62:177-181, 1998.

2. I.Stříţ, H.Pokorná, L.Zheng, J.Guzman, U.Costabel. Different expression of integrins by mononuclear phagocytes in peripheral blood and bronchoalveolar

lavage fluid. Resp.Med. 92:1326-1330, 1998

3. T.Mio, X.-D. Liu, Y.Adachi, Striz, I., C.M.Skold, D.J.Romberger, J.R.Spurzem, M.G.Illig, R.Ertl, S.I.Rennard. Human bronchial epithelial cells modulate

collagen gel contraction by fibroblasts. Am.J.Physiol. 274:L119-126, 1998.

4. Y.Adachi, T.Mio, K.Takigawa, I.Striz, D.J.Romberger, J.R.Spurzem, S.I.Rennard. Fibronectin production by cultured human lung fibroblasts in

three-dimensional collagen gel culture. In Vitro Cell.Dev.Biol.34:203-210, 1998.

5. M.Kraft, Striz, I., S.I.Rennard, K.Takigawa, T.Umino, R.J.Martin Expression of epithelial markers in nocturnal asthma. J.Allergy Clin.Immunol. 102: 376-381,

1998.

6. I.Stříţ, Mio, T., Adachi, Y., Heires, P., Robbins, R.A., Spurzem, J.R., Illig, M.J., Romberger, D.J., Rennard, S.I. IL-4 induces ICAM-1 expression in human bronchial

epithelial cells and potentiates TNF-alpha. Am.J.Physiol. 1999 277 (21): L58-L64.

7. I.Stříţ, Mio, T., Adachi, Y., Robbins, R.A., Romberger, D.J., Rennard, S.I. IL-4 and IL-13 stimulate human bronchial epithelial cells to release IL-8. Inflammation

1999, 23 (6): 545-555.

8. I.Stříţ, Mio, T., Adachi, Y., Romberger, D.J., Rennard, S.I. Th2-type cytokines modulate IL-6 release by human bronchial epithelial cells. Immunol.Lett. 1999, 70(2):

83-88.

9. I.Stříţ, Mio, T., Adachi, Y., Carnevali, S., Romberger, D.J., Rennard, S.I. Effects of interferons alpha and gamma on cytokine production and phenotypic pattern of

human bronchial epithelial cells. Int.J.Immunopharmacol. 2000, 22: 573-585

10. Stříţ I., Pokorná, H., Zheng, L., Jarešová, M., Guzman, J., Costabel, U. Calprotectin expression and mononuclear phagocyte subpopulations in peripheral blood and

bronchoalveolar lavage. Sarcoidosis Vasc. Diff. Lung Dis. 2001, 18: 57-63.

11. Stříţ I., Jarešová M., Lácha J., Sedláček J., Vítko Š. MRP8/14 and procalcitonin serum levels in organ transplantations. Ann.Transplant 2001, 6: 7-9.

12. Slavčev A. Mechanisms of allorecognition and organ transplantation. Ann Transplant 2002, 6:5-8.

13. Stříţ I., Slavčev A., Kalanin J., Jarešová M, Rennard S.I. Cell-cell contacts with epithelial cells modulate the phenotype of human macrophages. Inflammation 2001,

25(4): 241-246.

14. Slavčev A, Lácha J, Sajdlová H, Vítko Š, Horčičková M, Stříţ I, Ivašková E. Characterization of patient antibodies after kidney transplantation. Ann.Transplant 2001,

6:12-15.

15. Slavčev A, Stříţ I, Ivašková E, Breur-Vriesendorp BS. Alloresponses of cord blood cells in primary mixed lymphocyte cultures. Human Immunology 2002, 63:

155-163.

16. Tlaskalová-Hogenová H, Tučková L, Lodinová-Ţádniková R, Štěpánková R, Cukrowska B, Funda DP, Stříţ I, Kozáková H, Trebichavský I, Sokol D, Řeháková Z,

Šinkora J, Fundová P, Horáková D, Jelínková L, Sánchez D. Mucosal immunity: Its role in defense and allergy. Int Arch Allergy Immunol 2002; 128: 77-89.

17. Jarešová M, Bendukidze N, Ivaskova E, Striz I, Hlozanek I, Hatala M, Totusek P, Kosmoud Z. Human leukocyte antigen typing in Legionella-positive transplant

patients. In: Legionella. R. Marre ed, ASM Press, Washington, DC, 2002, pp 196-199.

18. Stříţ I Slavčev A, Krásná E, Valhová Š, Kronosová B, Jarešová M. Human lung epithelial cells express IL-18 receptors. In: Clinical Immunology and Allergy in

Medicine 2002 (in press)

19. Slavcev A, Lacha J, Honsova E, Sajdlova H, Lodererova A, Vitko S, Valhova S, Striz I, Ivaskova E. Clinical relevance of antibodies undetectable by the ctandard

complement dependent cytotoxicity test. Transplant Int (in press)

3_second_call_peroxisomes



Dear Colleagues,

We would like to join the program Genomics and biotechnology for health of 6th framework programme of European community

for research, technological development and demonstration activities. We are interested in the area



“Functional genomics approaches to the study of peroxisomes in health and disease” which belongs to the section

Multidisciplinary function genomics approaches to basic biological processes.



Our Laboratory of Molecular Pathology is involved in the study of the role of peroxisome proliferator-activated receptors

(PPARs) in glial cancerogenesis. We would be pleased if we could contribute to the project by the study “Effect of ligands of

peroxisome proliferator-activated receptors on cell cycle and apoptosis in human cancer cell lines.” The nuclear receptors PPARs are

transcription factors activated by specific ligands. PPARs play an important role in carcinogenesis, inflammation, atherosclerosis, lipid

metabolism and diabetes. There are evidences that activation of PPARs by specific ligands is able to suppress the growth of different

types of human cancer by mechanisms including the growth arrest, apoptosis and induction of differentiation. The detailed signalling

pathways have not been completely elucidated yet. We have examined the effect of synthetic ligands of PPAR and PPAR and we

have found that they affect the viability, proliferation, differentiation, apoptosis and expression of some cell cycle and apoptosis related

proteins in glial cancer cell lines.

We are able to offer the methods for global analysis of cell kinetic and gene expression including gene transfer and

biotechnology.



Selected publications:



Vavrusova N., Ehrmann J., Malikova J., Bartos J., Kolar Z.. Effect of peroxisome proliferators-activated receptor ligands on cell cycle and apoptosis of

human glial cancer cells; “PPARs: from basic science to clinical application”, Florence (Italy) March 2003 (abtract book of conference).



Vavrusova N., Ehrmann J., Bartos J., Malikova J., Rihakova P., Holinkova J., Pimrova E., Dolezel J., Kolar Z.. Peroxisome proliferator-activated receptors

agonists affect cell viability, apoptosis and expression of cell cycle related proteins in cell lines of glial tumors of brain. (submitted)



Ehrmann J., Vavrusova N., Collan Y., Kolar Z.. Peroxisome proliferator-activated receptors (PPARs) in the health and disease. Biomedical Papers 146(2):

11-14, 2002.

Vavrušová N., Ehrmann J., Kolář Z.. Peroxisome proliferator-activated receptor (PPAR) ligands affect cell viability, apoptosis and expression of cell

cycle related proteins in glial tumor cell lines. Pathologica 94 (2): 93, 2002.



Vavrušová N., Ehrmann J., Kolář Z.: The effect of fibrate on viability of glial cell lines. Biomedical Papers, 145: 39, 2001.



Ehrmann J. jr., Vavrušová N., Collan Y., Kolář Z.: Changes of expression of ”orphan“ receptor PPAR in breast carcinoma: imunohistochemical study.

Biomedical Papers, 145: 31, 2001.



The Laboratory of Molecular Pathology (LMP) was founded in 1995 as an integral part of the Centre of Molecular Biology and

Medicine of Palacký University in Olomouc and the Institute of Pathology, Faculty of Medicine UP Olomouc. LMP was founded for the

study of molecular mechanisms of cancerogenesis and the molecular aspects of diagnostics as well as the therapy of cancers.

Research activities of laboratory are primarily oriented to the basic and applied research in the field of general, experimental and

applied oncology. It also serves as a centre for postgraduate training. Members of the laboratory actively co-operate with other

scientific and clinical subjects in Czech Republic and abroad. A result of the cooperation is in development and realisation of joint

research projects. LMP is structured to four co-operative groups. A Laboratory of Morphometry and Computer Image Analysis

engages in automatic quantitative evaluation of histologic slides. A Laboratory of Cell Culture ensures in vitro cultivation and analysis

of cancer cell lines. Molecular mechanisms of cancerogenesis are studied in a Laboratory of Molecular Biology. A Laboratory of

Immunohistochemistry and in situ hybridisation participates in a various immunohistochemical investigations of protein expressions

and in situ detection of nucleic acids sequences. In detail see home page http://lmp.upol.cz.



Contact address:

Mgr. Nicol Vavrusova (vavrusova@seznam.cz)

Laboratory of Molecular Pathology UP,

Department of Pathology , http://lmp.upol.cz/

Palacký University

Hnevotinska 3

Olomouc

CZ-775 15

Phone: +420 585 632 451

Fax: +420 585 632 966

4_second_call_Korabecna



Proposals for participation in “Genomic and Biotechnology for health”



Department of Biology, Faculty of Medicine, Charles University

Karlovarska 48, 30166 Pilsen, Czech Republic

Head: Doc.RNDr.Josef Reischig, CSc.



Contact person:



RNDr.Marie Korabecna,

e-mail: marie.korabecna @lfp.cuni.cz

tel.: 00420 377593 262, 00420 377593 260



Topics for the second call:

 Global in situ gene expression analysis in rodent models and human tissues

 In vivo molecular imaging: identification of new markers for diagnostic purposes-new probes

 Molecular mechanisms of embryo implantation



We study the expression of proteins of fibrinolytic system (activators of plasminogen tPA and uPA and their inhibitor PAI-1) under

physiological and pathological conditions in human tissues using following methods:

in situ hybridization (ISH) to detect transcripts of Plasminogen Activator Inhibitor Type 1 (PAI-1) gene in paraffin-embedded samples

of human tissues, mainly in normal or atherosclerotic vessel walls and tumors and their surrounding normal tissue (grant no.1264 from

Ministry of Education). We use the DNA oligoprobes of our own design.

immunohistochemistry for selected proteins of fibrinolytic system (PAI-1, tPA and uPA) on the same material as above (grant no.1264

from Ministry of Education)

We are beginning with Real Time PCR to quantify the amount of mRNA for above-mentioned proteins in human tissues (grant no.2491

from Ministry of Education)



 Developing new molecular tools and approaches for high throughput molecular phenotyping of human population

 DNA damage and repair mechanisms in health and disease

 Medicine for children

 Development of genetic test allowing for harmonization, validation and standardization

We participate on the research project no. 52-201912 supported by the Grant Agency of the Czech Academy of Science, in which the

amount of fetal DNA in maternal plasma would be determined during normal and pathological pregnancies using the method of Real

Time PCR for detection Y chromosome related sequences. A diagnostic approach allowing the determination of Rh genotype of the

fetus in early pregnancy would be established during this study.





 Post genomic approaches to the study of human pathogens



We have studied the human fungal pathogens (Candida and non-Candida species) using PCR, in the internal transcribed spacers and

5.8 S rRNA gene, restriction analysis and fragment analysis on ABI PRISM 310. We have evaluated the diagnostic application of this

approach. The project has been supported by the grant no.117/1999C of the Grant Agency of Charles University). Our work has been

awarded by the European Confederation of Medical Mycology on its 7th Congress in Rhodes as the best poster presenting laboratory

methodology:

Korabečná, M., Liška, V., Fajfrlík, K.: The intraspecies variability in the internal transcribed spacers and 5.8 S rRNA gene region has

been found in clinical isolates of fungi using primers ITS1, ITS2 and ITS4. Mycoses, 44, (Supp.1), 2001: 38



Grants:

1994 - The Grant Agency of Ministry of Education, grant no.0665 - Development of activities of medical students in molecular genetics

1995-96 The Grant Agency of Charles University , grant no. 40/95 - Detection of mutation and PCR diagnostics in the gene for neurofibromatosis von

Recklinghausen, type 1 (NF1).

1997 - The Grant Agency of Ministry of Education , grant no. 1264 - Introduction of the in situ hybridization method for comparative histological studies

1998 - The Grant Agency of Ministry of Education, grant no. 1349 – Introduction of molecular genetic methods in the practical courses „Biology“ and

„Clinical Genetics“

1999 - The Grant Agency of Ministry of Education, grant no. 1378 – Study of the role of Epstein-Barr virus in tumorogenesis using molecular genetic

methods

2000 - The Grant Agency of Ministry of Education, grant no. G1738 Genetic study of the STR polymorphisms THO1, TPOX ans CSF1PO in the gypsy

population.

1999 – 2001 - The Grant Agency of Charles University , grant no. 117/1999 C Introduction of the methods of molecular genetics in the diagnostics of

mycoses

2002 - The Grant Agency of Ministry of Education, grant no. 2491 Workshop “Real Time PCR“ for gradueted students of biomedicine

2002 - The Grant Agency of Ministry of Education, grant no. 2492 Introduction of the FISH method for the needs of student scientific work

2003 - The Grant Agency of the Czech Academy of Sciences , grant no. 52-201912 Application of Real Time PCR in analysis of fetal DNA in maternal

plasma.

5_second_call_damborsky



 Standardisation and integration of genomic and phenotypic information to characterise bacterial diversity with

relevance to human health -> NETWORK OF EXCELLENCE.



The Protein Engineering Group (Masaryk University, Brno, Czech Republic; contact person: J. Damborsky – jiri@chemi.muni.cz)

could be involved in testing and validation of developed technologies with mycobacteria. In particular, the group is interested in

screening for the presence of specific mycobacterial genes potentially involved in pathogenesis.



 Development of an integrated software platform to tackle genomic sequence-structure-function relationships -

INTEGRATED PROJECT.



The Protein Engineering Group (Masaryk University, Brno, Czech Republic; contact person: J. Damborsky – jiri@chemi.muni.cz)

could be involved in development and integration of the software for modelling of biochemical reactions (currently the group develops

in-house software TRITON for site-directed mutagenesis and modelling of enzymatic reactions). The group also owns unique amount

of sequential, structural, kinetics, biochemical, etc. data collected for the family of enzymes haloalkane dehalogenases relevant for

study of sequence-structure-function relationships. These data could be uses for validation of the software developed within project.



 Computer assisted modelling for drug discovery and testing -> NETWORK OF EXCELLENCE.



The Protein Engineering Group (Masaryk University, Brno, Czech Republic; contact person: J. Damborsky – jiri@chemi.muni.cz)

could be involved in development and validation of methods for modelling and prediction of metabolism of drugs within a living cells.



 New bioassays and biosensors using post-genomic approaches for detection of harmful microbes – STREP



The Protein Engineering Group (Masaryk University, Brno, Czech Republic; contact person: J. Damborsky – jiri@chemi.muni.cz)

could be involved in development of biosensors using activity of dehalogenating enzymes widely distributed among bacteria. The

preliminary experiments confirmed that dehalogenases can be immobilised on biosensors and show good linearity in responses, as

well as an excellent sensitivity.

6_prediction_chemosenzitivity_Zimovjanova



Dear colleagues,



in Laboratory of Tumor Biology of The Oncology Department of General Faculty Hospital in Prague, Czech Republic, we

provide the method of chemoresistance prediction by MTT assay to measure the viability of tumor cells. We obtain part of tumor

(especially breast and ovarian) and make special suspenssion from tumor cells and also suspenssion of malignant pleural and

peritoneal effusions. We have experience with breast cancer cells passages, with short time cultivation of ovarian cancer cells and

with using malignant effusions as source of cancer cells. We have analyzed about 200 samples on which the MTT assey were realised

and predicted chemosenzitivity (cca. 10 cytostatics, e.g. tamoxifen).



We would be able to offer the cooperation in the sphere of the short in vitro tests (MTT) which is, in often cancer diagnosis,

successfully tested in our hospital laboratory. The goal of that is an individualization of chemoterapy for cancer patients. This is, as we

trust, the way of exclussion of ineffective therapy and minimalizing adverse events of chemotherapy.







Contact person:



Martina Zimovjanová, M.D. E-mail: zimov@seznam.cz

Oncology Department

The General Faculty Hospital

Prague 2

Czech Republic

7_pharmacoepidemiology-combmajdis_Perlik



Proposed Contribution of the Institute of Pharmacology in Prague to the Projects of the 6th Framework Program





Research projects of the Institute



The clinical pharmacology unit of the Institute currently performs studies aimed at characterization of genetic predispositions for

interindividual changes in pharmacokinetics, therapeutic efficacy and safety of selected drugs in healthy volunteers and patients under

naturalistic clinical conditions in hospital practice. Also possible effects of some pharmacotherapeutic schemes on the enzyme activity

are studied in hematooncological patients. Various single nucleotide polymorphisms in genes affecting activity and/or inducibility of

drug metabolizing enzymes and xenobiotic transporters are detected. The real activity of cytochrome P450 enzymes is assessed by

probe drugs.



Methodology



The relevant methodology available within the Institute is currently represented by genotyping techniques for detection and

characterization of single nucleotide polymorphisms including automated PCR, PCR-RFLP analysis, real-time PCR and phenotyping

methods based on HPLC analysis of probe drugs and their metabolites.





Possible involvement of the Institute in the projects



 In pharmacoepidemiological studies - the Institute is embedded in a large university hospital center with over 1000 beds. It

also cooperates with clinical departments in other large hospitals in Prague; the city with high number of students and over 1

million of inhabitants showing low migration. These factors offer good recruitment potential for pharmacogenetic studies among

patients as well as healthy volunteers.



 In combating major diseases – by applying pharmacogenetic approach and knowledge to individualize and improve therapy.



Contact persons:

Ass. Prof. Dr. František Perlík, DrSc. Dr. Ondřej Slanař

Head Clinical Pharmacology Unit,

Institute of Pharmacology Institute of Pharmacology

Albertov 4 Na Bojisti 1

Prague 2, 120 00 Prage 2, 128 08

Czech Republic Czech Republic

Email: fperl@lf1.cuni.cz Email: oslan@lf1.cuni.cz

Phone: +420 224968146 Phone: +420 224964135

8_fungi_Pazoutova



Exploitation of fungal genomics and application of filamentous fungal

biotechnology for the benefits of human health



Company Expertise

Title: Fungal genetics, taxonomy, ecology and biotechnology



Details:

Our current work involves research on fungi belonging to the Hypocreales. With the application of molecular markers, the genetic

variability has been studied in different symbiotic and phytopathogenic fungi (e.g., Claviceps sp., Geosmithia sp., phialophora sp.,

Ophiostoma sp.) in relationship to their spreading, vectors, habitat and host preferences, and population genetics. Methods of

molecular taxonomy (rDNA sequencing, RAPD, AFLP) as well as analysis of secondary metabolites (toxins, alkaloids,

polysaccharides and oligosaccharides)are used, also mathematical modelling of fungal growth and production of metabolites

(polysaccharides, alkaloids)



Research Interest: Genetics, Microbiology, Mycology, Biotechnology;



Contact person:



Dr. Sylvie Pazoutova

Insttitute of Microbiology ASCR

Videnska 1083

142 20 Praha 4

phone: (+4202) 9644 2332

fax: (+4202) 9644 2347

mail: pazouto@biomed.cas.cz

URL: http://www.biomed.cas.cz/~pazouto/pazouto.htm

9_gerontology-Ďoubal



Coordinating European research in ageing and longevity - CA. The goal is to provide a platform for the coordination of European

ageing research. Initiatives include workshops and meetings that address (i) development of common research strategies, (ii)

interspecies studies of ageing processes, and (iii) standardization of data collection (e.g. phenotype analysis) and data processing

including statistical analysis.



European research on ageing – SSA. The aim is to provide support for the organization of a conference on the state of the art and

future perspectives of European ageing research.



Contact:

Ďoubal Stanislav, Klemera Petr, doubal@faf.cuni.cz

Charles University Prague, Faculty of Pharmacy in Hradec Králové,

Department of Biophysics and Physical Chemistry

Heyrovského 1205

500 05 Hradec Králové,



Methodology of verification in gerontology

Summary

Among the most crucial problems in theoretical and experimental gerontology belongs the methodology of verification of theories of

aging. Extensive number of hypotheses of the nature of basic mechanisms of aging exists on the field of theoretical gerontology. This

situation claims the development of robust methodology of verification. Traditional ways of the verification were indirect and

insufficient. The progress in theoretical gerontology provides the possibility to verify the theories in more exact way.

Survey of the contemporary state in the theories of aging and available methods of verification is presented in the paper. The tools of

verification derived from survival curves and mortality curves are analyzed and discussed. Further the tools derived from biomarkers

of aging and batteries of biological age are survived.

Key words:

aging, verification, theories of aging, biological age, markers of aging



Visco-elastic Parameters of Human Skin – Measurement and Application in Gerontology, Dermatology and Cosmetics.

Abstract

The dynamics of deformation response of body surface depends on mechanical properties of skin and subcutaneous structures. The

determination of visco-elastic parameters of skin may be prospective tool of diagnostic in dermatology as well as potential source of

information in biological age assessment in gerontology. From the practical point of view, the analysis of deformation response of skin

(and its changes) can be useful for the assessment and control of effects of cosmetics.

The analysis of the dynamics of deformation response of the skin, the structure of rheological model and its typical parameters are

presented in the paper. The transient deformation response consists of two distinct exponential components. A “rapid” exponential

curve has time constant typically of order 10 ms, while “slow” exponential curve has a time constant of order 0.1 to 1s. The

corresponding model involves serial-parallel combination of two Hook’s and two Newton’s bodies. The time constant of the slow

exponential curve increases significantly with age. The increase is mainly connected with decrease of the value of parameter of

corresponding Hook’s body.

Demonstration of the application of the suggested methodology is further presented in the paper. The “antiaging” cosmetic cream

containing antioxidants and liposomes was used for demonstration. The time constant of the slow exponential curve decreases

significantly after application. Nevertheless, the decrease was connected with decrease of parameter of corresponding Newton’s

body. Consequently, the effect of the cream does not lie in reversing the aging of skin.

Key words: skin, aging, dermatology, cosmetics, diagnostics, biological age

Discussion

The measurement of deformation response of skin and following identification of rheological model seems to be potential source of

new information on its mechanical behavior [5, 6, 7.]. Especially important seems to be conclusion, that the response consists at least

of two exponential curves, differing in time constant. The explanation of this phenomenon probably lays in the structure of the skin and,

perhaps also in the structures of subcutaneous systems: the elastic behavior is determined by elastic fibers, forming helix-like

structures of on many levels, this elastic system is surrounding by amorphous matrix. The matrix is responsible for viscose behavior.

Such arrangements implied multiexponential response.The apparatus, applied in the experiment discussed in this paper works with

sensitivity 5 m and measured exponentials curves with constants in interval 100 s -1 do 1 s-1 . The apparatus enables to distinguish

two exponential curves in the response. It can’t be excluded, that application of more sensitive device or device with broader range of

time will reveal additional exponential curves in the response.

On the field of gerontology, the application of methodology may consist in assessment of biological age and revealing premature aging

[5]. In dermatology, the study of age-dependant changes of parameters of the model may contribute to better understanding of the

mechanisms of skin aging. The results of the work further demonstrates potential applicability of the methodology in cosmetics,

namely for assessment of positive as well as negative effects of cosmetics.

Mechanical impedance of biological materials: concept, meaning, applications and measurement

Summary

The quantitative methodology of assessment of mechanical behavior of visco-elastic materials is of crucial significance, among

others for pharmaceutical technology, research in cardiovascular system or for mechanical matching of implants. The mechanical

(rheological) properties of visco-elastic materials involve elastic as well as plastic elements. The mechanical behavior of these

materials is non-linear in many respects and it is different in cases of static and dynamic loading. Consequently, the satisfactory

description of mechanical behavior of biological materials is extremely difficult. The classical approach based on theory of elastic or

visco-elastic bodies often fails to provide adequate tools for solution of these problems. The concept of complex mechanical

impedance enables more universal and more adequate description of mechanical behavior of this category of materials. The concept

of mechanical impedance is analogical to the concept of impedance in theory of electric circuits. The mechanical impedance is

complex number defined as ratio between instantaneous complex values of stress and strain in steady state of cyclic dynamic loading.

The mechanical impedance enables to calculate the amplitude as well as phase of strain response and solve the problem of

mechanical matching. The theory of complex mechanical impedance as well as the methodology of identification of mechanical

models of visco-elastic materials is presented in the paper.



Appliance for measurement of creep curves of visco-elastic materials

Summary

The mechanical properties of biological materials depend on age and health status of the organism. They may be potentially used as

indicators of functional age or as diagnostic tools. Many biological materials exhibit both elastic and plastic (viscose) properties and

can not be simply categorized as solids or as liquids. The term visco-elastic materials or bodies is used for these substances. Skin, cell

walls, numerous structures of internal organs, tendons, cartilage and many other materials belong to this category. The currently used

methods of assessment of mechanical properties of biological materials are, as a rule, based on methods derived from the mechanics

of solids or liquids. However, the theory of rheology provides a more adequate description of mechanical properties of visco-elastic

bodies. The application of rheological approach is rare in biology and medicine. The reason consists in the limited availability of

convenient method of measurement of rheological characteristic of visco-elastic materials. The appliance for measurement of creep

curves of biological materials, was designed in our laboratory. The appliance enables the measurement of creep curves of biological

materials in vivo as well as in vitro. Examples of application on measurement of mechanical properties of human skin in vivo and skin

of rats in vitro are presented. The measurement of creep curves of non-biological materials is also possible, provided the visco-elastic

parameters of these materials are of similar range. The appliance was tested in our laboratory and is currently used for measurement

of changes of visco-elastic properties of human skin as a marker of biological age.

Key words: biological materials, measurement, visco-elasticity, diagnostic, biological age

10_insitu_gene_expresion_Fajkus



LABORATORY OF DNA-MOLECULAR COMPLEXES, INSTITUTE OF BIOPHYSICS, CZECH ACADEMY OF SCIENCES, AND DEPARTMENT OF

FUNCTIONAL GENOMICS AND PROTEOMICS, MASARYK UNIVERSITY BRNO



Would like to cooperate at the topic:

Global in situ gene expression analysis in rodent models and human tissues



Contact address: Jiri Fajkus, Institute of Biophysics, Kralovopolska 135, CZ-61265 Brno, Czech Republic.

phone: 420-541517199, FAX: 420-541211293, e-mail: fajkus@ibp.cz



Our present scientific projects aim at the nucleoprotein complexes, which form indispensable functional elements forming and

protecting the ends of linear eukaryotic chromosomes - telomeres. Telomeres are synthesised by a specialised reverse transcriptase,

telomerase. In the absence of telomerase, each round of DNA replication results in shortening of the telomeres due to incomplete

replication of the 3' end of the parental strand and, consequently, the number of cell doublings is limited by functionally critical length

of telomeric DNA.

In humans, telomerase activity is restricted to the germ-line, cancer, and possibly cycling stem cells of self-renewing tissues. It has

been shown that functioning telomere maintenance is a necessary factor of cellular immortalisation. The ability to bypass senescence

by circumventing telomere-based growth limitations is thought to be a critical step in the progression to malignancy. Today's telomere

research advanced from purely descriptive approach to promising applications in medicine. These applications include "passive"

ones, among which the use of analysis of telomeres and telomerase for cancer diagnostics is the best known. The "active"

applications involve targeted down- or up-regulation of telomere synthesis, either to mortalise immortal cancer cells or to re-juvenate

mortal somatic cells and tissues for cellular transplantations, respectively (see (Fajkus et al., 2002b) for review). Therefore, our

collaborative research with medical institutions is focused on biomedicine of telomeres (Malaska et al., 2000, Fajkus et al., 2003).

Besides, we also participate in development and application of molecular diagnostic techniques in general, namely in neuromuscular

disorders (Fajkusová et al., 2000; Fajkusová et al., 1997a; Fajkusová et al., 1997b; Fajkusová et al., 1997c; Fajkusova et al., 2001;

Fajkusová et al., 1998).

In plant cells, telomerase activity has been detected by our group in 1996 (Fajkus et al., 1996)and a developmental regulation of

telomere lengths and telomerase activity have been studied in model plant systems. (Fajkus et al., 1998; Riha et al., 1998; Riha et al.,

2000)It was shown, that telomerase activity is present in dividing plant cells and is absent (but inducible) in quiescent cells. A presence

of a regulatory mechanism has been demonstrated in plant cells, which controls telomerase action to compensate for replicative loss

of telomeric DNA. These observations are consistent with so-called totipotency of plant cells. Regulation of plant telomerase by

telomere-binding proteins from nuclei of telomerase-negative tissues has been observed recently. (Fulnečková and Fajkus,

2000)These proteins form salt-stable, sequence specific complexes with the G-rich telomeric strand and reduce its accessibility to

telomerase. Complete characterisation of these proteins, as well as a search for other telomere-binding proteins using combination of

biochemical, molecular-genetic, genomic and proteomic approaches is in progress. Besides studies on typical telomeres,

subtelomeres and their chromatin structure (Fajkus et al., 1995a; Fajkus et al., 1995b; Fajkus et al., 2002a; Fajkus and Trifonov, 2001;

Fajkus and Zentgraf, 2002; Fojtova et al., 2002; Sýkorová et al., 2003a; Sýkorová et al., 2001; Sýkorová et al., 2003b) we are

interested also in a structure of alternative telomeres, especially in plants. (Sýkorová et al., 2003b).





Fajkus, J., Borský, M., Kunická, Z., Kovaříková, M., Dvořáková, D., Hofmanová, J. and Kozubík, A. (2003) Changes in Telomerase Activity, Expression and

Splicing in Response to Differentiation of Normal and Carcinoma Colon Cells. Anticancer Res., 23, in press.

Fajkus, J., Fulnečková, J., Hulánová, M., Berková, K., Říha, K. and Matyášek, R. (1998) Plant cells express telomerase activity upon transfer to callus culture,

without extensively changing telomere lengths. Mol. Gen. Genet., 260, 470-474.

Fajkus, J., Kovařík, A. and Královics, R. (1996) Telomerase activity in plant cells. FEBS Lett., 391, 307-309.

Fajkus, J., Kovařík, A., Královics, R. and Bezděk, M. (1995a) Organization of telomeric and subtelomeric chromatin in the higher plant Nicotiana tabacum. Mol.

Gen. Genet., 247, 633-638.

Fajkus, J., Královics, R., Kovařík, A. and Fajkusová, L. (1995b) The telomeric sequence is directly attached to the HRS60 subtelomeric tandem repeat in tobacco

chromosomes. FEBS Lett., 364, 33-35.

Fajkus, J., Novotná, M. and Ptáček, J. (2002a) Analysis of chromosome termini in potato varieties. Rostlinná výroba, 48, 477-479.

Fajkus, J., Šimíčková, M. and Maláska, J. (2002b) Tiptoeing to chromosome tips: facts, promises and perils of today's human telomere biology. Phil. Trans. R.

Soc. Lond. Ser. B-Biol. Sci., 357, 545-562.

Fajkus, J. and Trifonov, E.N. (2001) Columnar Packing of Telomeric Nucleosomes. Biochem. Biophys. Res. Commun., 280, 961-963.

Fajkus, J. and Zentgraf, U. (2002) Structure and maintenance of chromosome ends in plants. In Krupp, G. and Parwaresch, R. (eds.), Telomerases, Telomeres

and Cancer. Landes Bioscience and Kluwer Academic, Georgetown and New York, pp. 314-331.

Fajkusová, L., Fajkus, J., Poláčková, K., Fulneček, J., Dvořáková, D. and Krahulcová, E. (2000) Detailed Mapping of Methylcytosine Positions at the CpG Island

Surrounding the Pa Promoter at the bcr-abl Locus in CML Patients and in Two Cell Lines, K562 and BV173. Blood Cells Mol. Dis., 26, 193-204.

Fajkusová, L., Hájek, J., Kuhrová, V. and Fajkus, J. (1997a) Relatioship between Genotype and Phenotype of Patients with the Diagnosis of Duchenne Muscular

Dystrophy. Čes a Slov. Neurol. Neurochir., 60/93, 236-239.

Fajkusová, L., Kuhrová, V., Hájek, J. and Fajkus, J. (1997b) Detection of Large Deletions and Duplications in the Dystrophin Gene. Čas. Lék. čes., 136, 148-150.

Fajkusová, L., Kuhrová, V., Hájek, J. and Fajkus, J. (1997c) Distribution of dystrophin gene deletions mapped by multiplex PCR in the Moravian population. Mol.

Cell. Probes, 11, 85-87.

Fajkusova, L., Lukas, Z., Tvrdikova, M., Kuhrova, V.V., Hajek, J. and Fajkus, J. (2001) Novel dystrophin mutations revealed by analysis of dystrophin mRNA:

alternative splicing suppresses the phenotypic effect of a nonsense mutation. Neuromuscul Disord, 11, 133-138.

Fajkusová, L., Pekařík, V., Hájek, V., Kuhrová, V., Blaţková, M. and Fajkus, J. (1998) Characterization of two nonsense mutations in the human dystrophin gene.

J. Neurogenet., 12, 183-189.

Fojtova, M., Fulneckova, J., Fajkus, J. and Kovarik, A. (2002) Recovery of tobacco cells from cadmium stress is accompanied by DNA repair and increased

telomerase activity. J Exp Bot, 53, 2151-8.

Fulnečková, J. and Fajkus, J. (2000) Inhibition of plant telomerase by telomere-binding proteins from nuclei of telomerase-negative tissues. FEBS Lett, 467,

305-310.

Malaska, J., Sklenickova, M., Krejci, K., Fajkusova, L., Bajer, M., Hrstkova, H. and Fajkus, J. (2000) Telomerase Activity and Expression and Telomere Analysis

in Situ in the Course of Treatment of Childhood Leukemias. Blood Cells Mol Dis, 26, 534-539.

Riha, K., Fajkus, J., Siroky, J. and Vyskot, B. (1998) Developmental control of telomere lengths and telomerase activity in plants. Plant Cell, 10, 1691-8.

Riha, K., McKnight, T.D., Fajkus, J., Vyskot, B. and Shippen, D.E. (2000) Analysis of the G-overhang structures on plant telomeres: evidence for two distinct

telomere architectures. Plant J, 23, 633-641.

Sýkorová, E., Cartagena, J., Horáková, M., Fukui, K. and Fajkus, J. (2003a) Characterisation of telomere-subtelomere junctions in Silene latifolia. Mol. Gen.

Genomics, in press.

Sýkorová, E., Fajkus, J., Mikako, I. and Fukui, K. (2001) Transition between two forms of heterochromatin at plant subtelomeres. Cromosome Res., 9, 309-323.

Sýkorová, E., Lim, K.Y., Chase, M.W., Knapp, S., Leitch, I.J., Leitch, A.R. and Fajkus, J. (2003b) The absence of Arabidopsis-type telomeres in Cestrum and

closely related genera Vestia and Sessea (Solanaceae); first evidence from eudicots. Plant J., in press.



Major techniques and equipment available at the Department: Electrophoretic techniques (from PAGE to PFGE),

chromatography (BioCad station), real-time PCR, mass spectrometry of proteins, automated DNA sequencing, oligonucleotide

synthesis, ultracentrifugation, FISH techniques, isotopic techniques (Southern hybridisation), Gel documentation system DIANA,

Phosphoimager Storm 860.

11_LFPlzen_clinicalstudies_Taborska



Department of Infectious Diseases (Faculty of Medicine in Plzen, Charles University) can offer clinical studies at the listed topics of the

2nd call:



Contact person:



Jana Táborská taborska@fnplzen.cz

Charles University, Faculty of Medicine in Plzen, Department of Infectious Diseases

Dr. E. Beneše 13

Plzeň 305 99

Czech Republic

Phone: +420 377402263





New improved vaccines based on genomic and proteomic information

Dendritic cells for novel immunotherapies

Eicosanoids and nitric oxide: mediators of cardiovascular, cerebral and neoplastic diseases

Coordination of clinical trials in Europe

Functional genomics of antibiotics-producing organisms

New molecular targets for the development of drugs against pathogens causing severe resistance problems

Novel approaches to address antimicrobial resistance through non-antimicrobial based therapies

Neuronal networks, learning and memory: from genes to behaviour

Molecular mechanisms of neuronal degeneration

12_SyfilisRTPCR_Stork



The Czech National Reference Laboratory for Diagnostics of Syfilis is interested in: "Real Time PCR test for detection of

Treponema pallidum subsp. pallidüm."



They would like to find a partners for a FP6 project (2nd call) at the area:



l.3 - i Advanced genomics and its applications fo health:

b) Development of new diagnostics -





Contact:



Hana Zákoucká

National Reference Laboratory for Diagnostics of Syfilis

Department of Dermatology, 1.st Faculty of Medicine, Charles University

Address: U Nemocnice 2, 128 08 Praha 2, Czech Republic

Phone: 224 920 610

Fax: 224 923 759

E-mail: kozni@lf1.cuni.cz

14_embrstemcells_Dvorak



Department of Molecular Embryology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic

http://uemweb.biomed.cas.cz/dvorak/dvorak.html



Contact person: Dr. Petr Dvorak

Phone: +425 45133298

Fax: + 425 45133298

E mail: dvorakp@mendelu.cz





Methodology available

- Cell culture (embryonic stem and embryonal carcinoma cells, hematopoetic cells, mouse oocytes, IVF in mouse)

- Aggregation chimeras

- Colony forming assay

- Hybridoma construction

- Microinjection

- Electroporation

- Recombinant DNA techniques (prokaryotic and eukaryotic gene expression, PCR, RT-PCR, etc.)

- Protein detection - Immunochemical techniques (1D and 2D electrophoresis, WB, IP, IIF)

- Radioisotope labelling, autoradiography, scintilation counting, etc.

- Confocal microscopy





Scientific expertise

- Fibroblast growth factor signalling (primarily its role in early embryogenesis and in hematopoetic malignancies)

- The role of cell cycle regulators (D-type cyclins CDK4/6, p27 CKI) in cell differentiation (primarily the significance of their interactions

in cells of embryonal origin)

- Oocyte development – functions of cell cycle regulators

- Derivation, propagation and differentiation of mouse embryonic stem cells (for example several ES lineages that are deficient in p27

CKI have been recently derived and are being currently used to study the role of p27 in proliferation and differentiation of ES cells)

- Human embryonic stem cell biology (human ES cell line H1 was recently obtained from WiCell company)

- Phenotyping of mouse embryonic stem cells using gene and protein markers (non-differentiated, differentiating into

neuroectodermal, endodermal, and mesodermal lineages)

- Development and testing of syntetic hydrogel suports suitable for propagation and/or differentiation of embryonic stem cells (in

collaboration with other institute of the AS CR)





Personell



Current number of workplaces in the Department of Molecular Embryology: 9



Name Position

Petr DVORAK Senior scientist – head of the department

Ales HAMPL Senior scientist

Jiri PACHERNIK Postdoctoral fellow

Vitezslav BRYJA Research associate

Jana KROUPOVA Research associate

Jitka FAITOVA Research associate

Iveta NEVRIVA Lab technician

Stanislava KOSKOVA Lab technician

Jana KANTOVA Accountant





Contributions to the project

By determining the quantities / interactions / activities of proteins of the cell cycle regulating machinery of embryonic stem cells, the

Department of Molecular Embryology seeks to establish new molecular criteria, which will contribute to more precise evaluation of

embryonic (possibly also adult) stem cells at the specific stages of their development (propagation, differentiation).



Since such criteria will refine all comparisons being made in cultured (possibly also transplanted) stem cells, they will be applicable in

various experiments carried out by collaborative laboratories, including for example:

- development of culture media

- development of culture techniques (testing of culture substrates/scaffolds, tridimensional cultures, etc.)

- production of clonally derived stem cell lineages

- differentiation toward specific pathways

Our experience in the field

The Department of Molecular Embryology builds up on about one decade long hands-on experience in mammalian gamete, early

embryo, and embryonic stem cell research.



The following topics were recently addressed, and the results were published in internationally recognised journals:



1) The functions of fibroblast growth factors (FGFs),their high affinity receptors (FGFRs), and non-signaling coreceptors in

early development in mammals

We have shown that FGF-2 low-affinity binding function is displayed by an embryoglycan-specific epitope recognized by TEC-1

antibody that corresponds to LeX trisaccharide Gal(14)-[Fuc(13)]GlcNAc or its isoforms. When we addressed the potential

roles of three naturally occuring isoforms of Lewis X (Le X) in FGF-2-mediated proliferation of embryonic stem (ES) cells, we have

found that (A) O-linked LeX oligosaccharides can regulate mitogenic activity of FGF-2 in embryonic cells, (B) and this ability varies with

subtle modifications in their structure. Our data represent the first insight into the mechanism of how growth factor activities might be

modulated by shedded embryoglycan ectodomains. We used targeted disruption of FGFR-1 to interfere with FGF-2 signalling. We

have demonstrated that in ES cells, FGFR-1 plays a dominant role in receptor-ligand interactions. However, the lack of functional

FGFR-1 does not contribute to basal as well as FGF-2-mediated proliferation of ES cells. Rather, it functions to regulate the

differentiation of ES cell-derived EBs. Specifically, we presented evidence that the absence of FGFR-1 causes down-regulation of

endoderm-specific genes. Moreover, it suppresses the formation of the visceral endoderm and the specification of outer layers of the

primitive ectoderm into the columnar epithelium, and thus leads to a block of cavitation of mammalian embryo.



2) The functions of cell cycle regulators in female reproductive organs, female germ cells, and cells of embryonal origin

We employ several cellular systems to further investigate functions of cell cycle regulators, particularly p27 CKI and D-type cyclins,

in cell differentiation. First, we recently offered the scenario how p27 and cyclin D3 may participate in driving development and

maintenance of differentiated phenotype of luteal cells of mouse ovary. Second, in studies employing the panel of embryonal

carcinoma (EC) cells that differ from each other by the expression of membrane carbohydrates, we found that increased amount of

p27 protein observed in differentiating EC cells might also, at least in its early phase, mediate the occurrence of phenomena that are

not directly linked to modification of cell cycle progression. Third, we investigated whether or nor G1/S regulators may play some role

in the regulation of peculiar development of mammalian female gametes – oocytes. We already described the dynamics of the

expression of D-type cyclins, p27, and CDK4 during growth and meiotic maturation of mouse oocytes. We also characterized

intracellulr localization of these molecules, and the changes that occur to their phosphorylation status during the progression of

meiotic maturation (manuscript submitted). Fourth, we derived mouse ES cell lines were that differ from each other by the presence or

absence of functional p27 gene. These lines were used to investigate the significance of p27 for embryonic stem cells in vitro

(manuscript in preparation).



3) Developments toward regulatable propagation and differentiation of mouse and human embryonic stem (ES) cells;

understanding the molecular mechanisms that underlie biological properties of ES cells

We concentrate on developing/improving the strategies that will allow for effective differentiation of ES cells into various neural

lineages. Recently, we have shown that differentiation protocol involving 2 days of culture in serum-containing media followed by

culture in media with only insulin, transferrin, selenium, and fibronectin, preferentially support the development of neural cells from

mouse ES cells. This differentiation approach may thus represent a novel alternative to the widely used protocols that invariably

employ formation of embryoid bodies. We further develop this protocol in order to serve us as the experimental system for studying

the molecular mechanisms involved in neurodifferentiation.



Selected publications



Anger, M., Bryja, V., Jirmanova, L., Hampl, A., Carrington, M., Motlik, J., Dvorak, P., Kubelka, M. (2003)

The appearance of truncated cyclin A2 correlates with differentiation of mouse embryonic stem cells.

Biochem. Biophys. Res. Commun., in press



Anger, M., Kues, W.A., Klima, J., Mielenz, M., Kubelka, M., Motlik, J., Esner, M., Dvorak, P., Carnwath, J.W., Niemann, H. (2003)

Cell cycle dependent expression of Plk1 in synchronized porcine fetal fibroblasts.

Mol. Reprod. Dev., in press



Horak, D., Dvorak, P. Hampl, A., Slouf, M. (2003)

Poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) as a mouse embryonic stem cell support.

J. Applied Polymer Sci., 87:425-432.



Pacherník, J., Esner, M., Bryja, V., Dvorak, P., Hampl, A. (2002)

Neural differentiation of mouse embryonic stem cells grown in monolayer.

Reprod. Nutr. Dev., 42:317-326.



Preclikova, H., Bryja, V., Pachernik, J., Dvorak, P., Hampl, A. (2002)

Early cycling-independent changes to p27, cyclin D2, and cyclin D3 in differentiating mouse embryonal carcinoma cells.

Cell Growth & Differ., 13:421-430.



Esner, M., Pachernik, J., Hampl, A., Dvorak, P. (2002)

Targeted disruption of fibroblast growth factor receptor 1 blocks maturation of visceral endoderm and cavitation in embryoid bodies.

Int. J. Develop. Biol., 46:817-825.



Jirmanova, L., Pacholikova, J., Krejci, P., Hampl, A., Dvorak, P. (1999)

O-linked carbohydrates are required for FGF-2-mediated proliferation of mouse embryonic cells.

Int. J. Develop. Biol., 43: 555-562.



Dvorak, P., Hampl, A., Jirmanova, L., Pacholikova, J., Kusakabe, M. (1998)

Embryoglycan ectodomains regulate biological activity of FGF-2 to embryonic stem cells.

J. Cell Sci., 111:2945-2952.



Hampl, A. and Eppig, J.J. (1995)

Analysis of the mechanism(s) of metaphase I arrest in maturing mouse oocytes.

Development, 121:925-933.





Contribution to the knowledge in the field

Our deep understanding of the biology of stem cells is required for establishing the theoretical platform for their safe and efficient

clinical use. One important strategy toward this goal is creation of a clear view of the intracellular protein world that underlies the

behaviour of stem cells under both ex vivo and in vivo conditions. Obviously, the ability of stem cells to govern their proliferation upon

the extra- and intracellular signals is of a major importance specifically in terms of their propagation and/or differentiation in vitro. This

fact necessarily brings our attention to the intricate network of the members of rather heterogeneous family of cell cycle regulating

proteins. Studying these molecules seems to be even more important because recent data distinguish cell cycle regulators also as

proteins that influence certain aspects of cell differentiation via mechanisms other then regulation of cell cycle progression. It is

believed that unravelling the interactions among the cell cycle regulators that are typical for proliferating/differentiating embryonic stem

cells (both mouse and human) will help to improve the theoretical basis for the development of culture systems, identify

proteins/interactions that may represent targets for genetical manipulation, or both. The results of this research will be mediated to the

scientific/medical community via publications in internationally recognised journals.

15_HPV16_cancer_Briza

Department of Gene Manipulations, Inst. of Plant Molecular Biology, Academy of Sciences of the Czech Republic

(http://www.umbr.cas.cz/807_www/index.htm), would like to participate at the 6FP project. We can offer:



The proposal will be aimed on construction of the expression systems for production of the antigens of the human

papilloma virus 16 (HPV16) in plants and on development of experimental vaccines based on these antigens for prophylaxy

and therapy of HPV16 associated cancer. The vaccines will include structural (L1) and nonstructural (E7) viral proteins in the form

of virus-like particles VLP-L1 or chimeric VLP-L1-E7 or in the form of fusion molecule with E. coli -glucuronidase. The nucleotide

sequence of viral genes in expression vectors will be modified in order to increase transcription and translation in plant cells, whereby

the transgenic plants will synthesize sufficient amount of recombinant virus protein for the induction of immune response. Nuclear

transformation will be done using Agrobacterium tumefaciens technique (strains LBA4404 and EHA105). Potato cultivars „Bintje” and

„Kamýk” will be transformed with the leave discs method modified for internodes (Horsch et al. 1985). Regenerated in vitro transgenic

plants will be assayed for the L1, E7 or L1/E7 expression, ability to form regular capsid structures (in the case of L1 or L1/E7

expression) and specific mRNA content. Parallel experiments will be set up with tomato cv. „Moneymaker” or “MicroTom” (cotyledon

leaves method, Fillatti et al. 1987), carrot cv. „Nantes”(hypocotyl transformation, Thomas et al. 1989) and with pea cv. „Bohatýr”

(transformation of immature embryonic axes, Schroeder et al. 1993).

Recent success in engineering of the chloroplast genome makes us for decision to use this approach in our project, too. We are

developing our own chloroplast transformation vector, and we plan to deliver transforming DNA to chloroplasts by both classical PEG

method (Koop et al. 1996) and by biolistic technique (Sanford et al. 1993), because the specialized apparatus for particle acceleration

is now available in the IPMB.

The immunogenicity of plant produced HPV16 antigens will be tested in cooperation with the Dept. of Exptl. Virology of the Inst.

of Haematology and Blood Transfusion, Prague, using the mouse model, by determination of specific humoral, cellular and anti-tumor

immune responses in vitro and in vivo.



Contact:

Doc. RNDr. Jindrich Briza, CSc., e-mail: briza@umbr.cas.cz

Institute of Plant Molecular Biology, ASCR

Branisovska 31

370 05 Ceske Budejovice, Czech Republic

Tel.: 387 775 515

Fax: 385 310 356

16_basic_clinic_pharmacology_martinkova



Dear Colleagues,

Let us declare our interest in collaboration with you that would be possibly accepted within the frame of 6FP.

Our Department of pharmacology is a part of Faculty of Medicine, the member of Charles University in Prague, The Czech Republic.



At present, our research is focused on both

BASIC PHARMACOLOGY

 In vitro studies related to CYP450 drug metabolism

CLINICAL PHARMACOLOGY

 Identifiable endogenous products in the bronchi as biomarkers of inflammatory processes

 Pharmacokinetic guided therapy in oncology:

high-dose methotrexate in children with ALL, the population kinetics with limited sampling strategy in toxicity of busulfan

 Pharmacokinetic guided therapy of severe psoriasis with LDMTX:



You are kindly invited to see our web-sites where you can find the information of us in more details (publications):

http://www.lfhk.cuni.cz/farmakol/



Please, find enclosed some short characteristics of our contemporary program.

Moreover, let me inform you that our department has an analytical laboratory working on the level of Good Laboratory Practice.

Since 1993 we have been participating in research programmes within European Concerted Action COST B1 and COST B15

supported by European Commission.

In our Institution some methods of molecular biology are also available so that we hope to be flexible enough in order to be able to join

and develop our possible contribution to your project.



Thank you very much in advance for your kind reply.



Contact:

Professor Jiřina Martínková, M.D., Ph.D. martinkova@lfhk.cuni.cz

Head on Department of Pharmacology

Prediction of drug-drug interactions



The purpose of our in vitro experiments is to evaluate drug-drug interactions at the level of cytochrome P450 enzymes (CYPs) and

selected transport proteins (multidrug resistance protein 1 - MDR1 and multidrug resistance associated protein 2 - MRP2) within the

liver. For these purpose, we are using pooled human and rat liver microsomes, cultured rat hepatocytes and isolated perfused rat

livers (IPRL) together with the palette of analytical methods that enables functional characteristic of the assessed metabolic or

transport pathway. The following assays are used in above mentioned biological models: ethoxyresorufin O-deethylation for CYP1A2,

coumarin 7-hydroxylation for CYP2A6, tolbutamide hydroxylation for CYP2C9, S-mephenytoin 4´-hydroxylation for CYP2C19,

dextromethorphan O-demethylation for CYP2D6, chlorzoxazone 6-hydroxylation for CYP2E1, nifedipine oxidation for CYP3A4,

rhodamine 123 for MDR1, and methotrexate for MRP2. Moreover, methods of Western blot and immunohistochemistry are developed

to study changes in the expression and localization of different CYPs and transporters during pretreatment in rats.



Biomarkers of inflammatory airways diseases

Introduction.



The prevalence of bronchial asthma over the world is rising and it´s origins shift into low age groups. Recent epidemiologic

surveys based on standardized simple questionnaire reported an increase in the prevalence of asthma in schoolchildren which is

higher than 10 % mainly in industrialized societies (Barry DMJ et al.Prevalence of asthma among 12 year old children in New Zealand

and South Wales: a comparative survey. Thorax 1991,46: 405-409. Strachan DP et al. A national survey of asthma prevalence,

severity and treatment in Great Britain. Arch Dis Child 1994, 70:174-178).

Airway inflammation plays an important role in diseases such as asthma and chronic bronchitis and is considered to be a major

cause for exacerbations and persisting structural alterations of the airways. The assessment of airway inflammation is important for

investigating underlying mechanisms of airway diseases. Futhermore, assessement of airway inflammation may reveal diseased

airways not detectable by symptoms, lung function or airway hyperresponsiveness. Airway inflammation has been directly assessed

in secretions and biopsies obtained during flexible bronchoscopy, but these methods are too invasive and not appropriate for

monitoring airway inflammation repeatedly particularly in children. In the past few years, research was therefore focused on less

invasive techniques such as the analysis of induced sputum and measurement of exhaled nitric oxide.

Traditional asthma biomarkers and clinical outcome measures include lung function, airway hyperresponsiveness and

symptom scores. They are characterized by a considerable interindividual and intraindividual variability which is increasing after

beginning of anti-inflammatory treatment. Moreover, the methodology of monitoring some of the biomarkers is unreliable (self

recorded asthma symptoms, monitoring of peak expiratory flow at home using the peak-flow-meters). Futhermore, all these outcome

measures are considered indirect and insufficiently specific for airway inflammation, therefore not surprisingly, airway unflammation

derived from indirect parameters might differ from results obtained by the direct invasive methods. From a clinical point of view,

described difficulties in identifying the degree of inflammatory airway process influence rational pharmacotherapy and conducting of

clinical studies comparing different anti-inflammatory drugs.

The aim of the project is to assess the value of new asthma biomarkers in establishing the diagnosis with bronchial asthma and

monitoring the level of achieved asthma control in the course of pharmacotherapy. The project would focus on evaluation of asthma

biomarkers in exhaled breath condensate.



Methods.

The standard collection of the matearial requires condensation of exhaled air and samples for analysis have to be deep-frozen and

kept in biologically inert containers. Measurement of the very low concentrations of some substances requires very sensitive

analytical methods. The assays developed and validated in our laboratory for measurement of various biomarkers in the breath

condensate are as follows:



 Leukotriene B4 and cysteinyl leukotrienes (C4, D4 and E4) using gas chromatography with mass-spectrometry. LTs are

inflammatory mediators derived from arachidonic acid via the 5-lipooxygenase. Cysteinyl leukotriens (LTC4, LTD4 a LTE4) are

potent pro-inflammatory mediators that contributes to pathophysiology of asthma. Leikotrienes are generated by mast cells,

macrophages, neutrophils, lymphocytes, eosinophils and other cells. They are responsible for bronchoconstriction, stimulation of

mucous secretion and decrease of mucociliary clearance. They have vasodilatating properties and increase vascular permeability,

recruit eosinophils into the airways and stimulate nitric oxide (NO) synthesis. (Lewis RA, Austen KF, Soberman RJ. Leukotrienes

and other products of 5-lipoxygenase pathway: Biochemistry and relation to pathophysiology in human disease. N Eng J Med

1990;323:645-55).



 Nitrate, nitrite, nitrotyrosine, chlorotyrosine, bromotyrosine and tyrosine. Nitrosoglutathione. Inflammatory cells

(particularly eosinophils) and airway epithelium produce superoxid anions and generate a high concentration of nitrogen oxides

such as nitric oxide. NO reacts with superoxide to yield peroxynitrite, or can be trapped by thiols-containing biomolecules (cystein

and glutathione) to form S-nitrosothiols. Nitrogen intermediates, particularly peroxynitrite, can induce a number of covalent

modifications in various biomolecules, for example 3-nitrotyrosine which is detectable in breath condensate and its concentrations

are correlated with levels of NO. Concentrations of nitrate, nitrite and nitrotyrosine reflect the nitrosative and oxidative stress in the

inflammed airways. Chlorotyrosine and bromotyrosine are further products of inflammatory cells (neutrophils and eosinofils) which

invade diseased airways.

 Amylase and total protein are used to check for contamination of condensate with saliva and to assess for its dilution by

water vapours.

Table 1: Bilogical properties of proposed biomarkers- leukotrienes.

Major site(s)

Molecule Major biological activities

of synthesis

monocytes, basophils,

induces leukocyte chemotaxis and aggregation, vascular

neutrophils,

LTB4 permeability, T-cell proliferation and secretion of

eosinophils, mast cells,

gamma-interferone (INF- , and interleukins IL-1 and IL-2

epithelial cells

monocytes and

component of slow-reacting substance of

alveolar macrophages,

anaphylaxis(SRS-A), induces vasodilation, vascular

LTC4 basophils, eosinophils,

permeability and bronchoconstriction and secretion of

mast cells, epithelial

INF-

cells

monocytes and

predominant component of SRS-A, induces vasodilation,

alveolar macrophages,

LTD4 vascular permeability and bronchoconstriction and secretion

eosinophils, mast cells,

of INF-

epithelial cells

mast cells and component of SRS-A, induces vasodilation and

LTE4

basophils bronchoconstriction



Proposed major research areas of interest:



- reference ranges for biomarkers in the breath condensate in healthy subjects. Levels of various biomarkers in asthmatics and

patients with chronic obstructive pulmonary disease. Does biomarkers reflect disease activity ? Relationship to the traditional

clinical surrogate markers and outcomes.

- biomarkers in the breath condensate in the course of antiinflammatory pharmacotherapy: sensitivity to detect disease worsening

during the step-down titration of the lowest effective dose

- biomarkers in the breath condensate in asthmatics after the bronchoprovocation test with histamin.

- proposed biomarkers as primary characteristics in comparative studies of inflammatory drugs

17_drugs_Rabiskova



The research group from Department of Pharmaceutics would like to find a partners for participation on the 6FP project. Our research

should be related to areas:





Development of new in vitro and in silico tests to replace animal experimentation

Combating, cardiovascular disease, diabetes and rare diseases



Research activities of the Department of Pharmaceutics, Faculty of Pharmacy, University of Veterinary and Pharmaceutical

Sciences, Brno – CZ: deal with polymeric excipients in the technology of dosage forms with controlled release of particular drug,

especially multiple dosage forms (pellets) and matrix tablets for oral application, their technologies, equipment and influence of

process variables on quality parameters of the final product. Technologies of wet granulation, extrusion/ spheronization,

rotoagglomeration and various coating processes are used in the production of solid dosage forms. Paddle and basket dissolution

methods are used for the establishment of drug release in vitro. The released drug is determined using UV-VIS spectroscopy or

HPLC. The quality parameters of prepared drug forms are proved by the pharmacopoeia methods according to Ph.B. and Ph.Eur. III.



Contact:



Miloslava Rabišková, rabiskovam@vfu.cz

Department of Pharmaceutics

Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences

Palackého 1-3

61242 Brno

18_genomics_wheat_Dolezel



Dear colleagues,



Our Laboratory of Molecular Cytogenetics and Cytometry would like to participate in the FP6 project at area:



 Structural genomics

 Comparative genomics and population genetics



Proposed topics for 6th FP:





Structural and functional genomics of wheat

This project will aim at developing the knowledge base, tools and resources needed to decipher the function of genes and gene

products in wheat relevant to human health and to explore their interactions with each other and with their environment.



Contact:



Doc. Ing. Jaroslav Doleţel, DrSc.

Laboratory of Molecular Cytogenetics and Cytometry

Institute of Experimental Botany, Academy of Sciences of the Czech Republic

Sokolovská 6

77200 Olomouc



Tel.: 585 228 521

Fax: 585 228 523



Email: dolezel@ueb.cas.cz

Web: www.ueb.cas.cz/olomouc1

19_RNA_terapeutictool_Svoboda



The Laboratory of Predictive Oncology from the Masaryk Memorial Cancer Institute, Czech Republic, would like to participate in FP6

project at the area:



 Innovative research in post-genomics, which has high potential for application



LSH-2003- 1.2.5-1 - RNA as a human therapeutic tool





Contact person:



Miroslav Svoboda, svoboda@mou.cz

Lab. of Predictive Oncology

Dpt. of Experimental Oncology

Masaryk Memorial Cancer Institute

Zluty kopec 7

656 53 Brno

20_Detection_mammaglobin_cytokeratin_Janku



Group from Dpt. of Oncology, 1st Faculty of Medicine, Charles University in The Czech Republic would like to cooperate at the

research in area:



Detection of mammaglobin and cytokeratin 19 in axillary lymph nodes, bone marrow and peripheral blood in the

assessment of minimal residual disease in eraly breast cancer patients.



Breast cancer is the most frequent malignancy in adult women in developed countries including the Czech Republic and is the

most frequent cause of death among women malignancies. Five year survival depends on the spread of disease at the time of

diagnosis and properly chosen adjuvant therapy. In the earliest stages the 5 year survival surpasses 90%. Adjuvant treatment could

reduce the risk of distant metastatic spread and prolonges survival. In the late ninties there were performed several trials

invetigating some molecular factors (like cytokeratin 19, MUC 1 etc.) in order to assess minimal residual disease which was not

detectable by rutin histopathological exam. In several trials there were proved cleare correlations between presence of minimal

residual disease and survival also supported by multivaritaion analyses (9). The next logical step would be to implement these

knowledges to the adjuvant treatment planning (10).

Mammaglobin (hMAM) belongs to the uteroglobin gene family which is specific for adult mammary gland (1). It codes

glycoprotein and it´s mRNA is frequently detectable in primary tumors, lymph nodes (2,3), peripheral blood, distant metastases. The

gene which codes mammaglobin is located on chromosome 11q13. Various mutaions of this part of human genoma are often related

to breast neoplasia (2,4).

Both cytokeratin 19 and mammaglobin seems to be promising markers in terms of detection of minimal residual disease. While

cytokeratin appears to be highly sensitive with relative lack of specificity, mammaglobin is less sensitive (approximately 80%) but

highly specific (about 100%).

In the recent studies there was observed strong mammaglobin positivity in approximately 80% of primary breast cancers. The

level of expression correlated with neither histologic type nor grade. Overexpression of human mammaglobin was also detactable in

infiltrated axilary lymph nodes. In lymph nodes without proven tumor involvement mammaglobin was not detected (5).

In another study there were tested 14 primary breast tumors, 56 axillary lymph nodes (11 positive on histopathology) for

mammaglobin B (homologous with mammaglobin A but not identical). As a control group served 15 nodes from patients without tumor.

Mammaglobin B was detected in all 14 primary breast tumors, and in all histologically positive lymph nodes. In addition 14 out of 45

histologically negative nodes were also positive for mammaglobin, which suggested the presence of micrometastases. In the control

group there were no positive results (7).

Another trial examined 114 specimens of peripheral blood from patients with breast cancer of various stage and 68 specimens from

patients without tumor. Mammaglobin overexpression was detected in 5 out 18 of patients (28%) at the time of diagnosis of breast

carcinoma, in 3 out of 53(6%) patients without tumor and in 21 out of 43 (49%) patients with metastatic breast cancer. All specimens

from patients with no malignancy were negative. Only 2 out of 41 specimens were positive among patients with other malignacies (8).

The crucial study addressing issue of minimal residual disease (MRD) using specific monoclonal antibody against cytokeratin in

bone marrow aspirates. The patients group consisted of 552 breast cancer stage I,II,III patientes who underwent complete resection of

the tumor. As control group served 191 specimens from patients without malignacies. Cytokeratin was found only in 2 out of 191

patients with no malignancy (1%) and in 199 out of 552 specimens from patients with breast cancer (36%). The presence of occult

metastatic cells in bone marrow did not correlate with axillary lymph nodes postivity, but there was apparent correlation between

appearance of distant metastases and cancer related death. Nevertheles there was no observed any relationship to the locoregional

recurrence.



The primary objective of our trial is to evaluate mammaglobin as marker for detection of minimal residual disease in

early breast cancer patients.



The secondary objective is to asses the correlation between overexpression of mammaglobin and disease free

interval and overall survival. With results of this research we would like to contribute to better tailoring of adjuvant

treatment based on special molecular features. It is becoming more and more obviuos that we should modifiy the adjuvant

therapy according to the heterogenity of tumors using certain molecular features.



We decided to use RT PCR for the detection of mammaglobin overexpression which appeared to be the most appropriate in

previous studies. With specific primers we will measuere mRNA specific for mammaglobin.

Within 3 years period we enroll 120 patients with breast cancer who underwent complete resection of tumor. Mammaglobin will be

examined in specimens of peripheral blood, bone marrow aspirates at the time of diagnosis. In addition to these examination we will

measure mammaglobin expression in axillary lymph nodes removed during the primary surgery. Peripheral blood and bone marrow

will be examined again either after the completition of adjuvant treatment or 6 month after beginning in case of hormonotherapy with

either tamoxifen or aromatase inhibitors.

References:

1) Watson MA, Fleming TP; Mammaglobin, a mammary-specific member of the uteroglobin gene family, is overexpressed in human breast cancer; Cancer Res

1996 Feb 15;56(4):860-5

2) Watson MA, Darrow C, Zimonjic DB; Structure and transcriptional regulation of the human mammaglobin gene, a breast cancer associated member of the

uteroglobin gene family localized to chromosome 11q13; Oncogene 1998, Feb 12; 16(6): 817-24

3) Leygue E, Snell L, Dotzlaw H; Mammaglobin, a potential marker of breast cancer nodal metastasis; J Pathol 1999 Sep; 189(1):28-33

4) Becker RM, Darrow C, Zimonjic DB; Identification of mammaglobin B, a novel member of the uteroglobin gene family; Genomics 1998 Nov 15;54(1): 70-8

5) Watson MA, Dintzis S, Darrow CM; Mammaglobin expression in primary, metastatic, and occult breast cancer; Cancer Res 1999 Jul 1;59(13): 3028-31

6) Min CJ, Tafra L, Verbanac KM; Identification of superior markers for polymerase chain reaction detection of breast cancer metastases in sentinel lymph nodes;

Cancer Res 1998 Oct 15;58(20): 4581-4

7) Aihara T, Fujiwara Y, Ooka M; Mammaglobin B as a novel marker for detection of breast cancer micrometastases in axillary lymph nodes by reverse

transcription-polymerase chain reaction; Breast Cancer Res Treat 1999 Nov; 58(2): 137-40

8) Zach O, Kasparu H, Krieger O; Detection of circulating mammary carcinoma cells in the peripheral blood of breast cancer patientes via a nested reverse

transcriptase polymerase chain reaction assay for mammaglobin mRNA; J Clin Oncol 1999 Jul; 17(7): 2015

9) Braun S, Pantel K, Janni W; Cytokeratin-postivie cells in the bone marrow and survival of patients with stage I, II or III breast cancer; N Engl J Med 2000 Feb

24;342 (8): 525-33

10) Braun S, Kentenich C, Janni W; Lack of effect of adjuvant chemotherapy on the elimination of single dormant tumor cells in bone marrow of high-risk breast

cancer patients.;J Clin Oncol 2000 Jan;18(1) : 80-6





Contact:

Filip Janku, E-mail: janku.filip@vfn.cz

1st Faculty of Medicine, Charles University

Department of Oncology

U Nemocnice 2

Prague 2 128 08

Czech Republic

Phone: +420 224962219 , +420 224917830

Fax: +420 224921716

21_Xlinkedsyndrome_Janout



The Department of Preventive Medicine, Faculty of Medicine, Palacky University, Czech Republic, would like to participate in the FP6

project. They can offer large-scale, long-term experience at area:



Epidemiology of Infectious Disease

Epidemiology of Cancer

Epidemiologiy of Cardiovascular Disease



Contact:



Prof.Vladimir Janout, MD.PhD.

Professor of Epidemiology

Department of Preventive Medicine

Faculty of Medicine, Palacky University

Hnevotinska 3, 77515 OLOMOUC

Czech Republic

Phone: 00420-68-5632651

Fax: 00420-68-5632668

E-mail: janout@tunw.upol.cz

22_genomicsproteomics_Sebo



Dear Colleagues,

Our laboratory of Molecular Biology of Bacterial Pathogens from the Academy of Sciences of the Czech Republic would like to

participate at the FP6 project. For the second call we can offer our long-term experience with genomics and proteomics at the fields:





LSH-2003-1.2.4-5 New improved vaccines based on genomic and proteomic information -INTEGRATED PROJECT.

LSH-2003-1.2.4-6 Dendritic cells for novel immunotherapies - NETWORK OF EXCELLENCE.

LSH-2003-1.2.5-2 Post-genomic approaches to the study of human pathogens - NETWORK OF EXCELLENCE.

LSH-2003- 1.2.5-4 New bioassays and biosensors using post-genomic approaches for detection of harmful microbes -

STREP.



Contact person:



Peter Sebo, PhD., sebo@biomed.cas.cz

Laboratory of Molecular Biology of Bacterial Pathogens

Cell and Molecular Microbiology Division

Czech Academy of Sciences

Institute of Microbiology

Videnska 1083

142 20 Prague 4

Czech Republic

phone: (+420) 241 062 762

(+420) 296 442 762

fax: (+420) 241 062 152

(+420) 296 442 152



http://www.biomed.cas.cz/mbu/Lab125/etox11

http://www.biomed.cas.cz/mbu/Lab125

http://www.hhmi.org/grants/awards/indiv/scholars/sebo.html

23_bioinformatics_Kypr



Dear Colleagues,



Our Laboratory of DNA Biophysics and Genome Bioinformatics, Institute of Biophysics, Academy of Sciences of the Czech Republic would

like to participate in the FP6 project:



LSH-2003-1.1.4-1 Bioinformatics grid for European genomics research – NoE



We can offer long-term eperience at this field as you can see at our web-page http://salsero.ibp.cz/



Contact person:



JAROSLAV KYPR

(Head of Laboratory)

Phone: (420) 541517198

Fax: (420) 541240497

E-mail: kypr@ibp.cz

http://salsero.ibp.cz/

24_pharmacology_Laznickova



Dear Colleagues,



Dpt. of Biophysics and Physical Chemistry and Dpt. of Pharmacology and Toxicology, Faculty of Phrmacy in Hradec Kralove, Charles

University, Czech Republic, would like to participate in the FP6 project at area:



b) Application of knowledge and technologies in the field of genomics and biotechnology for health

Development of new diagnostics



The aim of our projects is the research and development of new potential diagnostics and therapeutics on the basis of radioactively

labeled receptor-specific peptides. These new structures are parts of the sequences of larger biologically active peptides, which

maintain affinity to receptors of the original peptide but with better pharmacokinetic properties.

An important part of the research is also such modification of the peptidic structure which makes it possible to label the compound with

suitable radiochemical purity without losing of affinity of the structure to the adequate receptor. In the out-coming compounds which

have to posses suitable radiochemical purity, besides radio-receptor analysis and verification of internalization of the structures, the

biodistribution profiles and pharmaciokinetics in selected intact animals are studied together with the determination of the elimination

mechanisms on the perfused rat liver and kidney in situ.



Contact person:



Alice Laznickova

Charles University

Faculty of Pharmacy in Hradec Kralove

Heyrovskeho 1203

500 05 Hradec Kralove

tel: 495 067 478

fax: 495 518 002

E-mail: laznicko@faf.cuni.cz

25_PROJECT_Kunes



Dear Colleagues,

Our Department of Experimental Hypertension, Institute of Physiology , Academy of Sciences of the Czech Republic, Prague,

Czech Republic would like to find a partners to participate at the 2 nd call project:



LSH-2003-2.1.0 Eicosanoids and nitric oxide: mediators of cardiovascular, cerebral and neoplastic diseases - INTEGRATED

PROJECT



Contact person:

Kuneš Jaroslav (head of Dpt.) kunes@biomed.cas.cz

Dpt. of Experimental Hypertension, Institute of Physiology AS CR

Address: Videnska 1083

14220 Prague 4

Czech Republic

Phone +420-296442420

www http://www.biomed.cas.cz/fgu/





Possible contribution



Nitric oxide formation and inactivation in salt hypertension:

the role of inducible and constitutive NO synthase



The long-term control of blood pressure (BP) is based upon the balance of vasoactive systems which control not only the tone

of resistance vessels but also affect the growth of vascular smooth muscle cells (VSMC) and/or connective tissue. Sympathetic

nervous system (SNS) and nitric oxide (NO) represent two major vasoactive systems which are well balanced in normotensive beings.

Our recent studies [1-3] indicated that experimental hypertension in the rat is characterized by a considerable dysbalance of the two

systems in favor of augmented SNS. In last years our attention was focused to salt-dependent hypertension in Dahl rats in which we

have disclosed a major dysbalance between increased sympathetic vasoconstriction and attenuated NO-dependent vasodilation [1].

Increased sympathetic tone in Dahl salt hypertensive rats is due to CNS-mediated SNS activation involving abnormal action of brain

renin-angiotensin system[4,5], whereas reduction of NO-dependent vasodilation is caused by lower NO bioavailability [1,6]. Our data

indicate that diminished NO bioavailability does not result from decreased NO synthesis but it is a consequence of NO interaction with

superoxide anions the production of which is enhanced in salt hypertensive Dahl rats [1]. Both SNS hyperactivity and impaired

NO-dependent vasodilation were significantly associated with high BP in salt-loaded F2 hybrids derived from salt-sensitive (SS/Jr) and

salt-resistant (SR/Jr) Dahl rats [3].

It is well known that chronic excess salt intake elicits more severe hypertension in young than in adult rats [7,8]. Salt

hypertension induced in the two age groups is characterized by the difference in the spectrum of activate pressor systems and the

degree of alterations in NO bioavailability. Our previous studies disclosed that SNS and endogenous digoxin-like factor are

augmented in young animals with salt hypertension, whereas reserve pressor systems (such as vasopressin, angiotensin II or

endothelin-1) are enhanced in the adult hypertensive rats [9-11]. More pronounced SNS activity was also demonstrated in young salt

hypertensive Dahl rats in which NO contribution to BP regulation was substantially reduced compared to adult salt hypertensive

animals. Using acute tempol administration we have demonstrated greater superoxide production (and resulting decrease of NO

bioavailability) in young young than in young salt hypertensive Dahl rats [3]. The increased production of oxygen free radicals was

reported not only in spontaneous hypertension [12,13] but also in salt hypertensive Dahl rats [14-16]. Such a dysbalance between NO

and O2- production appears to be a common feature of experimental hypertensive models as well as of human hypertension [17-19].

In addition, NO and superoxide react to the powerful oxidant peroxynitrite, which can form hydroxyl radicals and nitrate protein

tyrosine residues resulting in impairment of signaling pathways [20] and vascular damage [17].

Our research effort will be focused to:



a) the evaluation of endothelial function, NO production and its hemodynamic action in salt hypertension of Dahl rats,

b) the study the interaction of NO and O2- in several models of experimental hypertension with different activity of NO

synthase (spontaneous hypertension, salt hypertension and NO-deficient hypertension), and

c) the elucidation of the effect of antioxidant therapy on blood pressure and NO synthase activity and expression in salt

hypertension.



ad a) A special attention will therefore be paid to particular NO synthase isoforms namely to inducible NOS (iNOS, NOS II) because

several polymorphisms in NOS2 gene were reported in SS/Jr Dahl rats [21-23]. iNOS inhibition accelerates the development of salt

hypertension in Dahl rats [24-26]. Progressive reduction of constitutive endothelial NOS (eNOS) during hypertension development

might be compensated by increased iNOS expression. Hemodynamic effects of NO synthesized by eNOS or iNOS should be

evaluated in normotensive and hypertensive rats because NO formed in non-endothelial cells or endothelium need not have the same

spatial relationship to target VSMC of resistance vessels (analogous to different heart regulation by NO formed by eNOS and nNOS).

ad b) Concerning NO inactivation in salt hypertensive animals, our effort will be focused on the interaction of NO with superoxide

anions and peroxynitrate formation. The production of oxygen free radicals and the capacity of antioxidant defense will be measured

in aortic, cardiac and renal tissue as a function of genotype, salt intake, age and hypertension stage.

ad c) The influence of diverse chronic antioxidant therapy (applied either in prepuberty or in adulthood) on blood pressure, vasoactive

balance and NO bioavailability will be examined in salt-loaded Dahl rats.



Particular Contributions Expected



1. to consider the role of inducible NO synthase in the pathogenesis of salt hypertension (from gene abnormalities up to

spatial confinement of NO formed)

2. to evaluate the contribution of NO/O2- dysbalance on the balance of vasoconstrictor and vasodilator systems during the

development of salt

3. to study the capability of NO and O2- to generate peroxynitrites and to elucidate the role of endothelium in the production

of these reactive species

4. to elucidate the effect of antioxidant therapy on blood pressure and NO synthase activity and expression in various forms

of hypertension



References

1. Zicha J, Dobesová Z, Kunes J. Relative deficiency of nitric oxide-dependent vasodilation in salt-hypertensive Dahl rats: the possible role of superoxide anions.

J Hypertens 2001; 19: 247-254.

2. Kunes J, Dobesová Z, Zicha J. Altered balance of main vasopressor and vasodepressor systems in rats with genetic hypertension and hypertriglyceridaemia.

Clin Sci 2002; 102: 269-277.

3. Dobesová Z, Kunes J, Zicha J. The altered balance between sympathetic nervous system and nitric oxide in salt hypertensive Dahl rats: ontogenetic and F2

hybrid studies. J Hypertens 2002; 20: 945-955.

4. Huang BS, Leenen FH. Both brain angiotensin II and "ouabain" contribute to sympathoexcitation and hypertension in Dahl S rats on high salt intake.

Hypertension 1998; 32: 1028-1033.

5. Leenen FH, Yuan B. Prevention of hypertension by irbesartan in Dahl S rats relates to central angiotensin II type 1 receptor blockade. Hypertension 2001; 37:

981-984.

6. Chen PY, Sanders PW. L-arginine abrogates salt-sensitive hypertension in Dahl/Rapp rats. J Clin Invest 1991; 88: 1559-1567.

7. Zicha J, Kunes J, Jelínek J. Experimental hypertension in young and adult animals. Hypertension 1986; 8: 1096-1104.

8. Zicha J, Kunes J. Ontogenetic aspects of hypertension development: analysis in the rat. Physiol Rev 1999; 79: 1227-1282.

9. Kunes J, Stolba P, Pohlová I, Jelínek J, Zicha J. The importance of endogenous digoxin-like factors in rats with various forms of experimental hypertension.

Clin Exp Hypertens A 1985; 7: 707-720.

10. Zicha J, Kunes J, Lébl M, Pohlová I, Jelínek J. Haemodynamics and the participation of pressor systems in young and adult rats with age-dependent

DOCA-salt hypertension. Physiol Bohemoslov 1987; 36: 89-92.

11. Zicha J, Kunes J, Lébl M, Pohlová I, Slaninová J, Jelínek J. Antidiuretic and pressor actions of vasopressin in age-dependent DOCA-salt hypertension. Am J

Physiol 1989; 256: R138-R145.

12. Grunfeld S, Hamilton CA, Mesaros S, McClain SW, Dominiczak AF, Bohr DF, Malinski T. Role of superoxide in the depressed nitric oxide production by the

endothelium of genetically hypertensive rats. Hypertension 1995; 26: 854-857.

13. Schnackenberg CG, Welch WJ, Wilcox CS. Normalization of blood pressure and renal vascular resistance in SHR with a membrane-permeable superoxide

dismutase mimetic: role of nitric oxide. Hypertension 1998; 32: 59-64.

14. Swei A, Lacy F, DeLano FA, Parks DA, Schmid-Schönbein GW. A mechanism of oxygen free radical production in the Dahl hypertensive rat. Microcirculation

1999; 6: 179-187.

15. Trolliet MR, Rudd MA, Loscalzo J. Oxidative stress and renal dysfunction in salt-sensitive hypertension. Kidney Blood Press Res 2001; 24: 116-123.

16. Meng S, Roberts LJ, Cason GW, Curry TS, Manning RDJ. Superoxide dismutase and oxidative stress in Dahl salt-sensitive and -resistant rats. Am J Physiol

2002; 283: R732-R738.

17. Berry C, Brosnan MJ, Fennell J, Hamilton CA, Dominiczak AF. Oxidative stress and vascular damage in hypertension. Hypertension 2001; 10: 247-255.

18. Zalba G, San Jose G, Moreno MU, Fortuno MA, Fortuno A, Beaumont FJ, Diez J. Oxidative stress in arterial hypertension: role of NAD(P)H oxidase.

Hypertension 2001; 38: 1395-1399.

19. Schnackenberg CG. Oxygen radicals in cardiovascular-renal disease. Curr Opin Pharmacol 2002; 2: 121-125.

20. Bouloumie A, Bauersachs J, Linz W, Scholkens BA, Wiemer G, Fleming I, Busse R. Endothelial dysfunction coincides with an enhanced nitric oxide synthase

expression and superoxide anion production. Hypertension 1997; 30: 934-941.

21. Deng AY, Rapp JP. Locus for the inducible, but not a constitutive, nitric oxide synthase cosegregates with blood pressure in the Dahl salt-sensitive rat. J Clin

Invest 1995; 95: 2170-2177.

22. Chen PY, Gladish RD, Sanders PW. Vascular smooth muscle nitric oxide synthase anomalies in Dahl/Rapp salt-sensitive rats. Hypertension 1998; 31:

918-924.

23. Deng AY. Is the nitric oxide system involved in genetic hypertension in Dahl rats? Kidney Int 1998; 53: 1501-1511.

24. Chen PY, Sanders PW. Role of nitric oxide synthesis in salt-sensitive hypertension in Dahl/Rapp rats. Hypertension 1993; 22: 812-818.

25. Rudd MA, Trolliet M, Hope S, Scribner AW, Daumerie G, Toolan G, et al. Salt-induced hypertension in Dahl salt-resistant and salt- sensitive rats with NOS II

inhibition. Am J Physiol 1999; 277: H732-H739.

26. Tan DY, Meng S, Cason GW, Manning RD. Mechanisms of salt-sensitive hypertension: role of inducible nitric oxide synthase. Am J Physiol

26_viralrepl_genetherapy_Ruml



Dear Colleagues,

Our group (consisting of Department of Biochemistry and Microbiology ICT Prague, Department of Protein Biochemistry of ASCR

and Center for Integrated Genomics) would like to find a partners for a FP6 project at the topics:



LSH-2003-1.1.2-1: Comparative structural biology of viral replication – INTEGRATED PROJECT

LSH-2003-1.2.4-1: Improved gene delivery systems for the therapy of severe acquired diseases – INTEGRATED PROJECT.



Contact persons:



Tomáš Ruml Tomas.Ruml@vscht.cz

Department of Biochemistry and Microbiology and Center for Integrated Genomics

Institute of Chemical Technology,

166 28, Prague 6,

Czech Republic.

www: http://biomikro.vscht.cz/indexen.html, http://cig.img.cas.cz/

phone: +420 224 353 022



Iva Pichová iva.pichova@uochb.cas.cz

Institute of Organic Chemistry and Biochemistry, Department of Protein Biochemistry,

Academy of Sciences of the Czech Republic,

Flemingovo nam.2,

166 10, Prague 6,

Czech Republic

www: http://www.uochb.cas.cz/

phone: +420 220 183 519



Our groups are focused on the research aimed at the mechanism of retroviral integration, capsid assembly and its maturation. We

have developed the approaches for the high level bacterial production and purification of precursor polyproteins. This allowed the first

demonstration of in vitro assembly of immature capsids of Mason-Pfizer monkey virus, which induces an AIDS like syndrome in

non-human primates and represents an attractive experimental model (Klikova et al., 1995, Rumlova et al., 2000, Nermut et al.,

2002), which now allows the dissection of mutant phenotypes and assay of potential peptide inhibitors of assembly that would not be

possible in cell-based systems.

Structural studies of M-PMV matrix protein (MA) that was expressed, isotopically labeled, and purified in our laboratory (Conte et

al, 1997) as well as analyses of some of mutants showing relevant phenotypic features in assembly, transport, membrane association

of capsids enabled to select functionally important mutations. Some of MA mutants showing relevant phenotypic features in

assembly, transport, membrane association of capsids have been expressed in E. coli (labeled) and purified for similar structural

studies that are currently under way.

Electron-microscopic studies of Gag deletion mutants expressed in E. coli revealed minimal domains required for capsid

assembly. The importance of putative domains required for the assembly are being currently analyzed in order to design and test a

peptide inhibitors of the assembly of immature capsid.

The ability to in vitro assemble capsids from purified proteins that bind nucleic acids will be employed for construction of model

particles in order to investigate whether such system could be used for construction of vectors for gene therapy. The fact that the in

vitro prepared capsids tolerate nonspecific N-terminal extensions that are exposed on the capsid surface will be used to provide

putative vectors with ligands that might interact with cell receptors of target cells.

The study of the role of truncated protease species in the viral replication cycle has been initiated by the finding that M-PMV

protease is autocatalytically truncated in the retrovirus life cycle (Pichova et al., 1998). We have also found specific processing of CA

protein with retroviral protease occurring probably in the early steps of the life cycle (Rumlova et al., 2003). The next step is to design

and introduce mutations within the processing sites in the protease that significantly decelerate the self-processing of protease and

analysis of the mutant phenotypes in mammalian cells.

We have recently solved a high resolution NMR structure of fully folded monomer of Cys7/Ala, Asp26/Asn, Cys106/Ala mutant of

the shortest form of M-PMV protease (PR). Coordinates of the 10 structures of the PRD26N/C7A/C106A with the lowest target functions

together with the associated restraint list have been deposited in the Protein Data Bank (accession code 1NSO). For further studies

series of protease mutants will be prepared and structural, biochemical, and infectivity analyses will be focused on the role of the

reversible oxidative modification in the regulation of maturation of M-PMV assembled immature capsids and on the investigation of the

mechanism of protease liberation from the precursor.

The study of integration will be aimed at characterization of M-PMV pre-integration complex, its composition, the interaction of

nucleic acids with viral and host cell proteins that are integral members of the pre-integration complex. Specific inhibitors of integrases

synthesized in our Institute (Snášel et al., 2001) will be used for structural studies of catalytic domain of M-PMV integrase.



Conte M.R., Kliková M., Hunter E., Ruml T., Matthews S.: The three-dimensional structure of the matrix protein from the type D retrovirus, the Mason-Pfizer

Monkey virus, and implications for the morphology of retroviral assembly EMBO J. 16, 5819-5826 (1997)

Kliková, M., Rhee, S.S., Hunter, E., Ruml, T.: Efficient in vivo and in vitro assembly of retroviral capsids from gag precursor proteins expressed in bacteria,

J.Virol. 69, 1093-1098 (1995)

Nermut, M.V., Bron, P., Thomas, D., Rumlová, M., Ruml, T., Hunter, E.: Molecular organisation of Mason-Pfizer monkey virus capsids assembled from Gag

polyprotein in E. coli. J. Virol. 76, 4321-4330 (2002).

Pichová, I., Zábranský, A., Košťálová, I., Hrušková, O., Andreanský, M., Hunter, E., and Ruml, T. Analysis of autoprocessing of Mason Pfizer monkey virus

proteinase in vitro: three active forms of proteinase. Structure and Function of Aspartic Proteinases: Adv. Exp. Med. Biol. 436, 105-108 (1998)

Rumlova, M., Ruml, T., Pohl J., Pichova, I.: Specific in vitro cleavage of Mason–Pfizer monkey virus capsid protein: evidence for a potential role of retroviral

protease in early stages of infection. Virology 310, 310-318 (2003)

Rumlova-Klikova, M., Hunter, E., Nermut, M., Pichova, I., Ruml, T.: Analysis of Mason Pfizer monkey virus Gag domains required for capsid assembly in

bacteria; role of the N-terminal proline residue of CA in directing the particle shape. J. Virol. 74, 8452-8459 (2000)

Snasel, J., Rejman, D., Liboska, R., Tocik, Z., Ruml, T., Rosenberg, I., Pichova I.: Inhibition of HIV-1 integrase by modified oligonucleotides derived from U5´

LTR. Eur. J. Biochem. 268, 980-986 (2001)