Annual Report 2008

ISSN 1334-854X design skala

Ruđer Bošković Institute Annual Report 2008

Ruđer Bošković Institute

Annual Report 2008

Zagreb, 2009. Editorial Board: Editor: Nela Pivac

Members: Stjepko Fazinić Kata Majerski Bogomil Obelić Karolj Skala David Smith Jadranka Stojanovski Mladen Žinić

Technical Support: Photographer: Josip Uhrl Graphic Design and Technical Processing: Faculty of Graphic Arts, University of Zagreb Printing: PRINTERA GRUPA d.o.o. Print run of 800 copies

Web edition: http://www.irb.hr/en/geninfo/reports/

Address: Ruđer Bošković Institute Bijenička cesta 54, P.O.Box 180 HR-10002 Zagreb, Croatia

Contact: URL: http://www.irb.hr e-mail: [email protected] tel: +385 1 45 61 111 fax: +385 1 46 80 084

Introduction ...... 1

Theoretical Physics Division ...... 13

Division of Experimental Physics ...... 17

Division of Materials Physics ...... 25

Division of Laser and Atomic Research and Development ...... 31

Division of Electronics ...... 35

Division of Physical Chemistry ...... 39

Division of Organic Chemistry and Biochemistry ...... 45

Division of Materials Chemistry ...... 55

Division of Molecular Biology ...... 61

Division of Molecular Medicine ...... 69

Division of Marine and Environmental Research ...... 79

Centre for Marine Research ...... 87

Centre for Informatics and Computing ...... 95

Centre for Nuclear Magnetic Resonance ...... 101

Library ...... 105

Rudjer Innovations Ltd...... 111 Dear reader,

Welcome to the 2008 Annual Report of the Ruđer Bošković Insti- Zagreb and Šibenik. These agreements are designed to further tute. The report is designed to provide an overview of the most strengthen our contribution to education in Croatia, particularly in important activities and achievements of Institute’s Laboratories regional centres. We also made several advancements towards and Divisions during the past year. Due to our position as the consolidating a sustainable infrastructure designed to fully utilize largest public research institute in natural sciences, biomedicine, the Institute’s intellectual property. Much progress was achieved marine research and environmental sciences in the country, through the ongoing expansion of Rudjer Innovations Ltd., a funded to a large extent by the Croatian Ministry of Sciences, Ed- company established and wholly owned by the Institute, which ucation and Sports, our mission is dependent upon the particular has been charged with handling the protection of intellectual needs of our society. Specifically, this involves exemplary per- property and some commercial aspects of the Institute’s work. formance on three principle fronts: the production of high-quality fundamental research, strong involvement in higher education, While a strong involvement in domestic affairs is an important and the provision of a leading contribution to the growth of the part of our function, it is clear that the current academic climate national economy through production of new technologies based also calls for an increased external focus. Our scientists are on our intellectual property and expertise. acutely aware of this and have an impressive rate of success in terms of gaining international projects. Naturally, becoming an Based on our desire to continue to fulfil our mission as to the integral part of the European Research Area is one of our key best of our ability, 2008 saw us lay the foundations for a series of strategic goals, and our ability to realize it is reflected by our suc- positive changes in the future. This included the drafting of a new cess in the 6th and increasing involvement in the 7th Framework statute governing the future operation and structure of the Insti- Programmes. Apart from this, our scientists have also enjoyed tute. This statute has been approved by both the Scientific Coun- noteworthy successes by obtaining projects from other external cil and the Board of Governors of the Institute and is currently sources such as IAEA, NATO, COST, NIH, as well as numerous being considered at the ministerial level. We also undertook a bilateral projects with foreign scientific institutions. systematic evaluation of all 86 of the Institute’s laboratories and their leaders. The successful completion of this evaluation by the In closing, I have the pleasant duty to thank the RBI scientific and end of the year places us in an ideal position to enter a new administrative staff for their honest efforts and enthusiasm as phase of operation at the Institute, fully aware of our strengths, well as their many excellent achievements throughout 2008. To weaknesses, opportunities and threats. you the readers of this 2008 Annual report I would like to express our sincere thanks for your interest and I would like to invite you Despite the preparations for potential reorganization, we con- to send us your opinions, suggestions for improvement and, by tinued to achieve visible results on all three of the principle all means, proposals for future collaboration. fronts mentioned above. Striving for excellence in fundamental research continued strongly during 2008 and the most significant results achieved throughout the year are described in the pages of this report. In addition to the substantial ongoing provision of undergraduate and graduate courses by our scientists at Higher Education Institutions all across the country, 2008 saw Prof. Dr. Mladen Žinić us sign additional agreements of cooperation with Institutions in Director General Introduction

In 2008, the Ruđer Bošković Institute (RBI) Council in Croatia, and Rosana Besednik, continued to build on its ever-expanding and the Arts, Science and Society Manager of highly important base of international rela- the same organization. We also received two tionships and collaborations. Almost 100 for- visits from dignitaries of the Slovak Republic: eign scientists delivered lectures ranging in in April, the Ambassador of the Slovak Re- subject from black holes to river sediments. public to Croatia, His Excellency, Jan Banas, With each and every lecture came the op- and in September, Mr. Dušan Čaplovič, Dep- portunity to strengthen existing ties or open uty Prime Minister of the Government of the up new avenues of collaboration between Slovak Republic for Knowledge-Based So- RBI scientists and our colleagues in the in- ciety, European Affairs, Human Rights and ternational community. While all lectures Minorities. A delegation from the Indonesian were important and integral parts of this en- Embassy in Zagreb, including His Excellen- deavour, special mention is warranted by the cy Mangasi Sihombing, the Indonesian Am- visits of members of our International Scien- bassador to Croatia, was hosted at the RBI tific Board (ISB). Namely, in May, we were in April. The month of June saw the visit of a fortunate enough to host Professor Egon Japanese delegation, including representa- Matijević, from Clarkson University in New tives from the Ministry of Education, Culture, York, when he delivered a fascinating semi- Sport, Science and Technology (MEXT), nar about colloid aspects of chemical me- the Japan Science and Technology Agency chanical planarization. Some months later, (JST), the Japan Society for the Promotion in September, we were honoured to receive of Science (JSPS), and the Japanese Em- Professor Roberto Peccei, who engaged us bassy in Zagreb. This visit was followed, in with his lecture on matter-antimatter asym- September, by a delegation comprised of metry in the universe and an arrow for time. representatives of various Japanese compa- The year of 2008 saw a large number of nies involved in the nuclear energy sector, official delegations visit the Institute. In Janu- including Mr. Toshikazu Hosoda, the presi- ary, we received His Excellency Mohammad dent of CHIYODA TECHNOL, with whom the H. Fadaifard, the Iranian Ambassador to RBI has enjoyed a productive collaboration Croatia, for discussions on possible collabo- for a number of years now. ration in fundamental research. In April, as In April, we received visits from the Ger- RBI Annual Report 2008. part of an information day on the European man Federal President, Mr Horst Köhler Commission, the RBI hosted Doctor Roland and Dr. Volker Wittwer, the acting director of Schenkel, Director-General of the European the Fraunhofer Institute for Solar Energy in Commission’s Joint Research Centre. In the Freiburg. Following these visits, a letter of in- same month, we were visited by delegations tent concerning collaboration in German and from the British Embassy and the British Croatian industrial and research projects in Council. In particular, we were pleased to the area of thin-film solar cells envisaged to host His Excellency Sir John Ramsden, the involve the RBI, the Fraunhofer Institute for British Ambassador to Croatia, Anamarija Solar Energy, INTERPANE Glas Industrie Jandrasek, from UK Trade and Investment, AG Lauenförde, and the Croatian company Adrian Chadwick, the Director of the British Lipik Glas, was signed.

1 In January, Christopher John Hull, Sec- for educational and scientific cooperation with retary General of the European Association the Australian Research Council’s Centre of of Research and Technology Organisations Excellence for Free Radical Chemistry and (EARTO), visited the RBI. Subsequently, Biochemistry. In the area of higher education, the Institute became a member of EARTO agreements were reached with the Agricul- in 2008. Accordingly, Croatia became a full tural Faculty in Zagreb and the Polytechnic member of EARTO, while the representa- College in Šibenik, while an agreement of tive of RBI, Neven Žarkovic, became a business cooperation was signed with the member of the EARTO executive board. town of Otočac. Finally, a joint agreement on The participation of RBI scientists in Eu- collaboration was signed by RBI, Ruđer Inno- ropean scientific networks remained one of vations Ltd. and TECNA S.R.L., a diagnostics the Institute’s top priorities in 2008. For ex- firm situated in Trieste, Italy. ample, in March, we staged an IAEA work- The RBI’s biannual Open Days were held shop entitled: “Regional Training Course on in late April of 2008. Thanks to the dedicat- How to Write Competitive Research Pro- ed effort of the organizing committee, these posals for Various Funding Programmes”. days were a great success in displaying the In July, we sent a delegation from RBI to work of the Institute to the general public. Brussels to present the Institute at a Work- Approximately 4200 people passed through shop on Croatian Research and Techno- the gates over the 3 days of festivities. This logical Development hosted by the Croa- included 7 different diplomatic delegations, tian Chamber of Economy. In addition to the Mayor of Zagreb and his entourage, vari- the 13 FP6 projects that are still ongoing at ous commercial representatives, members the Institute, 5 FP7 contracts were signed of the media, students and professors from in 2008. Numerous other proposals have 5 different university faculties and students been submitted and are awaiting evalua- from 76 schools originating from all over the tion. RBI scientists also took an active role country. We received very positive feedback in Management Committees of COST ac- from all sides and resounding encourage- tions. Krešimir Pavelić, head of the RBI’s ment to continue with this initiative into the Division of Molecular Medicine, was ap- future. Planning is already underway for the pointed in November as a Secretary Gener- 2010 event. al of the European Molecular Biology Con- ference (EMBC) and ex officio member of OVERVIEW the EMBO Council. Up until November, he was vice-president of the EMBC. Krešimir The RBI is the largest Croatian research cen- Pavelić is also member of the EMBC Strate- tre for basic sciences, participating also in sci- gic Working Party, Member of the Standing ence applications and higher education. The Committee, European Medical Research multidisciplinary character of the Institute is Council. Tarzan Legović, head of the Divi- reflected through the different research fields sion of Marine and Environmental Research in physics, chemistry, oceanography (includ- remains the Secretary General of the Inter- ing marine and environmental research and national Society for Ecological Modelling. geosciences), biology, biomedicine, com- The RBI signed several Memoranda of Un- puter science and electronics/engineering. derstanding in 2008. For example, a contract With an academic staff of 530, including 375 was signed with the Department of Public researchers and 155 Ph.D. students, the RBI Health “Andrija Štampar” concerning scientif- collaborates worldwide with many research

RBI Annual Report 2008. Annual Report 2008. RBI ic and technical cooperation in relation to joint institutions and universities. projects in the areas of public health and ecol- The RBI consists of eleven divisions, ogy. In addition, we also signed an agreement three centres, a library, as well as sections

2 for maintenance, technical services and ad- International Scientific Board. Their organi- ministration. The main bodies of the Institute zational integration with the remainder of the are the Board of Governors and the Scientific Institute is displayed below (Figure 1). Council, with an important role played by the RBI Annual Report 2008.

Figure 1. The organizational structure of the RBI.

3 • Rudolf Zechner, Institute for Molecular ORGANIZATION OF THE Biosciences, Graz, Austria INSTITUTE • Farooq Azam, University of California, San Diego CA, USA Director: Mladen Žinić • Walter Giger, Swiss Federal Institute Head of the Scientific Council: Neven Bilić for Aquatic Sciences and Technology, Chairman of the Board of Governors: Slavko Dübendorf/Zürich, Switzerland Krajcar • Thomas C. Malone, OceanUS Office for Integrated and Sustained Ocean Obser- International Scientific Board. vations, Arlington, VA, USA • Werner E.G. Müller, Johannes Guten- • Jean-Marie Lehn, Laboratoire de Chimie berg Universität, Mainz, Germany Supramoléculaire, ISIS/ULP, France • Nadia Pinardi, University of Bologna, • Harold Kroto, University of Sussex, UK Ravenna, Italy • Egon Matijević, Clarkson University, NY, USA • Helmut Schwarz, Technische Universität ACTIVITIES Berlin, Germany • Fritz Vögtle, Universität Bonn, Germany • Robert Blinc, Jožef Štefan Institute, Lju- Fundamental research bljana, Slovenia • Jonathan R. Ellis, CERN, Switzerland The total number of research articles pub- • Anthony R. Peaker, University of Man- lished by RBI scientists in 2008 was 446. chester, UK Amongst these, 357 were published in jour- • Bogdan Povh, MPI für Kernphysik, Hei- nals cited by Current Contents, the major- delberg, Germany ity of which were published in high ranking • Roberto D. Peccei, UCLA, Los Angeles, international Journals. Scientists from the CA, USA Division of Molecular Medicine authored a • Fernando Azorin, Institute of Molecular monograph on Peripheral Biological Markers Biology of Barcelona, Spain in Alcoholism, which was published by Nova • Bernd Kaina, Institut für Toxikologie, Science Publishers in New York, USA. RBI Mainz, Germany scientists also participated in the editorial • Werner E. G. Müller, Johannes Guten- process of a further 6 books, 18 book chap- berg Universität, Mainz, Germany ters and 2 collections of lecture notes con- • Miroslav Radman, Université René Des- cerning dating techniques. cartes-Paris V, France The details of the many important discov- • Jürgen Soll, Ludwig-Maximilians-Univer- eries made by RBI scientists in 2008 are to sität München, Germany be found in the subsequent sections of this • Vito Turk, Jožef Štefan Institute, Ljublja- report. Nevertheless, we present here a small na, Slovenia selection of highlights in order to convey a • Joseph Schlessinger, Yale University general impression of the kind of research School of Medicine, CT, USA carried out at the Institute. One breakthrough • Hans Joachim Seitz, Universität Ham- study, involving scientists from the Divisions burg, Germany of Molecular Biology and Molecular Medi- • Davor Solter, MPI für Immunbiologie, cine, was published in the highly cited journal,

RBI Annual Report 2008. Annual Report 2008. RBI Freiburg, Germany Blood. The research involved gene expres- • Peter J. Stambrook, University of Cincin- sion analysis of developmentally important nati Medical Centre, OH, USA transcription factors from the Ikaros family in

4 lymphocytes from patients with haematologi- pansion of the spectrum of projects offered cal malignancies, lymphoma, and focused on by the “Unity Through Knowledge Fund”, the differences in the distribution of their mes- recently introduced by the Croatian Ministry senger RNA (mRNA). Importantly, the results of Sciences, Education and Sports. In addi- show for the first time that the Aiolos mRNA is tion to the single project contracted from this overexpressed in primary lymphoma tissues source in 2007, three new contracts were of the non-Hodgkin lymphoma type. On a signed in 2008 and more funding is expected somewhat different front, scientists working in in this vein in 2009. Similarly, collaborative the Division of Physical Chemistry used mo- projects with the City of Zagreb were offered lecular modelling techniques to study aspects for the first time in 2008. One such project of the mechanism of Auxin Binding Protein 1 has been signed while a further 15 applica- (ABP1), which is a key component of the hor- tions are being considered. monal regulation of plants. Simulations of the An international consortium, including the hormone egress from ABP1 revealed three RBI, was granted a TEMPUS project in 2008. main routes by which an auxin molecule can In addition to the RBI, the project, entitled enter or leave the binding site and the signifi- “Opening University towards Society: Linking cance of these different pathways was related Education – Research – Innovation”, involves to the mechanism of action. An illustration de- 6 Croatian Universities, 6 Foreign Universi- scribing these results appeared on the front ties, 2 Government Ministries, the City of Za- cover of issue 1 of volume 94 of the Biophysi- greb, and 4 additional organizations. cal Journal. On the other end of the spectrum, scientists working in the Division of Ex- Organization of international perimental Physics actively participated in the conferences Crystal Ball collaboration, a new experimental program at the Mainz Microtron facility in As in previous years, the RBI continued Germany. The collaboration is devoted to ex- to support the organization of numerous in- periments using energy-tagged photons and ternational and domestic conferences. For among its major goals are the measurements example, the thirteenth biennial European X- of exotic phenomena such as the anomalous ray Spectrometry Conference was held from magnetic moment of the Delta resonance, the 16th to 20th June 2008 in Cavtat. Organized mass of the eta-meson and double pion pro- by RBI and co-chaired by Milko Jakšić and duction at threshold. In 2008, a paper describ- Stjepko Fazinić, the conference was attend- ing Incoherent Neutral Pion Photoproduction ed by 280 scientists from 41 countries and 22 on Carbon 12, co-authored by RBI scientists, industrial exhibitors. Selected papers were appeared in Physical Review Letters, which reviewed with regular procedure for publi- is one of the most respected and widely read cation in the X-Ray Spectrometry journal. journals in Physics. Similarly, the 23rd European Congress on RBI Annual Report 2008. Molecular Spectroscopy (EUCMOS-2008) Projects was held in Opatija from the 31st of August to the 5th of September, 2008. Co-chaired The RBI has 136 projects in basic re- by Svetozar Musić and Krešimir Furić, the search, which are funded by the Ministry of conference was great success with selected Sciences, Education and Sports. In addition, contributions to appear in a special issue of the Institute is involved with 41 international the Journal of Molecular Structure. In May projects (including: 5 FP7, 13 FP6, 6 IAEA, 5 2008, the Institute jointly with the University COST, 1 NIH, 3 NATO and 2 INTERREG), as of Dubrovnik, hosted for the first time the well as 67 applied and technological projects Annual Reporting Conference of the COST and 4 HITRA projects. This year saw the ex- (European Cooperation in scientific and

5 Technical Research) Domain Committee for and International FameLab 2008 awards, or- Chemistry, Molecular Sciences and Technol- ganized by the Festival of Science and the ogies. In November 2008, the RBI organized British council for the best scientific presen- the conference “Workshop on New Materi- tation. David Smith was the 2008 recipient als in Industry and Medicine: RTD Potential of the Leopold Ružička award for young sci- for Collaborative Projects”. The conference entists of the Croatian Chemical Society. Ina involved representatives of the partner in- Nemet was awarded the Juvenile Diabetes stitutes Jozef Stefan Institute from Slovenia Research Foundation Postdoctoral Fellow- and Joanneum Research Institute from Aus- ship Award (2008-2010). Ana Šarić won the tria and was organized within the scope of 2007 award for young scientists and artists in EARTOs Special Interest Group on “Novel the field of neuroscience from the Society of bioactive substances for industrial and bio- University Teachers, Scholars and Other Sci- medical use”. In September, the 10th Central entists - Zagreb. The same organization pre- European NMR Symposium was held at RBI sented the 2008 award in the field of biology in combination with the 10th Central Europe- to Branimir Bertoša. Finally, Fran Supek was an Bruker NMR Users Meeting. deservedly selected for the State Award for Several other equally noteworthy confer- Science for Ph.D. students in the category of ences were organized by scientists from the biotechnical sciences. RBI and further information concerning them can be found in the individual reports of the Education Divisions involved. In addition to their organizational efforts, RBI scientists also partici- In 2008, scientists from the Institute con- pated in many scientific meetings over the tributed in 78 undergraduate courses and 245 year, contributing in the form of invited and graduate courses to the program of higher accepted lectures as well as numerous post- education in Croatia. Their respective dis- er presentations. tributions amongst the seven universities at which they were conducted, as well as by the Awards and Recognition divisions and centres that contributed them are shown in Figures 2, 3, and 4. In addition The Croatian Academy of Science and to the coursework, 22 B.Sc., 6 M.Sc. and 22 Arts presented its 2008 award for the best Ph.D. theses were completed under the su- publishing achievement to the RBI for its pro- pervision of the RBI academic staff in 2008. duction of “Methods in Molecular Biology”, authored by a team of 11 of the Institutes scientists, led by Andreja Ambriović Ristov. Of the many other awards presented to RBI scientists for outstanding achievements in 2008, we have chosen to highlight those earned by the younger members of our staff this year. The RBI and SHIMADZU d.o.o. Zagreb gave the Annual Award of Excellence for the young researchers for the first time in 2008. On this Figure 2. Distribution of the RBI held undergraduate courses occasion, the award was given to Tomislav among the universities (78). Domazet Lošo for his work: A phylostratigraphy approach to uncover the genomic history In 2008, the first 30 students of the gradu-

RBI Annual Report 2008. Annual Report 2008. RBI of major adaptations in metazoan lineages, ate studies on Project Management gradu- published in Trends in Genetics in 2007. ated. The study is successfully organized as Marko Košiček received both the Croatian a joint study of the RBI and the College of

6 of intellectual property and its commercialization. In this context, various specific activities have been initiated and realized in this vein over the last few years. For example, the In- stitute’s Commission for Intellectual Property has been established. We have also established a company under the name Rudjer In- novations Ltd. This company, which is wholly owned by the RBI, engages in activities re- Figure 3. Distribution of the RBI held graduate courses among the lated to protection and commercialization of universities (245). knowledge arising from the RBI, other academic organizations, companies, and private persons. In 2008, we began regular weekly meetings between the Commission of Intel- lectual Property and representatives from Rudjer Innovations Ltd. We also undertook a cooperative relationship with a local legal firm to administer patent protection, both do- mestically and internationally. Presently, the portfolio of the Institute’s intellectual property Figure 4. Distribution of the RBI held graduate courses at domicile consists of 26 innovations classified under universities among Divisions and Centres (245). the broad banner of “know how”. Of these, 3 Business and Administration in Zaprešić. Final are very close to attaining commercial status. preparations for the postgraduate course of A total of 27 patent applications arising from Medicinal Chemistry, conducted jointly by RBI, within RBI, have been lodged, while a further the University of Rijeka and GlaxoSmithKline, 28 such applications have originated from were completed in 2008 and the course is set sources outside of the Institute. to commence in March 2009. The joint gradu- In March, a delegation from RBI and Rud- ate course of Biophysics, involving RBI and jer Innovations Ltd. visited the Finnish Fund- the University of Split was officially opened in ing Agency for Technology and Innovation, December. The National Council for Higher TEKES, in Helsinki. Education accepted the joint proposal for an undergraduate course in Marine Science, in- NEW EqUIPmENT volving the RBI and the University of Pula. To strengthen the collaboration with re- Rudjer-Medikol Cyclotron Ltd., a spin-off gional Universities and increase its contribu- company established by Rudjer Innovations tion in higher education in natural science Ltd., continued working towards the recon- RBI Annual Report 2008. and biomedicine, the RBI signed agree- struction of the cyclotron facility at RBI. In ments of collaboration and partnership with 2008, all licenses and permits were finalized the Agricultural Faculty in Zagreb and the for the reconstruction and it is expected that Polytechnic College in Šibenik. the facility will begin producing radioisotopes for use in Positron Emission Tomography in Intellectual Property the autumn of 2009. The new Laboratory for systems bio- Apart from fundamental research and edu- medicine which includes the Centre for Pro- cation, the activities of the RBI also result in teomics and Mass Spectrometry as well as various forms of intellectual creations. One the Centre for Transcriptomics, has been es- important mission of the RBI is the protection tablished in 2008. The Centre for Proteomics

7 and Mass Spectrometry offers commercial Ministry of Sciences Education and Sports. services which include amino-acid, pro- Compared to 2007, this support increased by tein and peptide sequencing upon isolation 12%. The comparison of the finances over the and purification. Additionally, the molecular period 2005-2008 (Table 1) shows a gradual weight analysis could be performed accord- increase. It should be also noted that the rev- ing to the MS and MS/MS measurements. enues originating from international, indus- Peptide and protein identification from com- trial and service contracts increased by an plex mixtures is performed by using special- impressive 84% between 2005 and 2008 al- ized software packages that are directly con- though they dropped marginally over the last nected with publicly open databases such as year. The total number of employees has con- The Protein Data Bank or SwissProt. tinued to rise since 2005. However, the recent A high-pressure liquid chromatography- trend in Ph.D. student numbers, for example, mass spectrometry (HPLC-MS) instrument constitutes some cause for concern. (Agilent Technologies) was purchased with the financial help of the Ministry of Sciences, Edu- Publication results of fundamental cation and Sports of the Republic of Croatia. research projects at RBI The acquisition of the HPLC-MS-MS instrument will contribute to the achievement of the Table 2 shows the projects led by RBI sci- scientific objectives in the majority of chemists entists which are ranked among the top 15% at the Institute and open possibilities for intro- in the country, according to the Croatian Sci- ducing new methods and scientific fields. entific Bibliography (CROSBI). The number With the support of the EU FP6 proj- of projects in a particular field of science is ect RBI-AF two quadrupole magnets were taken from the official list of the projects pro- added to the existing ion microprobe focus- vided by Ministry of Sciences, Education and sing facility to enable focussing of heavy ion Sports. The ranking is performed by the total beams, enabling focusing to submicron spot number of articles associated with a particular sizes of ions of up to 15 MeV mE/q2 rigid- project among the projects that began in 2007 ity. A laboratory for research in quantum in- - only research articles published in journals formation has been formed for the first time indexed in Currents Contents were counted, in Croatia. A setup for study of polarization up until March 1st, 2009 (web address: http:// entangled photon pairs was built and used bib.irb.hr/statistika?sto=p&period=2007&chse to measure quantum efficiency and single t=ASCII&lang=EN). The number of articles is photon timing resolution of a photon detector the total number of scientific papers appearing (constructed in the laboratory). in journals indexed in Currents Contents published on a particular project in 2008. The limi- Revenue and employees tation of the table is that it does not include an average journal impact factor, the number of In 2008, the major share of the finan- researchers/students working on the project, cial support for the RBI was provided by the and the financial support of the projects. RBI Annual Report 2008. Annual Report 2008. RBI

8 2008 / 2007 2008 / 2005 2005 2006 2007 2008 (%) (%) increased increased

Revenue from the Ministry of 17.293.472 20.072.940 23.090.639 25.818.444 11.8 49.29 Science Education and Sports (€)

Other revenue (international and industrial projects, 1.890.592 2.311.744 3.671.788 3.486.303 -5.3 84.4 services etc.) and donations (€) total 19.184.064 22.384.684 26.762.427 29.304.747 9.5 52.7

Employees

Scientific staff 325 317 320 322 0.6 -0.9 post-doctoral 30 40 42 53 26.2 76.7 students

Ph.D. students 159 158 177 155 -12.4 -2.5

Technicians and RBI Annual Report 2008. 127 134 127 145 14.2 14.2 other administration and 174 176 174 180 3.4 3.4 maintenance total 815 825 840 855 1.8 4.9

Table 1. Comparison of RBI Revenues (€) and employment during 2005-2008.

9 Number of Field of Science - Principal CC Articles Number of National Project Title Investigator Published in Projects in the Field 2008

Regulatory mechanisms of photosynthesis and BIOLOGY - 77 Hrvoje Fulgosi 6 plastid differentiation

Cell response to cytotoxic agents and resistance Maja Osmak 1 development

Physics and application of nanostructures and bulk PHYSICS - 85 Krešimir Furić 17 matter

Fundamental interactions in elementary particle Branko 12 physics and cosmology Guberina

Nuclear structure and reactions: experimental Suzana Szilner 6 approach

Basic properties of nanostructures and defects in Branko Pivac 10 semiconductors and dielectrics

Thin films of novel amorphous or nanostructured Nikola Radić 5 materials

Ion beam interactions and nanostructures Milko Jakšić 9

Massive neutrinos and astroparticles: from particle Ante Ljubičić 5 physics to cosmology

Interactions of trace metal species in an aquatic GEOSCIENCES - 65 Ivanka Pižeta 9 environment

Nature of organic matter, interaction with traces and Zlatica Kozarac 4 surfaces in environment

Radionuclides and trace elements in environmental Delko Barišić 3 systems

Synthesis and microstructure of metal oxides and CHEMISTRY - 73 Svetozar Musić 10 oxide glasses

Electroanalytical research on microcrystals and Milivoj Lovrić 12 traces of dissolved substances

RBI Annual Report 2008. Annual Report 2008. RBI Self-Assembly in gels and synthesis of functional Mladen Žinić 8 hybrid materials

10 NMR Spectroscopy and Modelling of Bioactive Dejan Plavšić 5 Molecules

Broensted and Lewis acids and bases in chemistry Zvonimir 2 and biochemistry Maksić

Molecular structure and dynamics in systems Boris Rakvin 9 containing paramagnetic particles

Spectroscopy, chemical properties and reactions of Branka Kovač 9 biologically active molecules

TECHNICAL Multispectral data analysis Ivica Kopriva 3 SCIENCE - 28

FUNDAMENTAL The role of different cell death responses to DNA- MEDICAL Marijeta Kralj 9 damage treatment SCIENCES - 175

Pharmacogenomics and proteomics of serotonergic Dorotea Mück- 7 and catecholaminergic system Šeler

Molecular basis and treatment of psychiatric and Nela Pivac 6 stress related disorders

Molecular characteristic of myofibroblasts derived Krešimir 11 from Dupuytren's contracture Pavelić

Gene therapy of tumors by modulating the Jasminka 5 molecules of immune system Pavelić

Lipids, free radicals and their messengers in Neven Žarković 5 integrative oncology

Molecular genetics and pharmacogenetics of Sanja 5 gastrointestinal tumors Kapitanović

Aberrant DNA methylation in HPV associated Magdalena 4 lesions Grce RBI Annual Report 2008.

Serotonergic neurotransmission: genes, proteins Branimir Jernej 3 and behavior

Table 2. Publication results of RBI fundamental research projects ranked among the top 15% Croatian projects in their respective field.

11 12 RBI Annual Report 2008. DIVISION OVERVIEW OFTHE Ph. D. theses. students completedtheir B. Sc., and Sc. M. at the University of and Zagreb anumber of continuedDivision to involved be in lecturing of members the the biomedicine. In 2008, of plication nonlinearmethods statistical in modellingmedical in and life theap science isnature inthe Division the activity of cial matter inphysics. condensed activity Aspe ogy. substantial is research addition, In there physicsphysics, and cosmol astroparticle physics, general and mathematicalparticle physics,vestigation such as of high-energy in thetheoretical with is mainly concerned consists ofthefollowinglaboratories: (ZTF) Division Physics Theoretical The Head: BrankoGuberina ORGANIZATION DIVISIONAL Theoretical PhysicsDivision The research performed in Division the researchThe performed a a a a

Dynamics, Mladen Martinis Dynamics, Group forLinearandNonlinear Meljanac Physics Group,Stjepan Theoretical andMathematical Group, NevenBilić Particle PhysicsandCosmology Brako Radovan Solid StatePhysicsGroup, - - - - TOP ACHIEVEm yield negativeyield entropy (Bilić, 2008). necessarily not does energy) dark (phantom claims, aviolation of null the energy condition stated to often equal to zero. contrary Hence, dark-energy iswith always associated greater than or entropy the that generally quite of k-essence. Itnetic has been type shown formalismthe has beenapplied to apurely ki particular, In temperature. finite at theory field of formalism the have using analyzed been of Thermodynamics Energy Dark the tachyoncondensatecosmological model. Figure 1.Evolutionofthebackground densityandpressurein Thermodynamic properties of energy dark properties Thermodynamic ENTS http//thphys.irb.hr -

1313 2008. Report Annual RBI ZTF Improved QCD Light-cone Sum Rule developed a systematic study for construct- ing realizations of noncommutative spaces. An improved QCD light-cone sum rule Star product and Drinfeld twist operator are (LCSR) calculation of the B -> K and Bs -> represented in terms of the coproduct (Mel- ZTF K form factors by including SU(3)-symmetry janac, Samsarov et al., 2008; Meljanac and breaking corrections is presented. By ap- Krešić-Jurić, 2008). Twisted statistics of kap- plying the method of the direct integration in pa-Minkowski space is analysed. the complex plane, the analytical extraction of the imaginary parts of LCSR hard-scat- Integrable systems and tering amplitudes becomes unnecessary applications in physics and therefore the complexity of the calculation is greatly reduced (Duplančić and A new analysis of the mechanism of elec- Melić, 2008). tronic capture by polar molecules has been presented. This analysis is based on theory Noncommutative chiral models of self-adjoint extension and the results show that a polar molecule can form a bound state In the noncommutative chiral gauge the- with electrons even when its dipole moment ories the 4-fermion vertices are shown to is less than the critical value of 1.63×10-18 be finite. The 4psi vertices appear in linear esu cm (Giri et al., 2008). A rational Calogero order in quantization of the theta-expanded model with additional interaction of Coulomb noncommutative gauge theories whereas type has been studied, and it was shown that in all previously considered models, based for certain values of the constants of inter- on Dirac fermions, the 4psi vertices were action the system allows for one-parametric divergent and nonrenormalizable (Burić et family of self-adjoint extensions which lead al., 2008). to novel solutions of this model (Basu-Mal- lick et al., 2008). Deeply virtual Compton scattering Homolumo gap and matrix model Combining dispersion and operator product expansion techniques, the conformal We discuss a dynamical matrix model by partial wave decomposition of the virtual which probability distribution is associated Compton scattering amplitude has been de- with Gaussian ensembles from random ma- rived in terms of complex conformal spin to trix theory, and interpret the matrix M as a twist-two accuracy. The perturbation theory Hamiltonian representing interaction of a bo- predictions for the deeply virtual Compton sonic system with a single fermion. We show scattering amplitude are presented in next- that a system of second-quantized fermions to-leading order for both the conformal and influences the ground state of the whole sys- modified minimal subtraction schemes. tem by producing a gap between the highest Within a conformal subtraction scheme, occupied eigenvalue and the lowest unoccu- where predictive power of conformal sym- pied eigenvalue (Andrić et al., 2008). metry is exploited, the radiative corrections are presented up to next-to-next-to-leading Enhanced van der Waals order accuracy (Kumerički et al., 2008). interaction at interfaces

Noncommutative spaces The excitation of surface polaritons by a

RBI Annual Report 2008. Annual Report 2008. RBI decaying atom or molecule and their sub- Kappa-Minkowski and generalized kap- sequent conversion into the radiation (pho- pa-deformed spaces are investigated. We tons) is at the core of surface-enhanced op-

14 tical processes such as fluorescence and PROJECTS AND PROGRAmS Raman scattering. We have considered the dispersion interaction between an excited Projects supported by the Ministry and a ground-state atom near an interface of Sciences, Education and Sports under the condition of resonant coupling of ZTF the excited atom to surface polaritons. We 1. Surfaces and nanostructures: Theoretical have demonstrated that the nonretarded approaches and numerical calculations, Ra- atom*-atom interaction energy at a vacuum- dovan Brako medium interface can be enhanced by sev- 2. Electronic properties of hybrid nanostruc- eral orders of magnitude in comparison with tures, Željko Crljen 3. Electromagnetic field fluctuations: the van der the van der Waals interaction energy of the Waals-Casimir forces, Marin-Slobodan Tomaš two isolated atoms. This promotes the van 4. Fundamental interactions in elementary parti- der Waals interaction as another example of cle physics and cosmology, Branko Guberina the surface enhanced phenomena (Tomaš, 5. Noncommutative spaces in high energy 2008). physics, Josip Trampetić 6. Matrix models, duality and field theory, Ivan From degree correlations to Andrić feedback in directed complex 7. Quantum field theory, noncommutative networks spaces and symmetries, Stjepan Meljanac 8. Heavy Majorana neutrinos in particle physics and cosmology, Davor Palle The reciprocity is a natural measure of feedback in complex systems representable as directed complex networks. The role of Programs supported by the one-vertex and two-vertex degree correla- Ministry of Sciences, Education tions in explaining the value of reciprocity and Sports has been studied analytically and in computer simulations using newly developed 1. High energy physics, gravity and cosmology, randomization algorithms. The hierarchy of Branko Guberina. importance of various degree correlations for the understanding of reciprocity has been Research, developmental and in- established and verified on a number of im- ternational projects portant empirical complex networks comprising world trade webs, neural networks of 1. QCD sum rules for exclusive decays of Caenorhabditis elegans, cortical networks, heavy hadrons, Blaženka Melić (Internation- food webs and Wikipedia networks (Zamo- al Research Project promoted by the Alexan- ra-López et al., 2008). der von Humboldt Foundation, with principal investigators from RBI and University of Sie- RBI Annual Report 2008. EDUCATION gen, Germany) 2. Aspects of Calogero models, noncommutative geometry and quantum physics, Stj- In 2008, the members of the Division con- epan Meljanac (Indo-Croatian Programme tinued to be involved in lecturing undergrad- of Cooperation in Science and Technology uate and graduate courses at the University for collaboration between RBI-ZTF, Saha of Zagreb, mostly at the Faculty of Science. Institute of Nuclear Physics, Calcutta, and A number of students completed their B. Sc., Institute of Mathematical Sciences, Chen- M. Sc. and Ph. D. theses. nai, India) 3. Nonabelian Cohomology and Applications in Geometry, Algebra and Physics, Zoran Škoda (International collaboration between RBI-ZTF

15 and Universität Hamburg, LMU München and SELECTED PUBLICATIONS Universität Göttingen, Germany) 4. Tools and Precision Calculations for Phys- 1. Andrić I, Jonke L, Jurman D, Nielsen H B. ics Discoveries at Colliders, Josip Trampetić Homolumo gap and matrix model. Phys Rev

ZTF (collaboration to the FW 6 EU RTN Network D 2008: 77: 127701. HEPTOOLS, no. MRTN-CT-2006-035505) 2. Basu-Mallick B, Gupta K S, Meljanac S, Samsarov A. Inequivalent quantization of the rational Calogero model with a Coulomb SELECTED INVITED LECTURES type interaction. Eur Phys J C 2008: 58: 159. 3. Bilić N. Thermodynamics of k-essence, Phys 1. Andraši A. Divergences in Coulomb gauge Rev D 2008: 78: 105012. QCD, A Triangle Workshop in Theoretical 4. Burić M, Latas D, Radovanović V, Trampetić Physics, Heviz, Hungary, January 23-25, J. Absence of the 4psi divergence in non- 2008. commutative chiral models, Phys Rev D 2. Škoda Z. Categorified actions and 2-repre- 2008: 77: 045031. sentations, Functional analysis X Conference, 5. Duplančić G, Melić B. B, B(s) -> K form fac- Dubrovnik, June 29 - July 5, 2008. tors: an update of light-cone sum rule results. 3. Melić B. B -> pi and B(s) -> K form factors and Phys Rev D 2008: 78: 054015. Vub determination, 34th International Confer- 6. Giri P R, Gupta K S, Meljanac S, Samsarov ence on the High Energy Physics ICHEP2008, A. Electron capture and scaling anomaly Philadelphia, USA, July 29 – October 5, 2008. in polar molecules. Phys Lett A 2008: 372: 4. Jonke L. U(1) gauge field theory on kappa- 29 67. Minkowski space, Supersymmetry and non- 7. Kumerički K, Müller D, Passek-Kumerički K. commutative quantum field theory, Workshop Towards a fitting procedure for deeply virtual in Memoriam Julius Wess, Vienna, Austria, Compton scattering at next-to-leading order December 4-6, 2008. and beyond. Nuclear Phys B 2008: 794: 244. 8. Meljanac S, Krešić-Jurić S. Generalized kappa-deformed spaces, star products and their realizations. J Phys A 2008: 41: 235203. SELECTED ORGANIZED CON- 9. Meljanac S, Samsarov A, Stojić M, Gupta K FERENCES S. Kappa-Minkowski spacetime and the star product realizations. Eur Phys J C 2008: 53: 1. Workshop on Black Holes in General Relativ- 295. ity and String Theory, V. Lošinj, Croatia, Au- 10. Tomaš M S. Enhanced van der Waals inter- gust 24-30, 2008, Larisa Jonke and Neven action at interfaces. J Phys A Math Theor Bilić, members of the Organizing Committee 2008: 41: 164020. 2. 3rd Croatian-Hungarian-Austrian Meeting – 11. Zamora-López G, Zlatić V, Zhou C, Štefančić Non Abelian Theories, Hot Matter and Cos- H, Kurths J. Reciprocity of networks with de- mology, Rab, Croatia, August 30 – Septem- gree correlations and arbitrary degree se- ber 4, 2008, organized by Ivan Dadić quences. Phys Rev E 2008: 77: 016106. RBI Annual Report 2008. Annual Report 2008. RBI

16 DIVISION OVERVIEW OFTHE recently also in quantum information. There information. quantum in also recently physics, astrophysics, and particle clear and nu theoretical experimentaland on focused laboratories: Physics Experimental (ZEF) consistsofthefollowing of Division The Tome Antičić (fromNov20,2008) 2008); 27, Sept (until Švarc Alfred Head: ORGANIZATION DIVISIONAL Division ofExperimentalPhysics h Dvso o Eprmna Pyis is Physics Experimental of Division The a a a a a a a a els, Alfred Švarc mod- QCD and experiments tween Vladivoj Valković the useofanalyticalmethods, and Group forthedevelopment physics, KrešoKadija for high energy Laboratory Obelić Bogomil activities, low-level for measurement of Laboratory Milko Jakšić interactions, for ion beam Laboratory Raul Horvat interactions, and weak for electromagnetic Laboratory Roman Čaplar for heavy ionphysics, Laboratory Neven Soić reactions, for nuclear Laboratory Laboratory for hadron physics inbe- for hadron Laboratory - first time. first of diamond for the properties electronic the modify to applied been now 1)has(Figure veloped previously pin diodes silicon on damage using microbeamde ion heavy beam (Borjanović et al., 2008). studied using irradiation by 2aMeV proton of nanodiamonds embedded inwas PDMS while changesin properties luminescence silica, in amorphous formation nanocrystal ofsuccessfully carbon applied in process nanodiamonds modification of and Ion beamassistedformation TOP ACHIEVEmENTS tes t sgiiaty nac is experi capabilities. mental its enhance significantly to others, was which used, among andSports cation of Edu Scienes othersources than Ministry from financing its of fraction large a ceived re reputation, international excellent its to applied physics research. TheDivision, due in both basic and tain astrong performance complexes abroad and in Croatia, and main experimental and experiments numerous in Ph.D.than 30 students. They are involved members, includingare over more staff 60 A technique for patterning radiation radiation patterning for technique A Implantation of1-2MeVcarbonionswas http://www.irb.hr/en/str/zef - - - - -

17 2008. Report Annual RBI ZEF Energy scans at the NA49 SPS experiment

An energy scan in Pb+Pb collisions at

ZEF the NA49 detector at the CERN-SPS was performed to understand the crossover region of the transition from normal matter to the quark-gluon plasma phase. Statisti- cal hadron gas models provided a reasonable description of the L and X yields, while string hadronic models failed to match the X multiplicities. Phi meson energy dependence was shown to be compatible with the assumption that partonic degrees of free- dom set in at low SPS energies. At 30A GeV Figure 1. Radiation damage structures induced in Si pin diode a change of the energy dependence for by 7 MeV carbon ions in a form of Piet Mondrian painting. yields as well as for the shape of the trans- Diode was imaged by IBIC technique using the same ions. Charge collection efficiency decreases from the highest (black) verse mass spectra is observed, compat- to the lowest (blue). ible with the prediction that the threshold for production of a state of deconfined matter pp→WZ analysis for the CMS at the early stage of the collisions is located Collaboration at LHC at low SPS energies (Alt et al., 2008).

Natural isotopes in environmental studies and radiocarbon dating

The new system for graphite preparation of micro-sized samples for 14C measurement by AMS technique was validated at the SUERC, Scotland. Dating of prehistoric and medieval sites from Croatia and Slov- enia by the LSC method continued. Carbon exchange processes in atmosphere, water and lake sediments was studied together with measurements of stable isotopes to asses possible anthropogenic contamina- Figure 2. One of the first images from CMS, showing the debris of 3 particles picked up in the detector's calorimeters and muon chambers. tion in Karst systems. The monitoring of H activity in precipitation in Croatia and Slove- The CMS potential for the observation of nia continued, as did that of biological sam- the pp→WZ reaction was investigated using ples and atmospheric CO2 near the nuclear simulated signal and background samples. power plant Krško. A training course dedi- New data-driven methods for the back- cated to dating methods within the regional ground determination have been developed. IAEA technical project RER/1/006 was or- A member of our group has been selected ganized in Zagreb. A workshop dedicated as convenor for all multiboson analyses in to valorization of monumental heritage and

RBI Annual Report 2008. Annual Report 2008. RBI the CMS Collaboration. We have also par- characterization of constructive materials ticipated in the analysis of the first cosmic was organized in Split. muons measured by CMS.

18 Scattering of protons and CLUNA). With aim to study the properties of deuterons at 135 MeV revisited the nuclear systems at extreme conditions, the measurements at the INFN-LLN Legn- Study of proton and deuteron scattering al- aro, INFN-LNS Catania and UCL Louvain- lows the inferring of information on the three- la-Neuve have been performed and new ZEF nucleon force for the smallest nuclear system experiments proposed by our group have possible. There has been a strong discrepan- been approved at the INFN-LLN and GANIL cy among existing data at 135 MeV/nucleon Caen facilities. (Figure 3). A precise measurement at this energy for the 2H(p,d)p and 1H(d,d)p reactions Search for solar hadronic axions have been carried out using polarized beams and liquid targets. The data differ significantly Axions (pseudoscalars that arise in from previous measurements and consist- models resolving the strong CP problem ently follow the energy dependence as ex- by the Peccei-Quin mechanism) could also pected from an interpolation of published data explain the mystery of dark matter in the (Gašparić et al., 2008). Universe. We developed a new approach to search for hadronic axions that is free from the large uncertainties associated with the estimation of the flavor-singlet axial-vector matrix element.

Large extra dimensions

In an experiment performed at the RBI we did not observe the bulk vector boson signal from the Sun. This result rules out the possibility of observing any signal at the LHC for two additional space dimensions (Horvat et al., 2008). Figure 3. Difference between theory and the measured cross sections for the elastic p+d reaction. The top graph shows the results Holographic dark energy from a standard calculation, while the bottom includes an additional Δ isobar. Solid circles are this work. Although the discrepancy is An extremely small entropy pertaining to reduced in the lower panel, inconsistencies remain. holographic dark energy models is explained for the first time with the aid of the entangle- Exotic nuclear phenomena ment entropy for the subsystems (the cos-

mic horizon and the interior) to show that RBI Annual Report 2008. The largest amount of knowledge in nu- via quantum correlations this entropy may clear physics is about nuclei close to the be responsible for the almost purity of the valley of stability, but recent studies have entire system (Horvat, 2008). moved towards the driplines and more exot- The holographic dark energy models, ic nuclear phenomena. Our current studies successful in describing the late-time dark concern proton-rich light nuclei and many- energy universe, are shown to have con- centre cluster structures in the neutron-rich ceptual problems when describing the ear- light nuclei. Design and construction of the lier cosmological epochs, so that a reas- detector array for nuclear structure and re- sessment of the whole concept is needed action research has been extended by inclu- (Horvat, 2008). sion of new electronic devices (FP7 project

19 OPERA neutrino oscillations experiment

Our scientists took part in data taking at OP- ZEF ERA (long-baseline experiment designed to investigate neutrino oscillations), which resulted in the first 1000 recorded neutrino events. They are also strongly involved in the electron- a) ics detector group and in data analysis.

Environmental Security of the Coastal Sea Floor

The detection and identification of im- properly disposed ammunition, explosives and chemical weapons at the sea floor and b) pollution of coastal sea sediments are problems of growing concern. While polluted sediments present a threat to the marine ecosystem and to the public health, ammunition and CW agent dumps are a seri- ous threat as well as possible objects of misuse. The research in this field has been established in LNAM (Valković et al., 2008). In 2007 we made the first prototype of the underwater system "Surveyor" containing a neutron generator, shielding and a gamma ray detector. In 2008 the “proof of principle” for the detection of explosive and chemical c) warfare agents has been established (Sudac et al., 2008). Figure 4. OPERA: (a) the detector, (b) a neutrino CC event (c) vertex tracks recorded. RBI Annual Report 2008. Annual Report 2008. RBI

Figure 5. Reported locations of ammunition on the floor of the Mediterranean (UNEP, 2007).

20 Matrix characterization in threat devoted to experiments using energy tagged material detection processes Bremsstrahlung photons and its major experiments are the measurements of the Matrix characterization is a key for the anomalous magnetic moment of the Delta neutron prototype systems used for threat resonance, of the mass of the eta-meson ZEF material inspection in cargo containers, and double pion production at threshold, and landmine detection or underwater threat others (Tarbet et al., 2008). materials inspections. For this purpose, the chemical composition of samples of con- Figure 7. The tainer cargo, soil and sea sediment have Crystal Ball Spectrometer. been analyzed using the Fast Neutron Acti- vation Method with Associate Alpha Particle and Energy Dispersive X-Ray Fluorescence (Obhođaš et al., 2008).

NEW EqUIPmENT

With the support of the EU FP6 project RBI-AF two quadrupole magnets were added to the existing ion microprobe focussing facility to enable focussing of heavy ion beams, enabling focusing to submicron spot sizes of ions of up to 15 MeV mE/q2 rigidity. Figure 6. The prototype of the underwater system "Surveyor" A laboratory for research in quantum in- containing neutron generator. formation has been formed for the first time in Croatia. A setup for study of polarization Poles as a true resonance signal entangled photon pairs was built and used to measure quantum efficiency and single The present manner in which the Particle photon timing resolution of a photon detec- Data Group is parameterizing nucleon reso- tor (constructed in the laboratory). nances in terms of Breit-Wigner parameters have been criticised as being inherently model

dependent. An appeal to change the harmful RBI Annual Report 2008. practice and use scattering matrix pole parameters instead is issued, and two new, model independent ways to extract pole parameters from partial wave data are presented.

The Crystal Ball Spectrometer

A new experimental program at the Mainz Microtron (MAMI) facility consists of the Figure 8. Series of five quadrupole magnets installed at the Crystal Ball, the TAPS detector and a cen- microprobe beam line to form spaced quintuplet system for ion tral tracker. The Crystal Ball collaboration is beam focusing.

21 Programs supported by the Ministry a) of Science, Education and Sports

1. High energy experimental physics within and

ZEF beyond the standard model, Krešo Kadija b) 2. Water in Karst - dynamics, geochemistry and isotopic processes, Bogomil Obelić

Figure 9. (a) the downconversion setup Research, developmental and utilizing a 405nm laser (b) a CCD picture of international projects downconversion light cones. 1. CLUustering phenomeNA in nuclear physics: EDUCATION strengthening of the Zagreb - Catania - Bir- mingham partnership (CLUNA), Neven Soić Members of the Division have been in- (FP7-REGPOT-2007-3 International Coopera- tion - Coordination and Support action, project volved in lecturing undergraduate and gradu- number 203200) ate courses at the Faculty of Science at the 2. Preparation of carbon samples for 14C dat- University of Zagreb, University of Rijeka, and ing by the AMS technique - AMS-14C, Ines at joint studies organized by RBI in cooperation Krajcar Bronić (EC FP6 program INCO- with the Universities of Osijek and Dubrovnik. CT-2006-043584) 3. Upgrade of the RBI Tandem Accelerator Facil- PROJECTS ity – RBI-AF, Stjepko Fazinić (EC FP6 program INCO Contract 043630) 4. EUROpean Nuclear Structure Integrated Infra- Projects supported by the Ministry structure Initiative – EURONS, Zoran Basrak of Sciences, Education and Sports (EC FP6 program, Contract 506065) 5. Development of frozen spin polarized target for 1. Experimental research of the nucleus: nucle- Crystal Ball Collaboration at MAMI, Ivan Su- ar structures and reactions, Suzana Szilner pek (University of Mainz for EU program I3HP 2. Ion beam interactions and nanostructures, TNA Contract) Milko Jakšić 6. TRAINMONHER - Valorization of Monumental 3. Hadronic physics and QCD, Ivan Supek Heritage through Higher Education and Pro- 4. Heavy-ion physics, Zoran Basrak fessional Training. Socioeconomic study and 5. Massive neutrinos and astro-particles: from analysis of National Policies on EU-MED-DEV particle physics to cosmology, Ante Ljubičić countries and EC Directives, Bogomil Obelić 6. Experimental physics at LHC energies, (EU FP6 project INCO-CT-2006-518697) Krešo Kadija 7. Eritr@C, European Riposte against ilicit tr@ 7. Experiments in quantum communication and ffiCking, Davorin Sudac (EU programme “Pre- quantum information, Mario Stipčević vention of and fight against crime”, Agreement 8. Photon-atom interactions and correlations, no. JLS/2007/ISEC/550) Tihomir Surić 8. EURITRACK, European Illicit Trafficking 9. Natural isotopes of weak activities and devel- Countermeasures Kit, Vladivoj Valković, (EU opment of instrumentation, Bogomil Obelić FP6- Specific Targeted Research or Inovation 10. Development and application of nuclear ana- Project) lytical methods, Jasmina Obhođaš 9. Nuclear Techniques for the Protection of Cul- 11. Development of methods for control of illicit tural Heritage Artifacts in the Mediterranean threat material trafficking, Dario Matika and Region, Stjepko Fazinić (National Coordinator, Davorin Sudac IAEA regional project RER/1/006) 12. Nuclear interactions, Ivo Šlaus 10. Measurements of differential cross sections 13. Development and application of nuclear 1 4

RBI Annual Report 2008. Annual Report 2008. RBI for elastic scattering of H and He ions from methods for investigation and protection of selected light elements, Ivančica Bogdanović cultural heritage, Vladan Desnica Radović (IAEA Research Contract 13269/RO)

22 11. Heavy ion acceleration in 1.0 and 6.0 MV elec- ++ trostatic accelerators, Milko Jakšić (IAEA Re- 26. Precise Measurement of the →Π e ν search Conract 13127/RO) Branching Ratio, Ivan Supek 12. Upgrade of PIXE and STIM imaging capabili- (International Collaboration between RBI and University of Virginia, Charlottesville, USA)

ties at Zagreb nuclear microprobe, Mladen Bo- ZEF govac (IAEA Research Contract 13258/RO) 13. Characterization of inorganic pigments used SELECTED INVITED LECTURES by selected painter(s) by nuclear microprobe, Stjepko Fazinić (IAEA Research Contract 1. Basrak Z. Selected effects of the NN cross 13050/RO) section on heavy-ion dynamics, Workshop on 14. Modification of electronic properties in insula- Nuclear Symmetry Energy at Medium Ener- tors using nuclear microprobe, Marko Karlušić gies, Catania and Militello in Val di Catania, (IAEA Research Contract 12925/RO) Italy, May 29-31, 2008. 15. Improvements of ERDA technique using TOF 2. Bogdanović Radović I. 3D imaging of light el- spectrometer, Zdravko Siketić (IAEA Research ements using elastic scattering coincidence th Contract 14580) technique, 11 International Conference on 16. Application of isotope techniques in investiga- Nuclear Microprobe Technology and Applica- tion of water resources and water protection in tions Debrecen, Hungary, July 20-25, 2008. the Karst area of Croatia, Nada Horvatinčić, (In 3. Brigljević V. Measurement of diboson produc- co-operation with the University of Rijeka; IAEA tion in early LHC data, Physics at LHC 2008, Technical co-operation project CRO/8/006) Split, Croatia, September 29-October 4, 2008. 17. Using Isotope Tracers as a Tool for Groundwa- 4. Jakšić, M. Accelerators of the Ruđer Bošković ter Vulnerability Assessment in the County of Institute: From the successful history to Split, Dalmatia, Nada Horvatinčić (In co-opera- promissing future, CoNuSS-2008, Belgrade, tion with the University of Rijeka; IAEA Techni- Serbia, September 22-25, 2008. cal co-operation project CRO/8/007) 5. Kiš M. New FOPI MMRPC ToF Barrel, Deut- 18. Isotope methods for management of drinking sche Physikalische Gesellshaft Frühjahrsta- water resources, Nada Horvatinčić (IAEA re- gung, Darmstadt, March 10-14, 2008. gional project RER/8/012) 6. Lakić B (for the CAST collaboration). Search 19. Photon detector for applications in quantum for solar axions with the CAST experiment. experiments, diagnostic and analytical meth- Identification of Dark Matter 2008, Stockholm, ods, Mario Stipčević (Technological project Sweden, August 18-22, 2008. financed by Croatian Institute of Technology) 7. Obelić B. Dating Techniques in Monumen- 20. Study of advantages and limitations of Si pin tal Heritage, Training course on Monumen- diodes as radiation detectors by ion beam tal Heritage within the EU project INCO- methods, Milko Jakšić (bilateral project with CT-2006-518697 “TRAINMONHER”, Marra- Hungary) kech, Morocco, April, 14-18, 2008. 21. Heavy ion physics, Roman Čaplar (Interna- 8. Obelić B. Técnicas de datación en el patri- tional collaboration project RBI-KFKI Research monio monumental, Universidad Michoacana Institute for Particle and Nuclear Physics, Bu- de San Nicolás de Hidalgo, Morelia (México), dapest via Croatian (HAZU) and Hungarian June 11, 2008. Academy of Science) 9. Obhođaš J, Sudac D, Valković V. Matrix char- RBI Annual Report 2008. 22. Heavy-ion reaction dynamics studies, Zoran acterization in threat material detection proc- th Basrak (bilateral research project Croatia-India) esses. 20 International Conference on the 23. Experiments in quantum communication and Application of Accelerators in Research and In- quantum information, Mario Stipčević (A bilater- dustry, Fort Worth, Texas, August 10-15, 2008. al research project Croatia-Germany (DAAD), 10. Szilner S. Nucleon-nucleon correlation ef- Contract number: 098-0352851-2873) fects in multinucleon transfer reactions, GAM- 24. OPERA collaboration, Ante Ljubičić (Interna- MAPOOL Workshop, Paris, May 27-30, 2008. tional collaboration between RBI, CERN (Swit- 11. Szilner S. Quasi-elastic reactions : a survey on zerland) and LNGS (Gran Sasso, Italy) recent results with PRISMA-CLARA, Fusion08 25. Axion Solar Telescope (CAST) experiment, - New Aspects of Heavy Ion Collisions Near the Milica Krčmar (International collaboration be- Coulomb Barrier, Chicago, Illinois, USA, Sep- tween RBI and CERN, Switzerland) tember 22-26, 2008.

23 12. Valković V, Obhođaš J, Sudac D, Matika D. En- 4. Wu Q et al., (RBI-NOMAD collaboration: Lakić vironmental Security of the Coastal Sea Sedi- B, Ljubičić A, Stipčević M). A precise measurements, 20th International Conference on the ment of the muon neutrino-nucleon inclusive Application of Accelerators in Research and In- charged current cross section off an isoscalar

ZEF dustry, Fort Worth, Texas, August 10-15, 2008. target in the energy range 2.5 < Eν < 40 GeV 13. Siketić. Quantitative analysis of hydrogen us- by NOMAD. Phys Lett B 2008: 660: 19. ing TOF ERDA spectroscopy, 20th International 5. Horvatinčić N, Barešić N, Babinka S, Obelić Conference on the Application of Accelerators B, Krajcar Bronić I, Vreča P, Suckow A. To- in Research and Industry, Fort Worth, Texas, wards a deeper understanding how car- August 10-15, 2008. bonate isotopes (14C, 13C, 18O) reflect en- 14. Bogdanović-Radović I. Materials analysis and vironmental changes: A study with recent modification using MeV heavy ions NIS Collo- 210Pb-dated sediments of the Plitvice Lakes, quium, Materials analysis and Modification by Croatia, Radiocarbon 2008: 50: 233.1. Ion Beams, University of Torino, Italy, Decem- 6. Horvat R. On the internal consist- ber 22, 2008. ency of holographic dark energy models. JCAP 2008: 10: 022. SELECTED ORGANIZED 7. Prakhov S, et al., (Supek I). Measurement of CONFERENCES the invariant-mass spectrum for the two photons from the eta --> pi0 gamma gamma de- The thirteenth biennial European X-ray Spec- cay. Phys Rev C 2008: 78: 015206. trometry Conference was held from 16th to 20th 8. Curtis N, et al., (Soić N). Breakup reaction June 2008 in Cavtat (EXRS-2008). Organized by study of the Brunnian nucleus 10C, Phys Rev RBI and co-chaired by M. Jakšić and S. Fazinić, the C 2008: 77: 021301-5. conference was attended by 280 scientists from 41 9. Valiente-Dobón JJ et al. (Szilner S.), Spec- countries and 22 industrial exhibitors. On the basis troscopy of neutron-rich 59-63Mn isotopes. of regular review procedure, selected papers were Phys Rev C 2008: 78: 024302-1. published in the X-Ray Spectrometry journal. 10. Ramazani-Moghaddam-Arani A, et al. (BINA The Crystal Ball Workshop was organized by Collaboration-IRB: Gašparić I). Elastic pro- I. Supek, and held in Dubrovnik from April 6 to 9, ton-deuteron scattering at intermediate ener- 2008 with attendance of over 50 scientists from all gies. Phys Rev C 2008 : 78: 014006. over the world. It was devoted to the development 11. Ceci S, Stahov J, Švarc A, Watson S, Zauner of experiments to investigate the strong interaction, B. Resolution of the multichannel anomaly in rare decays and symmetry breaking, as well as to the extraction of S-matrix resonance-pole pa- provide new insights in physics beyond the Stan- rameters. Phys Rev D 2008: 77: 116007-1. dard Model. 12. Ceci S, Švarc A, Zauner B, Manley M, Cap- stick S. Model-independent resonance pa- SELECTED PUBLICATIONS rameter extraction from the trace of K and T matrices. Phys Lett B 2008: 659: 228. 1. Borjanović V, Lawrence WG, Hens S, Jakšić 13. Alt C et al. (NA49 Collaboration-IRB: Antičić M, Zamboni I, Edson C, Vlasov I, Shenderova T, Kadija K, Nikolić V, Šuša T. Energy depend- O, McGuire GE. Effect of proton irradiation ence of Lambda and Xi production in central on photoluminescent properties of PDMS- Pb+Pb collisions at 20A, 30A, 40A, 80A, and nanodiamond composites. Nanotechnology 158A GeV measured at the CERN Super 2008: 19: 455701-1. Proton Synchrotron. Phys Rev C 2008: 78: 2. Bogdanović Radović I, Siketić Z, Jakšić M, 034918-1. Gurbich A. Measurement and parametriza- tion of proton elastic scattering cross-sec- Chapters in books tions for nitrogen. Journal of Applied Physics 2008: 104: 074905-1. 1. Lakić B, Horvat R, Krčmar M. Axions and 3. Horvat R, Kekez D, Krečak Z, Ljubičić A. Large Extra Dimensions. In: Axions: Theory, Constraining theories of low-scale quantum Cosmology, and Experimental Searches. RBI Annual Report 2008. Annual Report 2008. RBI gravity by nonobservation of the bulk vec- Lecture Notes in Physics 741. Editor: Kuster tor boson signal from the Sun. Phys Rev D M et al. Springer, Berlin Heidelberg, 2008, 2008: 78: 127101. pp 73-82.

24 OVERVIEW OFTHEDIVISION brational of spectroscopy range wide the of statephysics emphasis special placed vi on solid and molecular of field the in research microscopy,tron etc. AFM Fundamental ing Raman XRD, spectroscopy, SAXS, elec characterized by methods, different includ and bombardment), ion annealing, (thermal ion implantation) and subsequent treatments sputtering, (magnetron processing dynamic thermo non-equilibrium by produced been have materials Variousof nanophased kinds developments and research technology.in scientific fundamental both of direction tive and nanotechnology has been themost ac densedmatter andmolecules. Nanoscience of con properties and macroscopic scopic meso microscopic, the and connect scribe physicalparameters that de andprocesses fundamental on cused and applied studies of Division ofMaterialsPhysics The Division of Division The Materials Physics is fo Physics,KrešimirFurić NikolaRadić a a a laboratories: (ZFM) consistsofthefollowing The DivisionofMaterialsPhysics Head: NikolaRadić ORGANIZATION DIVISIONAL Laboratory forMolecular Laboratory for Thin Films, Branko Pivac Laboratory for Semiconductors, ------diamond (c-diamond), face-centred cubic (n- with cubic mation ofcarbonnanocrystals rich environment,leads to preferential for- silica, followedby in a annealing hydrogen- silica amorphous in formation diamond nanocrystal instudyof Selected results TOP ACHIEVEmENTS per paper of 1.85. rent Contents, an with average impact factor to28 journals the listed contributions in Cur out inwere theDivision published incarried of results research the 2008 During search. tems continue to subjects be of intensive re induced self-organization condensed sys interaction, and thespontaneous and in in laser-matter strongthe nonlinear effects samples other. the on and biological Finally, one on side, toceramics molecularcrystals systems metals, -from and semiconductors, Carbon ion implantation in amorphous ion implantation Carbon http://www.irb.hr/en/str/zfm - - - -

25 2008. Report Annual RBI ZFM Raman scattering on quadrupolar vibrational modes of spherical nanoparticles

ZFM In contrast to the symmetrical mode, the coupling coefficientsC ( ) of the quadrupolar vibrational modes of spherical nanoparticles embedded in a matrix consist of the longitudinal and transversal sound velocity contributions. Depending on the ratio of longitudinal and transverse sound velocities, these two contributions can interfere constructively or destructively resulting in enhancing or vanishing of some radial modes. The inverse problem of the determination of sound velocities of nanoparticles from the polarized low frequency Raman spectra by using the calculated C( ) and known size distribution of the nanoparticles was demonstrated (Ristić et al., 2008).

Figure 1. Transmission electron microscopy images (left side) and the corresponding selected area electron diffraction patterns (right side) of formed carbon nanocrystals after annealing. Observed phases depended on the implanted dose: [(a) and (b)] i-carbon nanophase was formed for D3=1x1017 C/cm2; [(c) and (d)] n-diamond was formed for D2=5x1016C/cm2; and [(e) and (f)] cubic diamond was dominant and n-diamond was a minor phase for D1=1x1016 C/cm2.

diamond), or simple cubic (i-carbon) carbon crystal lattices. The preferential formation of different carbon phases (diamond, n-diamond, or i-carbon) depends on implantation energy, implantation dose, and annealing conditions. Diamond nanocrystals formed at a relatively low carbon volume density are achieved by deeper implantation and/or lower implanted dose. Higher volume densi- ties led to n-diamond and finally to i-carbon crystal formation. The optical properties of different carbon nanocrystal phases were significantly different (Buljan et al., 2008).

RBI Annual Report 2008. Annual Report 2008. RBI Figure 2. Calculated frequencies of the vibrational modes of a quasi- free spherical nanoparticle in dependence on the vl / v t ratio. The full lines mark the longitudinal spheroidal modes.

26 Low temperature resistivity to the use of loose CNFs. Furthermore, the of heavily boron doped LPVCD Raman spectrum after immobilization of the polysilicon thin films CNFs on the lava support shows only the bands characteristic to carbon and CNTs, and

Heavily boron δ-doped polysilicon sam- those bands remain after the ODH reaction ZFM ples were prepared by horizontal low-pres- (Figure 4a). A slight shoulder (D’ band), typi- sure chemical vapour deposition (LPCVD) at cal for disordered carbon, which appeared af- 750 °C for 1 h and were annealed at 1200 ter reactions is in agreement with the findings °C for 1 h. The resistivity was measured from from high-resolution TEM (Figure 4b), where room temperatures down to 2K. A T1/2 de- a slightly disordered surface structure on the pendence of the conductivity in an unusually CNFs was observed. Thus, a promising use wide temperature interval, even up to 80K of a huge, inexpensive natural resource in was observed. Above 140K, the resistivity nanomaterials synthesis and in catalysis for can be described by the T3/2 dependence. production of butadiene and styrene is dem- The experimental results were analysed onstrated (Su et al., 2008). within the theories for the disordered metals (Žonja et al., 2008). a)

b) Figure 3. Conductivities of samples with different boron dop- ing concentration (B and C) as a function of T1/2. The samples beyond the critical concentration show metallic like behaviour. A rather wide interval of the T1/2 dependence of the conductivity is attributed to the strong hole-hole interaction due to the high boron concentration. At higher temperatures, from 140 K for sample C, the resistivity can be described by the T3/2 dependence, like in some amorphous materials. RBI Annual Report 2008.

Mount-Etna-Lava-Supported Nanocarbons for Oxidative Dehydrogenation Reactions

It was shown that the catalysis reaction rate in the oxidative dehydrogenation (ODH) for the production of butadiene from 1-butene, Figure 4. a) Raman spectra of (a) lava, (b) lava–CNFs before reaction, (c) lava–CNTs after ODH of ethylbenzene to styrene, and styrene from ethylbenzene is much faster and (d) lava–CNTs after ODH of butene to butadiene reaction. b) when the carbon nanofibers (CNF) supported HRTEM images of CNFs on lava stone after ODH of ethylben- on lava are used as catalyst in comparison zene to styrene reaction.

27 Laser-induced convection EDUCATION nanostructures on SiON/Si interface Members of Division of Materials Physics teach 7 graduate and 3 postgraduate cours-

ZFM The homogenized beam of an excimer es of physics and related topics at the Fac- KrF laser has been used to form rectangular ulty of Sciences, Faculty of Electrical Engi- millimeter-scale holes of vertical walls in the ~ neering and Computing, Faculty of Chemical 1 μm thick silicon-oxynitride (SiON) thin film Engineering and Technology in Zagreb and deposited on a Si <111> wafer. At the same elsewhere. time, horizontal thermal gradient causes the formation of the nanoscale Marangoni con- PROJECTS AND PROGRAmS vection structures at the SiON/Si interface. The inhomogeneous pattern of the roll struc- Projects supported by the Ministry tures can be divided into domains of regular, of Science, Education and Sports irregular and chaotic organization. Numerical simulation of the Marangoni domain roll struc- 1. Synergy of nanophases and nanocompos- tures based on the simple Swift-Hohenberg ites, Aleksandra Turković equation has reproduced all observed types 2. Basic properties of nanostructures and de- of the roll organization, including those which fects in semiconductors and dielectrics, show the evolution of dislocations from the Branko Pivac 3. Doped optoelectronic and ceramic nanoma- Eckhause instability (Maksimović et al., 2008). terials, Biserka Gržeta 4. The thin film silicon alloys on the amorphous to crystalline transition, Davor Gracin 5. Thin Films of Novel Amorphous or Nano- structured Materials, Nikola Radić 6. Semiconductor materials for optoelectronics and nanotechnology, Branko Šantić 7. Physics and application of nanostructures and bulk matter, Krešimir Furić 8. Organizational processes and optical interactions in condensed molecular systems, Stjepan Lugomer

Program supported by the Ministry of Sciences, Education and Sports

1. Advanced materials and applications for energy conversion and storage, Branko Pivac

Research, developmental and international projects

1. Research of defects in Si and Ge induced by fast neutrons, Branko Pivac (Croatia-Slovenia) Figure 5. Domains of Marangoni regular, and chaotic 2. Quantum effects in vibrational states of roll structures: a) SEM micrograph of the regular do- nanocrystalline silicon, Davor Gracin (Croa- main; b) Fourier spectrum of regular domain in Fig.a.; tia-Slovenia) RBI Annual Report 2008. Annual Report 2008. RBI c) SEM micrograph of the chaotic domain; d) Fourier spectrum of chaotic domain in Fig.c. 3. Thin ZnO layer optimization in amorphous silicon PV cells, Davor Gracin, (Croatia- Macedonia)

28 4. Laser-induced surface self-organization: for- SELECTED INVITED LECTURES mation of surfaces with special properties, Stjepan Lugomer (Croatia-Hungary) 1. Armellini C, Biljanović P, Berneschi S, Bhak- 5. Ion beam modifications of SiC for electron- tha SNB, Boulard B, Chiappini A, Chiasera A, ic and optoelectronic applications, Branko Arfuso Duverger C, Feron P, Ferrari M, Huy ZFM Šantić (Croatia-Hungary) PT, Ivanda M, Jestin Y, Moser E, Nunzi Conti 6. Research on silicon and germanium nano- G, Pelli S, Righini GC, Speranza G. Optical structures, Branko Pivac, (COGITO - Bilateral properties and fabrication of glass-based collaboration with France) erbium activated micro-nano photonic struc- 7. LPMAS, Davor Gracin (EU- FP6 -INCO- Proj- tures. MIPRO 2008, Opatija, Croatia, 26-30 ect No FP6-509178) May 26-30, 2008. 8. The origin of structural defects and their ef- 2. Ivanda M, Ristić D, Furić K, Musić S, Ristić M, fects upon the properties of silicate glass, Gotić M, Štefanić G, Crnjak Orel Z, Bitenc M, Davor Gracin, (National Science Foundation Montagna M, Ferrari M, Chisaera A, Jestin Y. of Croatia) Low-Frequency Raman Scattering in Materials Research, EUCMOS 2008 - XXIX European SELECTED ORGANIZED Congress on Molecular Spectroscopy, Opatija, CONFERENCES Croatia, August 31 – September 5, 2008.

SELECTED PUBLICATIONS

1. Su DS, Xiaowei C, Xi L, Delgado JJ, Schloegl R, Gajović A. Mount-Etna-Lava-Supported Nanocarbons for Oxidative Dehydrogenation Reactions. Adv Mater 2008: 20: 3597. 2. Kukovec BM, Vaz PD, Popović Z, Calhorda MJ, Furić K, Pavlović G, Rajić Linarić M. Pseudopolymorphism in nickel(II) complexes with 6-methylpicolinate. Synthesis, structural, spectroscopic, thermal and density functional theory studies. Cryst Growth Des 2008: 8 : 3465. 3. Kuitunen K, Tuomisto F, Slotte J, Capan I. Divacancy clustering in neutron-irradiated and annealed n-type germanium. Phys Rev B 2008: 78 : 033202. 4. Žonja S, Očko M, Ivanda M, Biljanović P. Low temperature resistivity of heavily boron doped LPVCD polysilicon thin films. J Phys Organizatori:

Hrvatsko vakuumsko društvo & Društvo za vakuumsko tehniko Slovenije D: Appl Phys 2008: 41: 162002. RBI Annual Report 2008. www.cro-vacuum.hr/15HS2008.html 5. Buljan M, Bogdanović Radović I, Jakšić M, Programski odbor: Organizacijski odbor: Desnica UV, Ivanda M, Saguy C, Kalish R, M. Jakšić M. Godec N. Radić B. Šetina B. Pivac D. Resnik H. Zorc S. Žižek Djerdj I, Tonejc A, Gamulin O. Implantation P. Pervan M. Čekada M. Pavlović A. Vesel Design by IC & NR S. Milošević M.Mozetič T. Car J. Kovač conditions for diamond nanocrystals forma- Autor fotografije: Ivo Pervan Ljubaznošću Hrvatske turističke zajednice tion in amorphous silica. J Appl Phys 2008: 104: 034315. The 15th International Meeting "Vacuum Sci- 6. Lugomer S, Geretovszky Z, Szorenyi T. La- ence and Technique", Varaždin, June 4, 2008, was ser generation of regular wavy patterns by organized by the Division members N. Radić, B. nonlinear instability of a metal nanolayer. J Pivac, I. Capan and T. Car on behalf of the Croa- Appl Phys 2008: 104: 054911. tian Vacuum Society. The attendance was 60 par- 7. Ristić D, Ivanda M, Furić K, Desnica UV, Bul- ticipants, and the Book of Abstracts was published. jan M, Montagna M, Ferrari M, Chiasera A,

29 Jestin Y. Raman scattering on quadrupolar CHAPTERS IN BOOkS: vibrational modes of spherical nanoparticles. J Appl Phys 2008: 104: 073519. 1. Turković A. SAXS Characterization of 8. Maksimović A, Lugomer S, Geretovszky Z, Mesoporous Thin Films: A Solar Energy Point Szorenyi T. Laser-Induced Convection Nano- of View, Chapter 11, Solar energy: Research, structures on SiON/Si Interface. J Appl Phys Technology and Applications. Nova Science 2008: 104: 124905. Publishers, Ed. William L. Olofsson and V.I. Bengtsson, 2008, pp 1-29. RBI Annual Report 2008. Annual Report 2008. RBI

30 OVERVIEW OFTHEDIVISION However, theanalysisofspectrophotometric for analysis of the refractive index of a mixture. fective mediumtheorieswas successfullyused Optical thinfilms TOP ACHIEVEmENTS processing. processing. signal andnanoclusters blind and semi-blind of metallic research plasmonic on properties theories, medium effective using mixtures eral strategic projects: modelling of thin films fields of medicine and national security. ofapplication thesebasic disciplines in the this,Besides are activities directed to the films. thin optical of fundamentals the and photonics optics, non-imaging and imaging of field the in knowledge the strengthen and consists ofthefollowinglaboratories: of Laserand The Division Atomic R&D Head: HrvojeZorc DIVISIONAL ORGANIZATION Research andDevelopment Division ofLaserand Atomic The modelling of thin film mixtures using ef sev on is currentlyworking Division The expand to is Division the of mission The a a

Eduard Švegel workshops, Multipurpose (deceased) Films, MladenPavlović for Optics and Laboratory Thin - - These films show unique optical properties optical unique show films These of noblemetals. evaporation controlled by a glasssubstratethatcan beproduced of nanometric metalclusters deposited on ensemble consists ofatwo-dimensional films of kind This films. island metal of ties started, focused onthe plasmonic proper reported (Janickietal.,2008). been has index) refractive of variation depth in- with filters (rugate coatings complex novel behaviour of mixtures. The characterization of native methodologytopredicttheabsorption tion coefficient has been proposed as an alter absorp the defining parameters the of ence of thecompositionaldepend rameterization theory (Sancho-Parramon et al., 2008a). A pa on thebasisofspectraldensityfunction weak absorptionranges,hasbeendeveloped in theories, these of failure the explains that framework, theoretical A 2008). Janicki, and (Sancho-Parramon coefficient absorption the such theoriesfailtodescribethevariationof that shown has mixtures niobia-silica of data A new research line in thin films has been http://www.irb.hr/en/str/lair - - - - -

31 2008. Report Annual RBI LAIR Signal processing

The research activities have been focused on the area of blind and semi-blind signal

LAIR processing: model-free blind deconvolution of temporally/spatially correlated signals, non- negative matrix factorization and sparse component analysis. Applications of the above mentioned blind signal processing methods were related to multispectral image decomposition, blind image deconvolution, compressed sensing, NMR and FT-IR spectroscopy.

Figure 1. Tuning of optical properties of metal island films deposited on glass substrates by modification of deposition parameters. EDUCATION because of the surface plasmon resonance Members of the Division teach three of electrons of isolated metal clusters. By courses at the Faculty of Electrical Engineer- varying the deposition conditions, such as ing, University of Osijek, and in the Polytech- deposited thickness, substrate tempera- nic College in Velika Gorica. ture or deposition rate, the structural and geometrical properties of the clusters can PATENTS be widely varied, enabling a broad tuning of optical properties of the films (Figure 1). 1. Kopriva I, Method for real time tumor visu- Structural and optical characterization of the alisation and demarcation by means of pho- films have been carried out using different todynamic diagnosis, WO 2008/132522 A1. techniques (AFM, GISAXS, ellipsometry) in 2. Szu H, Buss J, Kopriva I, Nonlinear blind the framework of international cooperation. demixing of single pixel underlying radiation A novel method for the dissolution of metal sources and digital spectrum local thermom- eter, US Patent 7,366,564, April 29, 2008. islands has been proposed, consisting of the 3. Kopriva I, Jerić I, Smrečki V, Method of and application of electric field and temperature system for blind extraction of more than two (Sancho-Parramon et al., 2008b). pure components out of spectroscopic or spectrometric measurements of only two mixtures by means of sparse component analysis, PCT /HR2008/000037. 4. Peršin A, Zorc H, Tisaj K, Stanišić V, Agatić N., Radman A, Soldo Roudnicky D, Lončarić M, Intelligent sequential device for photody- namic therapy, Patent P20060149

NEW EqUIPmENT

1. Digital Lock-in amplifier - Stanford research systems – SR 850. 2. Furnace - Lindberg/Bluem BS 51700 RBI Annual Report 2008. Annual Report 2008. RBI

Figure 2. Nanoclusters of silver produced under various conditions.

32 PROJECTS 2. Sancho-Parramon J, Janicki V, Zorc H. Com- positional dependence of absorption coefficient Projects supported by the Ministry and band-gap for Nb2O5-SiO2 mixture thin films. Thin Solid Films 2008a: 16: 5478. of Sciences, Education and Sports 3. Janicki V, Sancho-Parramon J, Zorc H. Refrac- tive index profile modelling of dielectric inhomo- LAIR 1. Analysis of multispectral data, Ivica Kopriva. geneous coatings using effective medium theo- 2. Optical properties of nanostructured layers, ries. Thin Solid Films 2008: 10: 3368. Hrvoje Zorc. 4. Sancho-Parramon J, Janicki V, Arbiol J, Zorc H, Peiro F. Electric field assisted dissolution of Research, developmental and metal clusters in metal island films for photon- international projects ic heterostructures. Appl Phys Lett 2008b: 16: 163108. 1. Optical properties of metal nanoparticles em- 5. Kopriva I, Seršić D. Wavelet Packets Approach bedded in dielectric multilayers, Hrvoje Zorc to Blind Separation of Statistically Dependent (International collaboration between RBI and Sources, Neurocomputing, 2008: 71: 1642. Institute of Nanostructured Materials and Pho- 6. Du Q, Kopriva I. Automated Target Detection tonics, Weiz, Austria) and Discrimination Using Constrained Kurtosis Maximization, IEEE Geoscience Remote Sens- SELECTED INVITED LECTURES ing Let 2008: 1: 38. 7. Du Q, Kopriva I. Dependent component analy- 1. Kopriva I. Blind separation of signal sources, sis for blind restoration of images degraded by Polytechnic of Turin, Laboratory for Engineering turbulent atmosphere, Neurocomputing, 2008: of the Neuromuscular Systems, May 21, 2008. 10: 1016. 8. Wasylkiwskyj W, Kopriva I. Second and Fourth SELECTED PUBLICATIONS Order Statistics - Based Reduced Polynomial Rooting Direction Finding Algorithms, Signal 1. Sancho-Parramon J, Janicki V. Effective me- Processing 2008: 10: 1016. dium theories for composite optical materials in spectral ranges of weak absorption: the case of Nb2O5-SiO2 mixtures. J Phys D: Appl Phys 2008: 21: 215304. RBI Annual Report 2008.

33 3434 RBI Annual Report 2008. OVERVIEW OFTHEDIVISION gramme “Computational knowledgediscov- for theresearch pro- nized a2dayworkshop 2008-2011.orga- Members oftheDivision ences, EducationandSports, for the period gy”, financed by the Croatian Ministry of Sci- of predictive modelsin computational biolo- research projectentitled“Machinelearning orations inmultidisciplinaryprojects. record oftheDivision’s members,andcollab publication the in reflected best is orientation ment techniques. The strong multi-disciplinary well asindevelopmentofadvancedmeasure computational biologyandbioinformatics,as biomedicine, in techniques these of plications formation systems,andvarietyoftailoredap in for representations knowledge techniques, of novelintelligentdataandsignalanalysis sion compriseresearchanddevelopment

DIVISIONAL ORGANIZATION Division ofElectronics In 2008, the Division was grantedanew theDivision In 2008, The maintopicsofresearchintheDivi aGroupforcomputationalbiologyand a a andonegroup: laboratories The Divisionofelectronicsconsiststwo Head: TomislavŠmuc

Branka MedvedRogina research, and processes for stochastic signals Laboratory Dragan Gamberger for information systems, Laboratory bioinformatics, TomislavŠmuc - - - - - PA R) ealn rlal determination reliable enabling RF), (PCA, techniques learning machine using essed a largernumberofmeasurements isproc- The methodinvolvesseveral stepsinwhich Department of Biology, Faculty of Science. from the tion withthegroupofKrsnik-Rasol collabora in developed been has phoresis), electro- gel or capillary instance mix- (for tures biomolecular of separations graphic from chromato- to measurementsderived signals Filtering proteomic TOP ACHIEVEmENTS ligence attheFacultyofScience. intel- artificial on course graduate a with ed the higher education curriculum was extend- with industry. The Division’sto contribution projects as R&D projects, aswell bilateral and HEARTFAID) project FP6 (EU tilateral mul- of international works ona number sion Divi- the that, Besides irb.hr/KDSA2008/). (http://lis. partners industrial and Zagreb of ers fromdifferent faculties oftheUniversity of research a number including the Division, 5 relatedresearchprojects,3ofthemwithin ery in scientific applications” comprised from Amethod, applied computational new http://www.irb.hr/en/str/zel - -

3535 2008. Report Annual RBI ZEL of relevant fractions for the particular dis- Finite-state data representation crimination problem, and improving compu- algorithms tational models for class distinction based on a filtered set of relevant fractions (Figure 1). An efficient method for the implemen- ZEL tation of a sub-sequential transducer has knowledge representation and been developed. A transducer is a finite reasoning for healthcare state automaton that, on every input sequence symbol, produces a specific output The R&D efforts within the HEARTFAID symbol during transition from state to state. project (EU6FP ICT-STREP) included the If the whole output sequence is associated coupling of Bayesian network reasoning to with the final state, the transducer is called the already developed ontology-based rea- sub-sequential. Our implementation is the soner. This extension significantly enhances most efficient one regarding space require- decision support capabilities of the system, ments while preserving high speed inherent providing reasoning in situations in which to automata structures. The applications for some information is missing. Besides this transducers are numerous and vary from work, extensive analyses of the proprietary natural language processing and human follow-up study database has been done in machine interface, to machine learning and order to form new models for the prognosis data mining. of elderly patients suffering from heart failure syndrome. Biomedical applications

Figure 2. Scaling exponents for human gait data.

Two applications in our current research focus are related to the human walk and human jaw movement. The first method com- prises the extraction of dynamic features of the human walk and the embedding of related time series data in high pseudo phase space. Subsequent projection of the embed-

RBI Annual Report 2008. Annual Report 2008. RBI Figure 1. Extraction of most informative gel windows using novel ded vectors on principal axes and/or on the computational method, from SDS PAGE measurements. main diagonal of embedding space enables extraction of fractal features from the data

36 AWARDS EDUCATION a deviceatspecific(high)clockfrequencies predict themetastability-inducedfailurerateof devices. Usingthesemethodsitispossibleto ters formetastabilityperformanceofbistable have been determinedascharacteristicparame (W) window metastability of width the (t tau constant time resolution The ers. new familiesofseveralleadingmanufactur were demonstratedonFPGA devicesfrom for evaluationofmetastabilitycharacteristics, ods, basedonincreasedpropagationdelay has beenproposed. Three different meth logic devicesinindustrialembeddedsystems, metastability characteristicsofprogrammable including different methods forevaluationof parameters, timing of verification for system systemdesign embedded FPGAbased of reliability of Methods for theassessment future studies. for necessary profiles standard the provides disorders symptoms oftemporomandibular cluding healthysubjectswithout any signsor University ofZagreb,astudyin- Medicine, with theSchool ofDental In collaboration andvelocityaremeasured. jaw acceleration vertical averaged of profiles accelerometric wherein sensor acceleration MEMS wireless is based on the measurements using tri-axial of Zagreb. University application The second with theFacultyforKinesiology,laboration col- our of part is research This 2). (Figure sciences. biotechnical in bioinformatics of field the in State Award for interdisciplinaryresearch at variousfacultiesoftheUniversityZagreb. A high-resolutionautomatedmeasurement Fran Supekwasawarded The Croatian The Divisionprovidesannually5courses ) and and ) . - - - . 1. and Sports Sciences,Education of Ministry bythe supported Programs 4. 3. 2. 1. Sciences,Education andSports of bytheMinistry supported Projects PROJECTS 3. 2. 1. SELECTED PUBLICATIONS 4. 3. 2. 1. projects international Research, developmental and entific applications,DraganGamberger discovery insci- knowledge Computational Computational Biology, Tomislav Šmuc of Machine Learning PredictiveModelsin ization, BrankaMedvedRogina Real LifeDataMeasurementandCharacter surement Systems,IvanMarić Methods inMea- Intelligence Computational cation, DraganGamberger their Appli- and Algorithms Learning Machine Šmuc T, Krizmanić I, Žinić B: Atypical cyto- Atypical B: Žinić I, Krizmanić T,Šmuc L, Šuman M, Marjanović, M, F,Kralj, Supek Inform ProcessManag2008: 44:325. cation onaCroatian-English ParallelCorpus. Offset:Morphology Language B: TextClassifi Malenica, M, Šmuc T, Šnajder J, Dalbelo Bašić teomics 2008:8:28. using machine learningalgorithms.Pro- T:power ofSDS-PAGEanalytical Enhanced F,Supek PeharecP,M, Šmuc Krsnik-Rasol Institute forElectricalEngineering) Medved Rogina (R&D project with the Končar embeddedsystems, in industrial Branka devices logic of programmable Reliability bilateral project) teomics, Tomislav Šmuc (Croatian-Slovenian Inductive Databasesfor Genomics andPro- (Croatian-Slovenian bilateralproject) Intelligent Data Analysis, DraganGamberger (EUFP6, ICT-STREP Gamberger project) Dragan population, elderly of heartfailurewithin management medical-clinical of servicesforsupporting HEARTFAID – Aplatform based knowledge - -

37 2008. Report Annual RBI ZEL static mechanism of N-1-sulfonylcytosine 4. Čož-Rakovac R, Šmuc T, Topić Popović N, derivatives determined by in vitro screen- Strunjak-Perović I, Hacmanjek M, Jadan M: ing and computational analysis. Invest New Novel methods for assesing fish blood bio- Drug 2008: 26: 97. chemical data. J Appl Ichthyol 2008: 24: 77. ZEL RBI Annual Report 2008. Annual Report 2008. RBI

38 OVERVIEW OFTHEDIVISION ternational collaborations demonstrates the ternational collaborations laborations. The largenumberoffruitfulin- col- contribu- international within realized those were tions of half Almost B. Review and Physical Journal hysChem, Biophysics & B,Physics,ChemP- Journal ofChemical Chemistry, JournalofPhysical Chemistry A try,Chemistry, Inorganic of Organic Journal ranking journalssuchas: Analytical Chemis highest the in published was part significant and chemicalanalyses,inbiosciences. A physical andchemicalprocesses,structural chemistry,chemistry, theoretical of modelling ic chemistry, chemical kinetics,structural inatmospher- lished nearly50contributions Head: Aleksandar Sabljić DIVISIONAL ORGANIZATION Division ofPhysicalChemistry In 2008, members of the Division pub- of theDivision In 2008,members a a a a a a

Ivan Habuš Laboratory for Analytical Chemistry, Boris Rakvin Laboratory forMagneticResonances, Marija Luić Crystallography,Biological and ofChemical Laboratory Tomislav Živković Theoretical ChemistryGroup, Nada Filipović-Vinceković ofRadiochemistry,Laboratory Branka Kovač Chemistry,and Atmospheric forChemicalKinetics Laboratory - Workshop) in2008. saga (nATOuniversal Research Advanced may assist in protonation and deprotonation may assistinprotonation anddeprotonation molecules water hydrogen-bonded the that site, was formed in all simulations suggesting binding ABP1 the in ligand zinc-coordinated the to water bulk the from leading molecules, water hydrogen-bonded of network A ecule. is stabilisedbythebindingofanauxinmol the positionofC-terminus,andonethem adopt two conformations, differing primarily in can ABP1 that showed simulations namics molecular modellingstudy. Moleculardy detailed a out carried we ABP1, of function In order tounderstandtheproposedreceptor affinity. and specificity high with mones) tous ingreenplants,bindsauxins(planthor with auxinbindingprotein auxininteraction Mechanism of TOP ACHIVEMENTS 11 conference international traditional ganized courses). Finally,or- members theDivision and graduateeducationinCroatia(about40 toundergraduate also contributeextensively ropean Research Area. Division members oftheDivisioninEu- strong presence th Auxin BindingProtein1(ABP1),ubiqui BRIJunI COnFEREnCE-Hydrogen: A http://www.irb.hr/en/str/zfk - - - -

39 2008. Report Annual RBI ZFK of auxin molecules and their egress from the ABP1 binding site. Simulations of the ligand egress from ABP1 revealed three main routes

ZFK by which an auxin molecule can enter or leave the ABP1 binding site (Bertoša et al., 2008). An illustration describing these results (Figure 1) appeared on the front cover of volume 94, issue 1 of Biophysical Journal. 8

Enhanced resolution for protein hydrogen/deuterium exchange

Solution-phase hydrogen/deuterium exchange, monitored by mass spectrometry, is

Biophysical a rapid method to study protein conforma- Journal Biophysical Journal tions and protein-protein interactions. Diges- tion efficiency for several proteins was opti- January 1, 2008 • Volume 94 • Number 1 Januar

y 1, 2008 – mized with pepsin and protease type XIII. The P ages 1–332 ages

Vol.No.1 94 protease type XIII produces more fragments BioFAST BJ articles online of shorter length and increases the signal to BJ Online: http://www.biophysj.org upon acceptance www.biophysj.org Online Manuscript Submission: http://submit.biophysj.org noise ratio, thus enhancing the sequence coverage for deuterium uptake and spatial Figure 1. The front cover of Biophysical Journal (volume 94, resolution. H/D exchange for myoglobin with issue 1) describing possible pathways used by auxin-related protease type XIII and pepsin confirms the molecules to enter/exit their binding site in ABP1 protein (Bertoša et al., 2008). 3-D solution structure of myoglobin by ac- curately locating fast- and slow-exchanging amide hydrogens in the loops and a-helices (Zhang et al., 2008). RBI Annual Report 2008. Annual Report 2008. RBI Figure 2. Exchange rates for increased sequence resolution for myoglobin segment 69-93. Amide hydrogens from the loop region 78-85 are shown in red. From the exchange rates of 11 overlapping fragments, the number of fast-, medium- and slow-exchanging hydrogens was assigned.

40 Electron-spin relaxation for two Lipase-catalysed secondary solid ethanol phases in the boson- alcohol esterification peak temperature region

The approach offers the unique possibility ZFK to switch from one state of molecular packing to another within the same ethanol sample in the course of an EPR experiment. The incor- porated spin probe bears information on the local dynamics and structural constraints of the glassy and crystalline environment (Kve- der et al., 2008).

Double cyclopalladated complexes of azobenzenes

Figure 4. Comparison of binding modes of E1 ester in crystal (in red rectangular) and the one found by molecular modelling.

As a continuation of our study of the en- antioselectivity towards secondary alcohols of Burkholderia cepacia lipase (BCL), we accomplished theoretical, MM, MC and QM/MM studies of R- and S-1-phenoxy-2-hydroxy- butane-BCL complexes and determined the crystal structure of BCL complexed with a Figure 3. The solvent ligands (dmso, dmf, py) exchange routes phosphonate analogue of its S-ester. The cal- and cis/trans isomerization in the double cyclopalladated complexes of azobenzenes. culations showed that the reaction is not fea- sible from the crystallographically determined Since doubly cyclopalladated complexes binding mode, but proceeds smoothly from of azobenzenes have two metalated phenyl the modelled binding mode (Luić et al., 2008). rings, they are promising candidates for much wider application in organic synthesis, cataly- AWARDS AND RECOGNITION sis and photochemistry than their singly cy-

clopalladated analogues. We have prepared The 2008 award for young scientists and RBI Annual Report 2008. and characterized a new set of doubly cyclo- artists in the field of biology from the Society palladated azobenzenes. Their crystal struc- of university Teachers, Scholars and Other tures have been resolved and for the first time Scientists – Zagreb was presented to Brani- it was demonstrated that the cyclopalladation mir Bertoša. may take place at an azobenzene aromatic ring with a strong electron withdrawing sub- EDUCATIONAL ACTIVITIES stituent at the para position. The experimental results, complemented by a theoretical study, The Division provided 21 undergraduate explained cis/trans isomerism in isolated and 18 graduate courses at universities in complexes, their aromaticity and the nature of Zagreb, Split, Rijeka, Osijek and Dubrovnik. the electronic transitions (Babić et al., 2008).

41 PROJECTS sation of the novel SGnH-hydrolase family from Streptomyces and mapping of Fusani- Projects supported by the Ministry um parasites, I. Leščić Ašler (Bilateral project of Sciences, Education and Sport with Austria)

ZFK 3. Theoretical study of the reactivity of metallo 1. Molecular structure and dynamics of systems centres in proteins, S. Tomić (Bilateral proj- with paramagnetic particles, Boris Rakvin ect with Austria) 2. Surfactants, processes in solutions and at in- 4. Combined experimental and theoretical terfaces, Nada Filipović-Vinceković study of structure and dynamics of hydrogen 3. Measurement and effect of atmospheric oxi- bonded systems, Nađa Došlić (Bilateral proj- dants, Leo Klasinc ect with France, Program "COGITO") 4. Advanced studies on chemical reactivity, 5. Applications of advanced Pulsed EPR tech- Aleksandar Sabljić niques in the research of new fullerene-based 5. Developing methods for modelling properties materials: Structural properties of Li4C60, B. of bioactive molecules and proteins, nenad Rakvin (Bilateral project with Slovenia) Trinajstić 6. Computer simulations of structure and dy- 6. Design, synthesis and properties of organic namics of proteins, S. Tomić, (Bilateral proj- ligands and their metal complexes, Ljerka ect with Slovenia) Tušek-Božić 7. “Investigations of calcium phosphate based 7. Protein-ligand interactions at atomic level, biomaterials”, FP6 Specific Support Action Marija Luić “Creating international cooperation teams of 8. Spectroscopy, chemical properties and reac- excellence in the field of emerging biomate- tions of biologically active molecules, Branka rial surface research”, Maja Dutour Sikirić Kovač 8. COST physics P-15 action “Advanced Para- 9. Control of atomic and molecular dynamics by magnetic Resonance Methods in Molecular shaped electromagnetic fields, Nađa Došlić Biophysics”, Boris Rakvin 10. Computational study of bio-macromolecules and development of new algorithms, Sanja SELECTED INVITED LECTURES Tomić 11. Development of mathematical methods for 1. Rakvin B. Dynamic properties of the stable the description of molecular structure, dynam- paramagnetic centres in the L-alanine crys- ics and reactivity, Tomislav Živković tal lattice. 6th Asia Pacific EPR/ESR Sympo- 12. Amino-beta-lactams-synthrons for biologically sium, Cairns, Australia, June 13-17, 2008. interesting compounds, Ivan Habuš 2. Živković T. A new mathematical approach for the treatment of the vibrational isotope effect. Programs supported by the 6th Congress of the International Society for Ministry of Sciences, Education Theoretical Chemical Physics, Vancouver, and Sports Canada, July 18-27, 2008. 3. Došlić N. Multidimensional quantum dynam- 1. Molecular structure, dynamics and reactivity, ics of large amplitude motion. XXIX Euro- Boris Rakvin pean Congress on Molecular Spectroscopy 2. Spectroscopy and modelling of bioactive (EuCMOS-08), Opatija, August 31 – Sep- molecules, Ante Graovac tember 05, 2008.

Research, developmental and inter- SELECTED ORGANIZED national projects CONFERENCES

th 1. Chemical applications of advanced ESR- 1. 11 BRIJunI COnFEREnCE - Hydrogen: A techniques, B. Rakvin (Bilateral project with universal saga (nATO Advanced Research

RBI Annual Report 2008. Annual Report 2008. RBI Austria) Workshop), Brijuni, 25 -29 August 2008. 2. Application of MALDI mass spectrometry in protein and intact cell analysis: characteri-

42 SELECTED PUbLICATIONS 6. Cambré S, Wenseleers W, Čulin J, Van Door- slaer S, Fonseca A, nagy JB, Goovaerts E: Review articles Characterisation of nanohybrids of porphy- rins with metallic and semiconducting carbon 1. Kralj M, Tušek-Božić Lj. Frkanec L: Biomedi- nanotubes by electron paramagnetic reso- ZFK cal potentials of crown ethers: Prospective nance and optical spectroscopy. ChemPhy- antitumor agents. ChemMedChem 2008: 3: sChem 2008: 9: 1930. 1478. 7. Kveder M, Merunka D, Jokić M, Rakvin B: Electron-spin relaxation in crystalline and Research articles glassy state of solid ethanol in the boson- peak temperature region. Phys Rev B 2008: 1. Zhang H, Kazazić S, Schaub T, Tipton J, 77: 094202. Emmett M, Marshall A: Enhanced digestion 8. Matanović I, Došlić N, Johnson B: General- efficiency, peptide ionization efficiency, and ized approximation to the reaction path: the sequence resolution for protein hydrogen/ formic acid dimer case. J Chem Phys 2008: deuterium exchange monitored by FT-ICR 128: 084103-1-084103-10. mass spectrometry. Anal Chem 2008: 80: 9. Makong O, Flyunt R, Tobien T, naumov S, 9034. Bonifačić M: Dimethylselenide as a probe for 2. Babić D, Ćurić M, Molčanov K, Ilc G, Plavec reactions of halogenated alkoxyl radicals in J: Synthesis and characterization of dicyclo- aqueous solution. Degradation of dichloro- palladated complexes of azobenzene de- and dibromomethane. J Phys Chem A 2008: rivatives by experimental and computational 112: 5916. methods. Inorg Chem 2008: 47: 10446. 10. Friščić T, Klasinc L, Kovač B, MacGillivray 3. Luić M, Štefanić Z, Ceilinger I, Hodošček M, L: HeI photoelectron spectra and gas-phase Janežić D, Lenac T, Leščić Ašler I, Šepac D, electronic structures of end-functionalized Tomić S: Combined X-Ray Diffraction and [3]- and [5]-ladderanes. J Phys Chem A QM/MM Study of the Burkholderia cepacia 2008:112: 1493. Lipase-Catalyzed Secondary Alcohol Esteri- 11. Novak I, Kovač B: Electronic structure of fication. J Phys Chem B 2008: 112: 4876. substituted benzoquinones and quinonechlo- 4. Bertoša B, Kojić-Prodić B, Wade R, Tomić S: roimides. J Phys Chem A 2008: 112: 3061. Mechanism of Auxin Interaction with Auxin 12. Alberti A, Galasso V, Kovač B, Modelli A, Pi- Binding Protein (ABP1): A Molecular Dynam- chierri A: Probing the molecular and electronics Simulation Study. Biophys J 2008: 94: 27. ic structure of capsaicin: A spectroscopic and 5. Vujasinović I, Veljković J, Molčanov K, Kojić- quantum mechanical study. J Phys Chem A Prodić B, Mlinarić-Majerski K: Thiamacrocy- 2008: 112: 5700. clic lactones: New Ag(I)-ionophores. J Org 13. Galasso V, Kovač B, Modelli A, Ottaviani MF, Chem 2008: 73: 9221. Pichierri F: Spectroscopic and theoretical study of the electronic structure of curcumin and related fragment molecules. J Phys Chem A 2008: 112: 2331. RBI Annual Report 2008.

43 44 RBI Annual Report 2008. OVERVIEW OFTHEDIVISION of topics such assyntheticandphysicalor- range in abroad important discoveries eral sev- were There chemistry. bioorganic and organic of fields the in research basic the to devoted was effort work the of majority The maintained inthe Division throughout 2008. following laboratories: Biochemistry (ZOKB)consistsofthe and of OrganicChemistry The Division June, till Kata Majerski Eckert-Maksić Mirjana Head: DIVISIONAL ORGANIZATION and Biochemistry Division ofOrganicChemistry The excellence in scientific research was research scientific in excellence The a a a a a a a a formolecularspectros- Laboratory forsupramolecularand Laboratory

chemistry, David Smith chemistry, David Group forquantumorganic copy, GoranBaranović chemistry, MirjanaEckert-Maksić for physical organic Laboratory Marija Abramić nucleoside chemistry,nucleoside MladenŽinić chemistry, KataMajerski for synthetic organic Laboratory Zdenko Hameršak catalysis andbiocatalysis, for stereoselective Laboratory Štefica Horvat tide andglycopeptidechemistry, Laboratory forcarbohydrate,pep- Laboratory forcellularbiochemistry,

members ofseveraleditorial boards. and bodiesserveas theeditorsor active innationalandinternational societies M.Sc. (1) and Ph.D. (2) thesis. They arealso doctoral levelandbysupervising B. Sc. (6) education to higher and courses atundergraduate by providing contributions nificant tion, 5patentapplicationsweresubmitted. In addi- chemicaljournals. in highranking mostly appeared which papers, scientific 59 enzymology, and quantumorganicchemistry. molecular and biochemistry py; experimental andcomputationalprotein and peptidomimetics;molecularspectrosco- glycopeptides of peptides, RnA, chemistry DNA/ with molecules small of interactions gels, andhost-guestinteractions; including and catalysis; supramolecular chemistry, ganic chemistry; stereoselective synthesis Members of the Division have madesig- Members oftheDivision in published are work the of results The http://www.irb.hr/en/str/zokb

45 2008. Report Annual RBI ZOKB TOP ACHIEVEMENTS Interactions of novel benzimidazole derivatives with DNA/RNA and The first structure of dipeptidyl biological activity peptidase III ZOKB

Figure 2. General structures of studied benzimidazole derivatives. Detailed studies of the interactions between novel “non-fused” benzimidazole derivatives (Figure 2A) and their “fused” analogues (Figure 2B) with natural and synthetic double stranded DnA and RnA unambiguously revealed that the “non-fused” derivatives (A) bind into DnA minor groove, while their “fused” analogues Figure 1. Structure of the Saccharomyces cerevisiae DPP III (B) intercalate in both, DnA and RnA. Differ- enzyme. The catalytic zinc ion is shown in yellow. ent in vitro antitumor activity mechanisms of “non-fused” and “fused” derivatives were di- Dipeptidyl peptidase III (DPP III) is a rectly correlated to the DnA binding modes of zinc-dependent enzyme with an implied studied compounds (Hranjec et al., 2008) role in the pain-modulatory system and en- dogenous defence against oxidative stress Atypical cytostatic mechanism of in mammals. Two members of the DPP III N-1-sulfonylcytosine derivatives family were studied in parallel. For the human orthologue, a functional role of Tyr318 was predicted based on the mutagenesis approach, which resulted in a publication in Biological Chemistry. Yeast DPP III was cloned, heterologously expressed and the 1.95-Å crystal structure was resolved, representing the prototype for the whole family (Figure 1). It shows a novel protein fold and provides insight into the catalytic mechanism and mode of substrate binding. The yeast enzyme shows a high degree of conservation to mammalian DPP III in the active site and thus provides the basis for rational drug design (Baral et al., 2008). Figure 3. A self-organizing map constructed using i2SOM soft- The latter article was selected as a Pa- ware contains 537 compounds belonging to one of 12 mechanis- per of the Week in the Journal of Biological tic classes plus the two BZ compounds.

RBI Annual Report 2008. Annual Report 2008. RBI Chemistry (JBC) and was also included in a cumulative collection of JBC Papers of N-1-Sulfonylpyrimidine derivatives have the Week. strong antiproliferative activity, whereby 1-(p-

46 toluenesulfonyl)cytosine, BZ-1 showed a se- tuted oxazolidinones in high yields and with lective effect to normal cells. Supervised ma- high enantiopurity (69-98% ee). This is the chine learning methodology (Random Forest first example of the biocatalytic conversion classifier) was used for analysis of cytostatic of a range of epoxides to the corresponding activity profiles (Figure 3). The computa- oxazolidinones (Majerić Elenkov et al., 2008).

tional results, taken together with cell cycle ZOKB perturbation and apoptosis analysis, point Hydrogen bonding in 1,1′-bi-2- to an unusual mechanism of cytostatic ac- naphthol within the polarizable tion, possibly a combination of nucleic acid continuum model antimetabolite activity and a novel molecular mechanism (Supek et al., 2008). The intra- and intermolecular hydrogen bonding of 1,1′-bi-2-naphthol in a series of Domino photochemistry of N-(1- solvents and in the solid phase has been adamantyl)phthalimide investigated by means of mid-IR spectroscopy and DFT reaction-field calculations. The photochemical reaction of N-(1- The results show that the relative stability adamantyl)phthalimide (Figure 4) yields of isomers, differing in the positions of the the novel hexacyclic benzazepine deriva- hydroxyl groups, are the same in hydrogen- tive of 2,4-methanoadamantane (2), as a bond non-accepting solvents and the gas clean single product. Its structure, char- phase, although the less stable isomers are acterized by X-ray analysis, represents more probable in solvents of higher relative the first example of the 2-azahexacy- permittivity. In hydrogen-bond forming sol- clo[8.7.1.11,4.04,9.011,16.012,18]nonadeca- vents, the least stable isomer is most prob- 4,6,8-triene skeleton. The product is formed ably prevalent due to the additional stabiliza- by a domino process of two consecutive ex- tion through intermolecular hydrogen bonds cited state intramolecular hydrogen transfer with solvent molecules. A detailed vibrational reactions. Base hydrolysis of the benzaz- analysis revealed the spectral regions spe- epine (2) gives the keto derivative of the cific to the OH vibrations with the observed 1,2-substituted adamantane ε-amino acid solvent effects concerning the redistribution (3) in high yield (Basarić et al., 2008). of vibrational intensities rather than wave- number shifts (Biliškov et al., 2008). Epoxides to chiral oxazolidinones Surface-enhanced Raman Halohydrin dehalogenase from Agrobac- scattering on colloid gels terium radiobacter catalyzed the enantiose- lective ring opening of terminal epoxides with Surface-enhanced Raman scattering (SERS) has been applied to study weak in- cyanate as a nucleophile, yielding 5-substi- RBI Annual Report 2008.

Figure 4. Domino photochemistry of 1.

47 termolecular interactions between small or- complexes Ag13 and Ag(13)2 (Figure 6) sug- ganic gelling molecules involved in the silver gest that preferred ambidentate tetracoordina- and gold nanoparticle-hydrogel composite tion of Ag+ ions is favourable for the molecules formation. Strong Raman signals dominate with flexible rings (Vujasinović et al., 2008). in SERS spectra of hydrogels containing Successful characterization of ZOKB silver nanoparticles prepared by the citrate and borohydride reduction methods, where- mixed-ligand Fe(II) complexes as broad bands of low intensity are detected in the spectra of gold colloid gels. Transmis- Formation of novel mixed-ligand iron sion electron microscopy reveals a dense complexes, containing 1,10-phenanthroline, gel structure in the close vicinity of the en- 1,10-phenanthroline-5,6-dione, and nCS- as hancing metal particles for both silver colloid ligands, were analyzed by electrospray ion- gels (Miljanić et al., 2008). ization ion trap MS/MS. Under the applied electrospray ionization mass spectrometry (ESI-MS) conditions, MeOH, water, and EtOH formed solvent clusters around the free or complexed 1,10-phenanthroline-5,6- dione. Owing to the solvent-ligand hydrogen- bond formation, the solvent-ligand clusters were formed in the polar protic solvents. The Figure 5. (a) TEM images of silver citrate colloid hydrogel of number of protic solvent molecules per com- bis(S-phenylalanine)oxalyl amide, magnification 25 000 x and plex ion in cluster depended on the number (b) its SERS spectrum. of 1,10-phenanthroline-5,6-dione ligands in the complex ion. Unlike MeOH, EtOH, or wa- New Ag(I)-ionophores ter, ACN was not involved in the formation of the solvent clusters with the iron complexes containing 1,10-phenanthroline-5,6-dione as ligand (Kobetić et al., 2008).

Guanidinium ions separated by para-phenylene spacer

Figure 6. Ball-and-stick representation of [4:2] silver complex with thialactone ligand Ag(13)2 determined by X-ray structure analysis.

New macrocyclic hosts, varying in size of Figure 7. Schematic presentation of the optimized structure of macrocyclic ring, the number of flexible or ad- double protonated para-bisguanidylbenzene dication. amantane moieties and the number of donor atoms, were prepared, and their complexing The stability and fragmentation mecha- ability toward transition and heavy metal cat- nism of the mono- and the doubly pro- ions (Ag+, Cu2+, Zn2+, Cd2+, Pb2+) was stud- tonated guanidinium ions, generated via

RBI Annual Report 2008. Annual Report 2008. RBI ied. In picrate extraction surveys, it was possi- electrospray ionization of para-bisguanidyl ble to show that most of the hosts studied are benzene and its permethylated derivatives, good Ag+ acceptors. The structural analysis of were investigated and rationalized using

48 DFT calculations. The obtained dications are the first examples of multiply charged cations of this type generated in the gas phase (Tintaru et al., 2008).

Reactivity and oxidative potential ZOKB of sugars in peptide-sugar model systems

Fructose is a sugar that participates in the formation of toxic advanced glycation products, which appear to play a role in the patho- Figure 8. Undecacyanofluoradene is the first neutral hyperacid genesis of the vascular, renal and ocular as predicted by computational chemistry. complications of diabetes. The reactivities of fructose and glucose in model systems con- Patent applications taining bioactive peptides (enkephalins) were compared. The obtained results indicate that Patent Application WO2008102127 (A3), glucose is more reactive than fructose, with Čaplar V, Frkanec L, Jokić M, Makarević K, respect to the formation of N-glycated pep- Portada T, Žinić M, Jelčić Ž. (Pliva Hrvatska tides. However, fructose has the higher oxida- d.o.o.), Gel forming compounds. tive potential to damage methionine residues Patent Application WO2008113992 (A3), in peptides (Jakas et al., 2008). Čaplar V, Frkanec L, Jokić M, Makarević K, Portada T, Žinić M, Jelčić Ž. (Pliva Hrvatska Novel chloroenyne-modified amino d.o.o.), Gel compositions. acid derivatives Patent Application WO2008/114067 (A1), Basarić N, Renić M, Mlinarić-Majerski K. naturally occurring enediyne com- Adamantane-dipyrromethane derivatives, pounds are among the most effective an- method of preparation and applications in ticancer agents known, and synthetically anion sensing. modified enediynes are lead chemothera- Patent number P2080102A, Landek G, peutics today. Three groups of chloroe- Kontrec D, Vinković V. New Chiral Station- nyne-modified amino acids carrying differ- ary Phases for Chromatography Based on ent protecting groups were synthesized. Aromatic Allyl Amines. The optimal conditions for the coupling of Patent number PCT/HR2008/000037, Ko- amino acid-derived acetylenes with alkenyl priva I, Jerić I, Smrečki V. Method of and sys- chlorides were described and elucidated tem for blind extraction of more than two pure

(Gredičak et al., 2008). components out of spectroscopic and spec- RBI Annual Report 2008. trometric measurements of only two mixtures Superacids: How far can one go? by means of sparse component analysis.

Computational studies of neutral organic New equipment superacids were continued and the most powerful hyperacid was designed by using The high-pressure liquid chromatogra- polycyanated extended molecular frame- phy-mass spectrometry (HPLC-MS) instru- work of Rees’ annulenes. The manuscript ment (Agilent Technologies) was purchased describing the results was published in the with the financial help of the Ministry of Sci- New Journal of Chemistry, where it was se- ences, Education and Sports of the Republic lected as a “hot article”. of Croatia.

49 The acquisition of a HPLC-MS-MS instru- molecules. Synthesis and reactivity, Zdenko ment will contribute to the achievement of Hameršak the scientific objectives in Division and open 5. Chemical transformations of natural com- possibilities for introducing new methods pounds, Štefica Horvat 6. Cage compounds: Building blocks for molecu- and scientific fields. lar architecture, Kata Majerski 7. Brønsted and Lewis acids and bases in chem- EDUCATION istry and biochemistry, Zvonimir Maksić 8. Host-guest interactions in policyclic systems, The Division provides annually over 27 Davor Margetić undergraduate and graduate courses at uni- 9. Design, synthesis and study of interactions of versities Zagreb, Osijek and Dubrovnik. small molecules with DNA, RNA and proteins, Ivo Piantanida AWARDS AND RECOGNITION 10. Computational studies of protein structure and function, David Smith David Smith: Leopold Ružička award for 11. Chiral organic materials - synthetic, structural young scientists of the Croatian Chemical and functional research, Vladimir Vinković 12. Synthesis of novel biologically active nucleo- Society. base and nucleotide derivatives, Biserka Žinić Ina nemet, Juvenile Diabetes Research 13. Supramolecular chemistry of gels. Self-as- Foundation Postdoctoral Fellowship Award, sembly approach to functional hybrid materi- “Novel Pathways of Glycation Damage in als, Mladen Žinić Diabetic Complications” (2008-2010). Borislav Kovačević: Postdoctoral Fellow- Programs supported by the Ministry ship from the national Foundation for Sci- of Sciences, Education and Sports ence, Higher Education and Technological Development of the Republic of Croatia: 1. Design, synthesis and reactivity of (bio)organ- “Computational Investigation of the Bio- ic molecular systems, Mirjana Eckert-Maksić 2. New small molecules targeting macromole- logical Mechanism of Glycerol Dehydration” cules of tumour and inflammatory processes, (1.11.2007-30.10.2008). Ivo Piantanida Danijela Barić: Postdoctoral Fellow- ship from the national Foundation for Sci- Research, developmental and ence, Higher Education and Technological international projects Development of the Republic of Croatia: “Computational Investigation of the Coen- 1. Reinforcement of the Centre for Computa- zyme B -Dependent Fermentation of Diols” tional Solutions in the Life Sciences, David 12 th (15.02-15.08.2008). Smith (6 Framework Programme, EU-FP6- 043749-ReCompSoLS) 2. Computational prediction of structure and PROJECTS AND PROGRAMS catalytic activity of new organic superacids, Unity through Knowledge Fund project for Projects supported by the Ministry young researchers and professionals under of Sciences, Education and Sports the call “My First Research Topic” Grant co- financed by the APO Environmental Protec- 1. Molecular enzymology and protein interaction Services Ltd. Zagreb, Robert Vianello tions of hydrolases, Marija Abramić 3. Artificial Receptors for Bacillus anthracis 2. Macrocyclic ligands, structures in solu- Specific Anthrose Detection, Andreja Jakas, tions and molecular spectroscopies, Goran nato Science for Peace and Security Pro- Baranović gramme; CBP.EAP.SFP.983154

RBI Annual Report 2008. Annual Report 2008. RBI 3. Organic and bioorganic processes in ground 4. Photodynamical simulation of bioorganic and excited states, Mirjana Eckert-Maksić processes, Mirjana Eckert-Maksić (Croatian- 4. Chiral building blocks for biologically active Austrian bilateral project)

50 5. The amide linkage and its implications in es, Croatian Academy of Arts and Sciences, molecular biology, Robert Vianello (Croatian- Zoran Glasovac Austrian bilateral project) 6. Protein engineering of halohydrin dehaloge- SELECTED INVITED LECTURES nases for the production of fine chemicals and pharmaceutical intermediates, Maja Majerić

Elenkov (Croatian-Chinese bilateral project, 1. Basarić N: Domino photochemictry of ada- ZOKB 2007-2009) mantane phthalimides, Central European 7. Microheterogeneity in Aqueous Mixtures: An Conference on Photochemistry, Bad Hofgas- Investigation by Molecular Spectroscopy and tein, Austria, February 10-14, 2008. Theoretical Methods, Goran Baranović (Croa- 2. Maksić ZB: Acidity and basicity in solutions – a tian-French program “Cogito”) selection of the best model and implication for 8. New functional dendritic materials: synthesis grid applications, COST D37 meeting, Barce- and self-organization, Andreja Lesac (Croa- lona, Spain, May 22–23, 2008. tian-French program “Cogito”) 3. Smith DM: Computational Investigations of 9. Photochemical transformation of adamantane Enzyme Mechanisms: An Application to the derivatives activated by phthalimides, nikola Dehydration of 1,2-Diols, From Solid State to Basarić (Croatian-German bilateral project) BioPhysics, Cavtat, Croatia, June 06-13, 2008 10. Experimental and Computational Study of Pro- 4. Smith DM: Computational Investigation of tonated Organic Molecules, Mirjana Eckert- Enzyme Mechanisms: An Application to the Maksić (Croatian-German bilateral project) B12-Independent Glycerol Dehydratase, 11. Computer-assisted Design of Strong and ultra- Trends in Enzymology, Saint Malo, France, strong Bases and their Applications, Zvonimir July 02-05, 2008. Maksić (Croatian-German bilateral project) 5. Maksić ZB: From concepts to computations 12. Metal-binding ability of Leu-enkephalin, re- and vice versa, Electron Correlation and Mo- lated glycoconjugates and peptidomimetics: lecular Dynamics for Excited States and Pho- comparative CD and FTIR spectroscopic tochemistry, Wien, Austria, July 03–04, 2008 studies, Andreja Jakas (Croatian-Hungarian 6. Majerski K: Influence of the rigid spacer to macrocyclization of poly(thialactones): syn- bilateral project) th 13. Pores and Channels by Assembly of Cyclic thesis and computational analysis, 19 Peptides: Design, Molecular Modelling and IuPAC Conference on Physical Organic Synthesis, Kata Majerski (Croatian-Indian bi- Chemistry, Santiago de Compostela, Spain, lateral project) July 13–18, 2008. 14. Theoretical Study of Bioactive Molecules with 7. Eckert-Maksić M: Dynamics simulations of Property of Releasing nitrogen Monoxide photodissociation of formamide and its proton- th (nO): n-nitrosohydroxylamine and its n- and ated formin the gas phase, 19 IuPAC Confer- O- alkyl Derivatives, Mirjana Eckert-Maksić ence on Physical Organic Chemistry, Santiago (Croatian-Slovenian bilateral project) de Compostela, Spain, July 13–18, 2008 15. Theoretical and Experimental Investigations 8. Maksić ZB: Acidity and basicity of 20+2 a- of the Intra- and Intermolecular Hydrogen amino acids in vacuo and water solutions, 19th IuPAC conference on physical organic Bonds, Zvonimir Maksić (Croatian-Slovenian RBI Annual Report 2008. bilateral project) chemistry, Santiago de Compostela, Spain, 16. Thermally processed foods: possible health July 13–18, 2008. implication, Štefica Horvat and Andreja Jakas 9. Maksić ZB: Design of organic superacids and (COST 927, WG1 and WG5) superbases "ex machina" – an interplay be- 17. Organising non-Covalent Chemical Sys- tween conceptual and computational chem- th tems with Selected Functions, Mladen Žinić istry, 7 European Conference on Compu- (COST D31) tational Chemistry, Venice, Italy, September 18. Design, synthesis and molecular interactions 11–15, 2008. of bis-porphyrin molecular receptors, Croatian 10. Smith DM: A Computational Investigation of Academy of Arts and Sciences, Davor Margetić Enzyme Mechanisms: An Application to the 19. Polyfunctional guanidines. Design, synthesis Dehydration of 1,2-Diols, The Eighth Trien- and catalytic properties of novel superbas- nial Congress of the World Association of

51 Theoretical and Computational Chemists ne by a Domino Photochemistry of n-(1-ada- (WATOC 08), Sydney, Australia, September mantyl)phthalimide. Org Lett 2008: 18: 3965. 14-19, 2008. 5. Majerić Elenkov M, Tang L, Hauer B, Janssen 11. Smith DM: Computational Investigations of BD: Formation of enantiopure 5-substituted ox- the Mechanism of Enzyme Action: An Appli- azolidinones through enzyme-catalysed reso- cation to the Dehydration of 1,2-Diols, The lution of epoxides. Org Lett 2008: 10: 2417.

ZOKB International Conference on the Theory and 6. Biliškov N, Baranović G: Hydrogen Bonding Applications of Computational Chemistry in in 1,1′-Bi-2-naphthol within the Polarizable 2008 (TACC2008), Shanghai, China, Septem- Continuum Model, J Phys Chem B 2008: ber 23-27, 2008. 112: 10638. 12. Eckert-Maksić M: Photodissociation of for- 7. Vujasinović I, Veljković J, Molčanov K, Kojić- mamide and its protonated forms – An ab Prodić B, Mlinarić-Majerski K: Thiamacrocy- initio surface hopping dynamics simulations, clic Lactones: New Ag(I)-Ionophores. J Org The Centre for Computational Chemistry, uni- Chem 2008: 73: 9221. versity of Georgia, Athens, uSA, September 8. Miljanić S, Frkanec L, Biljan T, Meić Z, Žinić 25, 2008. M: Surface-Enhanced Raman Scattering on 13. Maksić ZB: From concepts to computations Colloid Gels Originated from Low Molecular and back – design of strong organic super- Weight Gelator, J Raman Spectrosc 2008: acids and superbases, Twenty second an- 39: 1799. nual Charles A. Coulson lecture, university of 9. Kobetić R, Gembarovski D, Baranovi G, Georgia, Athens, Georgia, u.S.A., September Gabelica V: ESI-MS studies of mixed-ligand 30, 2008. Fe(II) complexes containing 1,10-phenanth- 14. Vianello R: Extremely acidic neutral organic roline and 1,10-phenanthroline-5,6-dione as superacids – computationally predicted mole- ligands. J Mass Spectrom 2008: 43: 753. cules awaiting experimental synthesis, Work- 10. Tintaru A, Roithová J, Schröder D, Charles shop on new materials in industry & medicine, L, Jušinski I, Glasovac Z, Eckert-Maksić M: Zagreb, Croatia, november 25–26, 2008. Generation and Dissociation Pathways of Singly and Doubly Protonated Bisguanidines SELECTED PUbLICATIONS in the Gas Phase. J Phys Chem A 2008: 112: 12097. 1. Sandala GM, Smith DM, Radom L: The Car- 11. Eckert-Maksić M, Glasovac Z, Trošelj P, Kütt bon-Skeleton Rearrangement in Tropane Al- A, Rodima T, Koppel I, and Koppel IA: Basici- kaloid Biosynthesis. J Am Chem Soc 2008: ty of Guanidines with Heteroalkyl Side Chains 130: 10684. in Acetonitrile. Eur J Org Chem 2008: 5176. 2. Baral PK, Jajčanin-Jozić N, Deller S, Ma- 12. Supek F, Kralj M, Marjanović M, Šuman L, cheroux P, Abramić M, Gruber K: The first Šmuc T, Krizmanić I, Žinić B: Atypical cyto- structure of dipeptidyl-peptidase III pro- static mechanism of N-1-sulfonylcytosine vides insight into the catalytic mechanism derivatives determined by in vitro screen- and mode of substrate binding. J Biol Chem ing and computational analysis. Invest New 2008: 283: 22316. Drugs 2008: 26: 97. 3. Hranjec M, Piantanida I, Kralj M, Šuman 13. Gredičak M, Kolonić A, Jerić I: Novel chlo- L, Pavelić K, Karminski-Zamola G: Novel roenyne-modified amino acid derivatives. amidino-substituted thienyl- and furyl-vinyl- Amino Acids 2008: 35: 185. benzimidazole derivatives and their pho- 14. Jakas A, Horvat Š: Reactivity and oxidative tochemical conversion into corresponding potential of fructose and glucose in enkepha- diaza-cyclopenta[c]fluorenes. Synthesis, lin-sugar model systems. Amino Acids 2008: interactions with DNA and RNA and antitu- 34: 329. mor evaluation. Part 4. J Med Chem 2008: 15. Vianello R, Maksić ZB: Rees polycyanated 51: 4899. hydrocarbons and related compounds are ex- 4. Basarić N, Horvat M, Mlinarić-Majerski K, tremely powerful Brønsted superacids in the RBI Annual Report 2008. Annual Report 2008. RBI Zimmermann E, Neudörfl J, Griesbeck AG: gas-phase and DMSO – a density functional Novel 2,4-Methanoadamantane-Benzazepi- B3LYP study. New J Chem 2008: 32: 413.

52 CHAPTERS IN bOOKS 2. Monnier VM, Sell DR, Dai Z, Nemet I, Collard F, Zhang J: The role of the Amadori product 1. Roje M, Portada T: Three-membered Rings with in the complications of diabetes. In The Mail- Two Oxygen and/or Sulfur Atoms. In: Compre- lard Reaction: Recent Advances in Food and hensive heterocyclic chemistry III. Editor: Ka- Biomedical Sciences. Editors: Schleicher E, tritzky A. Oxford : Elsevier, 2008. pp. 641-678. Somoza V, Schieberle P. New York : Blackwell Publishing, 2008, pp 81-88. ZOKB RBI Annual Report 2008.

53 54 RBI Annual Report 2008. OVERVIEW OFTHEDIVISION laboratory at the division is theonlyexisting laboratory atthedivision tems. dosimetry chemistry and The radiation in differentmechanisms sys- precipitation of thekinetics and tion intheinvestigation metal hydrides. and tradi- There isalong organic polymers, intermetallic compounds and metalclustercompounds, polynuclear are in metal oxides, glass-ceramics, zeolites, interests synthesis. Ourprimary of materials methods new developing are we Also, als. and physical propertiesof various materi- chemical, microstructural are investigating centre of excellence inmaterialsscience. We consists ofthefollowinglaboratories: The Division of Materials Chemistry(ZKM) Head: SvetozarMusić DIVISIONAL ORGANISATION Division ofMaterialsChemistry The Division of MaterialsChemistryisa The Division a a a a a a

Rozelindra Čož-Rakovac Rozelindra materials, biological – Group forichtiopathology chemistry, PavicaPlaninić Laboratory forcomplexcompounds Želimir Blažina Laboratory forsolidstatechemistry, and dosimetry, DušanRažem chemistry for radiation Laboratory Damir Kralj processes, for precipitation Laboratory Boris Subotić materials, for synthesis ofnew Laboratory

(Gotić andMusić,2008). obtained were particles hematite nanosized presence the of ethanolandfreeacetic acid,exclusively In obtained. was phase tite and someofthehema- octanol, magnetite formed. Inthepresenceofpure exclusively were particles magnetite nanosized ethanol, pure in autoclaved was acetate iron(III) sic ba- When developed. was system alcohol acid/ the iron(III)/acetic in esteri- reaction an fication of participation the with proach oxide particlesbyusinga solvothermal ap- oxidesnanosized iron New methodinthesynthesisof TOP ACHIEVEMENTS pitals, stateinstitutionsandfaculties. numerous cooperations with industries, hos- and Sports. ences, Education There arealso Sci- of Ministry the by sponsored financially recognition. Ourmainresearchactivitiesare international received and developed were and high-dosechemicaldosimetrysystems diations and their applications. The low-dose ra- ionizing of effects physico-chemical the of aspects all covers which Croatia in unit h nw ytei o nnszd iron nanosized of synthesis new The http://www.irb.hr/en/str/zkm

55 2008. Report Annual RBI ZKM Precipitation of calcium carbonate drothermal treatment (heating at 353 K) indicates that the particles of the partially and/or Different soluble polysaccharides: cat- fully crystalline phase are nuclei (Figure 1A) ionic, anionic and non-ionic dextrans and for further crystallization of zeolite (Figure 1B

ZKM soluble starch have been used as additives and C) (Kosanović et al., 2008). in the precipitation system of calcium carbonates. The study investigated the role of ionic Lipidomics charge, molecular masses and concentration of selected polysaccharides on the size The combination of studies in lipido- distribution, morphology and mineralogical mics with those of free radical modifica- composition of precipitate. In addition, some tions of lipids forms a basis for a chemical general conclusions on the mode of substrate biology approach to the study of molecular / macromolecule interactions in electrolyte mechanisms in a biological environment. solutions were made (Kontrec et al., 2008). The search for the correlations between our studies in free radical lipid peroxidations and Study of microstructure of lipid isomerizations forms the subject of the amorphous aluminosilicate gel interdisciplinary collaboration among the Eu- before and after its hydrothermal ropean research groups within the COST treatment Action “Free Radicals in Chemical Biology“ (Chatgilialoglu et al., 2008). Analyses of freshly prepared sodium aluminosilicate hydrogel as well as during its hydrothermal treatment at 353 K by different methods have shown that the freshly prepared gel is mainly composed of disc-shaped primary particles, but also partially or even fully crystalline entities. To arrive at this conclusion, techniques such as powder X-ray diffraction, Fourier transform infrared spectroscopy, Dif- ferential thermal gravimetry, High-resolution transmission electron microscopy and Atomic force microscopy, were used. Atomic force microscopy analysis of the solids separated Figure 2. Particle size analyzer Mastersizer 2000. from the hydrogel at various stages of its hy- Organic polymers

Initiation of crosslinking of unsaturated polyester (UPE) resins by ionizing radiation helped to identify the real cause of double peaks that often appear in crosslinking DSC thermograms of those resins and are usually Figure 1. AFM image of the features appearing in the solid phase assigned to initiator effects. We excluded of the reaction mixture (initially aluminosilicate hydrogel) during the initiator by radiation initiation of the re- its hydrothermal treatment at 80 oC for (A) 30 min (“pyramidal- action and nMR spectroscopy detected the shaped” particles which represent the first visualization of zeolite presence of ortho-phthalic saturated units nuclei), (B) 90 min (zeolite A microcrystals formed by the growth

RBI Annual Report 2008. Annual Report 2008. RBI of nuclei: top of nucleus can be observed near the centre of the in polyester of such resin. In the uPE-resin- 001 crystal faces of each microcrystal) and (C) 240 min (final containing iso-phthalic units, a single peak product; zeolite A crystals with typical growing terraces). appeared in DSC thermograms. Presence of

56 ortho-phthalic units in polyester reduces its compatibility with styrene, probably because of steric hindrances what lead to a reaction- induced phase separation that increases homopolymerization, lowers the extent of ZKM crosslinking and causes the appearance of double peaks. Further literature reviewing revealed that double peaks in DSC thermograms almost exclusively appeared in ortho- phthalic-containig UPE resins while single peaks are characteristic of iso-phthalic-containing resins (Pucić et al., 2008).

Unusual oxidation of the intermetallic compound Zr50Cu50 Figure 3. The QAE contacts comprising four bpy ligands from the 2+ two neighbouring [M(bpy)3] cations in the orthorhombic crystal form of the new solvatomorphs. The oxidation behaviour of selected zir- 2+ conium based hydrogen-storage materials bouring [M(bpy)3] cations – quadruple aryl was investigated. Alloys of the composition embrace (QAE) contact – has been revealed Zr50Cu50 were prepared and their interaction in the series of nine (9) new compounds of the with dry oxygen at high temperatures was composition [M(bpy)3]2[nbO(C2O4)3]Cl·nH2O studied (Paljević et al., 2008). A preferential (M = Fe2+, Co2+, ni2+, Cu2+ and Zn2+; bpy = oxidation of zirconium occurs within the tem- 2,2’-bipyridine), crystallizing in the monoclinic perature region 770 - 970 K, while the excess space group P21/c (n = 11) or in the orthorhom- of copper is accumulated at the alloy-oxide in- bic space group P212121 (n = 12). The mono- terface forming the Zr14Cu51 phase. At 1100 clinic form is a racemic structure containing an 2+ K, after a strong exothermic reaction, the com- equal number of different [M(bpy)3] enan- plete oxidation of the alloy into ZrO2 and CuO tiomers (δ and λ), whereas the orthorhombic occurs after 21 hours. The oxidation process form is an enantiopure structure containing 2+ showed an anomalous decrease of oxygen only one type of [M(bpy)3] enantiomers (δ consumption in the temperature region 900 – or λ). Transformation of the monoclinic crys- 1000 K. This increase of oxidation resistivity tals into the more stable orthorhombic form was ascribed to preferentially oriented crystal- during crystallization is a process of sponta- lites of ZrO2 which have been formed within neous resolution of the racemic compounds 2+ the oxide layer during oxidation. The reaction [M(bpy)3]2[nbO(C2O4)3]Cl·11H2O (M = Fe , kinetics obeys a parabolic law with an activa- Co2+, ni2+, Zn2+) into the racemic conglomer-

tion energy of about 92 kJ/mol. ates [M(bpy)3]2[nbO(C2O4)3]Cl·12H2O. The RBI Annual Report 2008. two structural forms differ in composition just Supramolecular motifs and solvato- in the number of solvate (water) molecules morphism within the compounds (11 versus 12); therefore, this series of com- 2+ containing [M(bpy)3] entities pounds exhibits the phenomenon of solvatomorphism (Jurić et al., 2008). Modern ideas in the design of new molecular solids with desirable physical properties Novel methods for assessing fish are based on the analysis of controlled supra- blood biochemical data molecular aggregation of molecular entities. A specific type of supramolecular contact com- using novel machine learning techniques, prising four bipyridine ligands from two neigh- the authors created and generated compre-

57 hensible classification models for exploring PROJECTS AND PROGRAMS the importance of blood chemistry parameters, strength, mutual interactions or depen- Projects supported by the Ministry dencies, and reliability of particular param- of Sciences, Education and Sports

ZKM eters within the seasonal groups, for the first time (Čož-Rakovac et al., 2008). 1. Synthesis and microstructure of metal oxides and oxide glasses, Svetozar Musić 2. Polynuclear metal systems – synthesis and NEW EQUIPMENT properties, Pavica Planinić 3. Metal hydrides in clean energy systems, A new dynamic laser light scattering parti- Želimir Blažina cle size analyzer Mastersizer 2000 (Malvern) 4. Study of influence of aluminosilicate precur- was obtained. The measurement range is 20 sors on their transformations, Boris Subotić – 3000 nm of small quantity (50 – 100 mg) of 5. Precipitation mechanism of inorganic bio- solid sample dispersed in 1 – 2 ml of solvent compatible and related materials, Damir Kralj (aqueous and/or organic). The instrument 6. Structure-property relationships of modified is used within a cooperative effort involving polymer materials, Ivan Šmit Ruđer Bošković Institute and Bartex-Bartol. 7. Physico-chemical effects of ionizing radia- tions in materials, Dušan Ražem As part of a cooperative effort involv- 8. Subcellular biochemical and phylogenetic ing Ruđer Bošković Institute and Chiyoda diversity of aquatic organisms, Rozelindra Technol, we secured a radiophotolumines- Čož-Rakovac cent reader with dosimeters (FGD - 1000 for GD-300 series). A Varian capillary gas chro- Programs supported by the matograph GC 450 equipped with a flame Ministry of Sciences, Education ionization detector was obtained. and Sports In addition, the Division obtained an Elec- trophoresis set, a DnA imaging system and 1. New functional materials, Svetozar Musić a PCR thermal cycler. Research, developmental and EDUCATION international projects

Scientists from the Division contributed to 1. Metal oxides: structural and magnetic prop- 17 undergraduate and postgraduate courses erties, Mira Ristić (Croatian-Serbian Scien- tific Cooperation Programme for 2008-2010). in 2008 as part of the involvement in the edu- 2. Free Radicals in Chemical Biology (CHEM- cational programs of universities in Zagreb, BIORADICAL), Branka Mihaljević; Project Osijek and Dubrovnik. number COST Action CM0603 3. Solid state dosimetry systems for various PATENTS dosimetry fields, Maria Ranogajec-Komor; Bilateral scientific and technical co-operation Patent number P20070240A. Kosanović between Croatian Academy of Sciences and C, Subotić B. Preparation for chemical treat- Arts and Hungarian Academy of Science (2007 – 2009). ment of sand-treated glass surfaces and hy- 4. Characterization, intercomparison and ap- drophobization of other glass, ceramic and plication of radiophotoluminescence (RPL) rock surfaces. dosimetry system according to international standards and protocols, Maria Ranogajec- Komor; Scientific co-operation between

RBI Annual Report 2008. Annual Report 2008. RBI Ruđer Bošković Institute and Chiyoda Tech- nol. Corporation, Japan; Signed 2 Septem- ber 2008.

58 5. nuclear techniques for the protection of the ture”, Gacka d.o.o., Natalija Topić Popović cultural heritage in the Mediterranean Region, (Ministry of Agriculture, Fisheries and Rural Branka Katušin-Ražem; International Atomic Development 324-01/08-01/393) Energy Agency Regional Technical Co-opera- 16. Scientific/professional management of a tion Project; Project number: RER/1/006 project: “Breeding and Selection in Aquacul- ZKM 6. Quality control methods and procedures for ture”, Fishery 1961 d.o.o., Ivančica Strunjak- radiation technology, Dušan Ražem; Interna- Perović (Ministry of Agriculture, Fisheries tional Atomic Energy Agency Regional Tech- and Rural Development 324-01/08-01/401) nical Co-operation Project; Project number: 17. Aquatic animal health monitoring – contracts RER/8/010 with 8 international and national companies, 7. Optimization of the synthesis process of zeo- Rozelindra Čož-Rakovac, Mato Hacmanjek lite A with special emphasis on the control of particulate properties (size and shape of zeo- INVITED LECTURES lite A crystals), Boris Subotić (Bartex-Bartol and Ruđer Bošković Institute co-operation nd 1. Topić Popović, N. Good laboratory practice in scientific research – 2 phase). manipulation with fish as a model in biomedi- 8. Atomic-force microscopy study of the crys- cal research. 5th scientific-professional con- tallization of zeolites A, X and silicalite ference on autochthonous karstic species, from amorphous (alumino)silicates, Cleo Otočac, Croatia, June 27, 2008. Kosanović (Croatian-Hungarian Intergovern- 2. Jadan, M. Genetic structure of brown trout mental Science and Technology Cooperation population, 5th scientific-professional con- Programme for 2007-2009). ference on autochthonous karstic species, 9. PHARE project: “Trout and Tourists”, Roze- Otočac, Croatia, June 27, 2008. lindra Čož-Rakovac (Department for Financ- 3. Strunjak-Perović, I. Diseases of crayfish, 5th ing Eu Assistance Programmes and Proj- scientific-professional conference on autoch- ects, Central Finance and Contracting unit, thonous karstic species, Otočac, Croatia, 2005-0808-010101) June 27, 2008. 10. VIP project: “Model of revitalization and 4. Čož-Rakovac, R. Crayfish Farming. 5th sci- breeding of brown trout”, Rozelindra Čož- entific-professional conference on autoch- Rakovac (Ministry of Agriculture, Forestry thonous karstic species, Otočac, Croatia, and Water Management MAFWM, VI-1- June 27, 2008. 10/05) 5. Ranogajec-Komor, M. Application of solid 11. VIP project: “Preservation of oyster produc- state dosimeters in individual, medical and tion by asserting its autochthony” Ivančica environmental dosimetry. Sapientia univer- Strunjak-Perović (Ministry of Agriculture, Fish- sity, Cluj, Romania, 1 April 2008. eries and Rural Development, VIII-5-50/08) 6. Ranogajec-Komor, M. Environmental moni- 12. “Determination of genetic structure and toring with solid state dosimeters. Advanced restoration of autochthonous population Training Course “New Techniques for the De- of brown trout in the National Park Plitvice tection of nuclear and Radioactive Agents“, Lakes”, Rozelindra Čož-Rakovac (National Mugla, Turkey, 26 – 30 May 2008. RBI Annual Report 2008. Park Plitvice Lakes/Ministry of Environmen- 7. Ražem, D. Effects of radiation on controlled tal Protection, Physical Planning and Con- drug delivery and release systems. 15th In- struction 21320/06) ternational Meeting on Radiation Processing. 13. Scientific/professional management of a Workshop on Radiation Sterilization of Drug project: “Breeding and Selection in Aquacul- – Device Combination Products. London, ture”, Fishery 1961 d.o.o., Mato Hacmanjek united Kingdom, 21 – 25 September 2008. (MAFWM, 324-01/06-01/202) 8. Miljanić, S. Double dosimetry in intervention- 14. Scientific/professional management of a proj- al radiology – practice, evaluation and rec- ect: “Breeding and Selection in Aquaculture”, ommendatations. 4th International Workshop Fishery Vrnjika, Rozelindra Čož-Rakovac on Individual Monitoring, Oarai, Japan, 1-3 (MAFWM, 324-01/06-01/215) December, 2009. 15. Scientific/professional management of a project: “Breeding and Selection in Aquacul-

59 ORGANIZED CONFERENCES 6. Paljević M, Tudja M. Unusual oxidation behaviour of Zr50Cu50 alloy at high tempera- XXIX. European Congress on Molecular tures. Corros Sci 2008: 50: 818. Spectroscopy (EuCMOS-2008), Opatija, 31.08.- 7. Jurić M, Perić B, Brničević N, Planinić P, Pajić D, Zadro K, Giester G, Kaitner B. Supramo-

ZKM 05.09.2008., Chairpersons: Svetozar Musić and Krešimir Furić (Ruđer Bošković Institute). lecular motifs and solvatomorphism within The First Croatian Symposium on Zeolites, the compounds [M(bpy)3]2[nbO(C2O4)3] 2+ 2+ 2+ 2+ Split (Croatia) 26-27.09.2008. Organization: Cl·nH2O (M = Fe , Co , ni , Cu and Croatian Zeolite Association, Ruđer Bošković Zn2+; n = 11, 12). Syntheses, structures and Institute and university of Split. President of magnetic properties. Dalton Trans 2008: 742. the Organizing Committee: Josip Bronić (Ruđer 8. Čož-Rakovac R, Šmuc T, Topić Popović N, Bošković Institute). Strunjak-Perović I, Hacmanjek M, Jadan M. Novel methods for assessing fish blood biochemical data. J Appl Ichthyol 2008: 24: 77. SELECTED PUbLICATIONS Chapters in books 1. Gotić M, Musić S. Synthesis of nanocrystalline iron oxide particles in the iron(III)acetate/ 1. Subotić B, Bronić J, Antonić Jelić T. Theoreti- alcohol/acetic acid system. Eur J Inorg Chem cal and Practical Aspects of Zeolite nucleation. 2008: 966. In: Ordered Porous Solids: Recent, Advances 2. Kontrec J, Kralj D, Brečević Lj, Falini G. In- and Prospects. Editors: Mintova, Svetlana; fluence of some polysaccharides on the pro- Valtchev, Valentin; Tsapatsis, Michael. Else- duction of calcium carbonate filler particles. J vier, Amsterdam, 2008, pp 127-185. Cryst Growth 2008: 310: 4554. 2. Ražem D. Radiation sterilization of pharma- 3. Kosanović C, Bosnar S, Subotić B, ceuticals: An overview of the literature. In: Svetličić V, Mišić T, Dražić G, Havenscak K. Trends in Radiation Sterilization of Health Study of the microstructure of amorphous Care Products. International Atomic Energy aluminosilicate gel before and after its hydro- Agency, Vienna, 2008, pp 175-185. thermal treatment. Micropor Mesopor Mat 3. Chu RDH, Desrosiers MF, Inokuti M, Klas- 2008: 2-3: 177. sen NV, Kovacs A, McLaughlin WL, Miller 4. Chatgilialoglu C, Ferreri C, Hermetter A, A, Ražem D, Sharpe PHG, Shortt K, Selt- Lacote E, Mihaljević B, Nicolaides A, Sia- zer SM, Takehisa M, Tanaka R, Whittaker B, faka-Kapadai A. Lipidomics and free radical Wieser A. Dosimetry systems. In: Dosimetry modification of lipids. Chimia (Basel) 2008: Systems for use in Radiation Processing. In- 62: 713. ternational Commission on Radiation units 5. Pucić I, Jurkin T. Radiation and Postirradia- and Measurements (ICRu) Report no. 80. tion Crosslinking and Structure of Two Un- ICRu, Bethesda, MD, 2008, pp. 29-70. saturated Polyester Resins. Polym Engin Sci 2008: 48: 1768. RBI Annual Report 2008. Annual Report 2008. RBI

60 OVERVIEW OFTHEDIVISION genetics, biophotonics and bioinformatics. genetics, biophotonics biology,molecular biochemistry, cellbiology, biology is based onthe methods of modern consists ofthefollowinglaboratories: The Division of Molecular Biology(ZMB) Head: IgorWeber DIVISIONAL ORGANISATION Division ofMolecularBiology The research in the Division ofmolecular The researchintheDivision a a a a a a a a a a a a

Mariastefania Antica Immunology,Molecular and forCellular Laboratory Andrija ŽeljkoLovrić Investigations, forBiocenotic Laboratory Branka SalopekSondi for Chemical Biology,Laboratory Hrvoje Fulgosi for Electron Microscopy,Laboratory Branimir Jernej neurobiology,Molecular for neurochemistry and Laboratory Maja Osmak for Genotoxic Laboratory Agents, Cancerology, IvicaRubelj for Experimental Laboratory Mary Sopta Laboratory,Gene Regulation of Eukaryotes,MiroslavPlohl for Molecular Genetics Laboratory Dušica Vujaklija for Molecular Genetics, Laboratory Microbiology, MirjanaPetranović for Molecular Laboratory Brčić-Kostić Krunoslav forMicrobialGenetics, Laboratory and biotechnology. lecular biosciences, biomedicine including mo- of field the in work professional for tists of life, as well as the training of young scien- principles level andtheunderlying molecular our knowledge of biological processes at the of broadening projects isageneral research and genomes. The primarypurposeofthese of genes in thecytoskeleton;andevolution and ecologyof fungi; dynamical processes taxonomy,diversity including biogeography tioxidant activity of polyphenols; fungalbio- an- of planthormones; biology and structural of photosynthesis;physiology, biochemistry neurotransmission; regulatorymechanisms background and regulatory mechanismsof tance to cytostatics and antibiotics;genetic to toxicagentsandresis- responses cellular sion, growth, differentiation and senescence; of celldivi- regulation in molecular duction (transcription andtranslation);signaltrans- quences; expressionof genomic information genome organization and repetitive DNA se- (DnA andrepair); replication, recombination of genomevariation integrity andregulation genome of maintenance study: of fields ing follow- the comprise broadly Division our in plants andmammaliancells. The projects lular slimemoulds,severalinvertebrates, other fungi,cel- bacteria, yeastand clude Model organismsusedinthesestudies-

http://www.irb.hr/en/str/zmb 61 2008. Report Annual RBI ZMB In 2008, members of the Division of mo- malignant counterparts, our results would lecular biology participated in the teaching of indicate a disregulation of a developmental more than 30 undergraduate and postgradu- pathway in follicular centre cell lymphoma ate courses at Croatian universities. During (FCC-NHL). Our results show for the first

ZMB that year they also supervised more than 20 time Aiolos overexpression in primary lym- diploma, M.Sc., and Ph.D. theses. A series of phoma tissues (Antica et al., 2008). practical courses in biology and medicine was organized in our Division by Andreja Ambriović Transcription of centromeric DNA Ristov (http://www.tecajevi-irb.com). non-coding RnA deriving from centro- TOP ACHEIVEMENTS meric regions is proposed to plays an active role in the formation of pericentromeric and Gene expression and transcription- centromeric heterochromatin, both of them al regulation in lymphoma important for proper centromere function. We have identified and characterized stable, We analyzed gene expression and tran- RnA polymerase II dependant transcripts scriptional regulation in lymphocytes from of abundant centromeric satellite DnA, not patients with lymphoma compared to nor- regulated by RnAi, in beetle Tribolium cas- mal lymphocytes. We tackled the question taneum (Pezer and Ugarković, 2008a). The whether there is a quantitative difference functional studies indicate that slight chang- in distribution of Ikaros, Aiolos, and Helios es in expression of non-coding centromeric mRNA between Hodgkin lymphoma (HL) RnA could induce chromosome instability, and non-Hodgkin lymphoma (nHL). Forma- mis-segregation and aneuploidy, facilitating lin-fixed and paraffin embedded sections of lymph nodes from patients were analyzed by real time qRT-PCR. Ikaros and early B-cell factor (EBF) transcription factors regulate lambda 5 expression of pre-B-cell receptor (BCR) at the pre-BI stage of B-cell development. The transition from pre-BI to pre-BII is marked by pre-BCR down-regulation due to higher Aiolos expression. Because one approach to understanding neoplastic transformation is by comparing normal cells to their

Figure 2. Link between centromeric RNA and aneuploidy. Aber- rant expression of centromeric satellite DNA affects centromere/ RBI Annual Report 2008. Annual Report 2008. RBI kinetochore function and causes abnormality in chromosome segregation. Defects in RNA metabolism could affect hetero- Figure 1. Mitogen-stimulated lymphocytes, TEM. chromatin maintenance and fidelity in mitosis.

62 finally tumourigenesis (reviewed in Pezer MODERN FACILITIES, METHODS and Ugarković, 2008b). AND EQUIPMENT

Integrin-mediated drug resistance Centre for DNA sequencing ZMB Recently, we found the up-regulation of The DnA centre for DnA sequencing, un- αvβ3 integrin in human laryngeal carcinoma der the supervision of Helena Ćetković as part cells resistant to cisplatin. We show here, on of the Laboratory for Molecular Genetics, con- the model of human laryngeal carcinoma- tinued to provide services during 2008. Be- derived αvβ3 integrin-expressing cells, the sides DnA sequence analyses, it also offers a appearance of resistance to several anti- microsatellite genotyping method for external cancer drugs (cisplatin, mytomycin C and users. More than 2500 sequence analyses doxorubicin). Our results describe a novel were performed in this year at the DNA centre mechanism mediated by αvβ3 integrin that is using ABI-Prism 3100 Sequencer. the consequence of glutathione-dependent increased ability of αvβ3 integrin-expressing Confocal laser scanning cells to eliminate drug-induced reactive oxi- microscope dative species (Brozović et al., 2008). The confocal laser scanning microscope An ancient evolutionary origin of Leica TCS SP2 AOBS is equipped with eight human disease genes laser excitation lines and four photomultiplier detectors. Instead of filters and dichroic mir- rors, it uses acoustic-optical elements for spectral separation of fluorescence signals.

GbOX EF Gel Documentation System

A new, cost-effective gel documentation system from Syngene is capable of accu- rately producing images of gels and blots stained with both visible and low-light emit- ting fluorescent dyes. Figure 3. An artistic illustration of phylostratigraphy.

Genomic phylostratigraphy of human genetic diseases shows that evolutionary origin

of disease genes is not random. Surprising- RBI Annual Report 2008. ly, there is a clear bias towards old genes, whereas disease genes specific to the mammalian lineage are almost absent. These regularities show that genetic diseases are an inescapable component of life and that all living organisms today, i.e. not only humans, will be affected by similar genetic diseases. The article was evaluated in “Faculty of 1000 Biology” and reports about it were published in “New Scientist” and “The Economist” (Domazet-Lošo and Tautz, 2008). Figure 4. The new gel documentation system.

63 64 RBI Annual Report 2008. ZMB AWARDS 6. 5. 4. 3. 2. 1. Sciences,Education andSports of bytheMinistry supported Projects PROJECTS ANDPROGRAMS EDUCATION Report (JasenkaPiljacŽegarac). technology“ accordingtotheJournalCitation sities inZagreb,Split,DubrovnikandOsijek try, biophysicsandbiomedicineatthe postgraduate coursesinbiology, biochemis ogy teachover10undergraduateand20 4 chem.2008.07.048). This journalisranked Chem 2008(http://dx.doi.org/10.1016/j.food dark fruitjuicesinrefrigeratedstorage.Food phenolic contentandantioxidantcapacityof the in Fluctuations A. Belščak S, Martinez L, ValekJ, Piljac-Žegarac article: the for Sports, and Education Croatian MinistryofSciences, in chief: Andreja Ambriović Ristov). biology,(Methods inmolecular ologiji” Editor bi- u molekularnoj ”Metode for thebook 2007 in naturalsciences in Croatianlanguage and Science Arts forthebestpublication of Academy Croatian the by Award” mayer Stross- Juraj “Josip the awarded lisher,was th of 103 in the category “Food science and of103inthecategory“Foodscienceand Members oftheDivisionmolecularbiol by granted Award Excellence Scientific pub- the as Institute, Bošković Ruđer myces biology, DušicaVujaklija Fundamental molecularstudies of Strepto- tion andrepair, DavorZahradka Molecular mechanismsof DnA recombina Orešković Darko fluid, cerebrospinal of Hydrodynamics Branka Salopek-Sondi Molecular regulationof plant development, and behavior, Branimir Jernej transmission: genes,proteins Serotonergic Ambriović Ristov effi- transduction cacy andresistanceto cytostatics, Andreja adenovirus of Increase u niver- . - - - - 17. 16. 15. 14. 13. 12. 11. 10. 9. 8. 7. 1. national projects Research, developmental andinter- 1. Sciences,Education andSports of bytheMinistry supported Program 5. 4. 3. 2.

Plohl DnAtions ofsatellite Miroslav sequences, interac- and functional Evolution, properties Mary Sopta Transcriptional regulationin eukaryotes, Mariastefania Antica entiation, interactions inlymphocytedifferMolecular - tance development,MajaOsmak to cytotoxicagentsandresis- response Cell Lipa Čičin-Šain Serotonergic mechanismsin alcoholism, genome evolution,KrunoslavBrčić-Kostić in DnAThe roleofrecombination repairand immortalization and cellularaging,IvicaRubelj of mechanisms Molecular cell motilityandcytokinesis,IgorWeber Regulation of the cytoskeleton dynamicsin and differentiation ofplastids, HrvojeFulgosi Regulatory mechanismsof photosynthesis and evolutions,HelenaĆetković genomes: structures,functions Genes and of eukaryoticgenome,ĐurđicaUgarković portion Evolution andfunctionoffastevolving castaneum DnAheterochromatic ing insect in Structural andfunctionalanalysisof noncod es, MiroslavPlohl. process- fundaments ofbiological Molecular uclua lclzto o guahoe and cysteine incyanobacteria, HrvojeFulgosi glutathione of localization Subcellular project with Austria, 910-08/07-01/00129) cells, Mariastefania Antica (MSES, bilateral Transcriptionalin humanleukemic regulation Agreement 9/07) Pase proteins,IgorWeber (uKF1A Grant bysmallGT actin cytoskeletondynamics Biophotonics approachto regulation of the EW 07-032) grant, ESF- Science Foundation (European Miroslav Plohl to epigenetics, sequences structure andfunction:fromrepetitiveDnA heterochromatin on workshop Exploratory MTKD-CT-2006-042248) project Knowledge of Transfer Curie Marie Đria Ugarković Đurđica ,

(EC FP6 Tribolium - - 15. 14. 13. 12. 11. 10. 9. 8. 7. 6. 1. SELECTED INVITEDLECTURES

tional ResearchProgram,no:L129) VujaklijaDušica - application, Transla(FWF biocatalytic, agriculturaland environmental Bacterial endophytes, a novel biosourcefor (Maraška Ltd.,MPŠVG,24-14/07) Ćetković Helena juice, maraska cherry sour on of productsbased the quality Improving plied collaborativeproject) county,Primorsko-goranska altitudes, ap- at high for agriculture (Centre Salopek-Sondi berry (Vaccinium corymbosum Propagation of the American highbushblue TRA–TEST, 381-01/06-02/00032) HI- (MSES, Ristov Ambriović Andreja knee, of the cartilage of articular Regeneration Žegarac (HITRA-TEST, E38-2005) oxidants infoodproducts,JasenkaPiljac ofanti- the analysis for laboratory Certified 919-08/06- 01/00208) Slovenia, with project bilateral (MSES, proaches, BrankaSalopek-Sondi ap- and molecular stress usingbiochemical Plant hormones indevelopmentandbiotic ny, 910-08/07-01/00145) Germa- with project bilateral DAAD (MSES, drugs, MajaOsmak to platinum susceptibility Molecular mechanismsdeterminingcellular ny, 910-08/07-01/00143) Germa- with project bilateral DAAD (MSES, and cellmigration,IgorWeberphagocytosis Analysis of cytoskeleton dynamicsduring 910-08/06-01/00098) France, with project bilateral Cogito (MSES, Ristov Ambriović Andreja fibrosis, cystic of therapy in gene application n andpotential Adenovirus retargetingto aminopeptidase projet withFrance,910-08/06-01/00093) bilateral (MSES, Cogito Plohl gyne, Miroslav root-knot nematodesofthegenusMeloido- interactions in holocentric chromosomesof of DnA,proteincomponentsandtheir Study 08/07-01/00125) 910- Austria, with project bilateral (MSES, Osmak M, Brozović A, Advances inOnclogyand101 platin- resistance.13 cis- in role their and cisplatin with treatment by the proteinsinduced es incelladhesion Chang A: Ristov Ambriović G, Fritz D, jhen th

Čimbora-Zovko Čimbora-Zovko T, Ma- Worldon Congress th International L.),Branka - - - 3. 7. 6. 5. 4. 2. 10. 9. 8. VujaklijaD: tion. Postojna,Slovenia,May26-29,2008. ics tointerac- understand plant-nematode Medicine. Symposium onMolecular species: thecaseof Mravinac B: Satellite DnAsincloselyrelated ber 20-21,2008. Biology inCroatia.Zagreb,Croatia,novem- Molecular of 50 Years Symposium Scientific Fulgosi H: Photosynthesis requires TROL. Croatia, September23-24,2008. therapy.to gene from basicbiology Zadar, mo- its biology.lecular FEMScourse, Adenoviruses: and structure Virus of adenoviruses: properties General A: Ambriović-Ristov tember 20-23,2008. Stubica, Croatia,Sep- Donja to epigenetics. DnAfunction: fromrepetitive and sequences ry Workshopstructure onHeterochromatin in (peri)centromericregions.ESF Explorato Plohl M: Tandem repetitiveDnA sequences 19-22, 2008. International November Slovenia, Portorož, Participation. with Society Microbiological of theSlovenian terial species.Congress bac- distant SSBs fromtaxonomically terial Meloidogyne genus the of nematodes root-knot with study tribution in phylogenetic analysis:a case P: Relevance ofsatelliteDnA genomicdis - Castagnone-Sereno M, Plohl N, Meštrović sonissos, Greece,October9-11, 2008. f iceity n Mlclr ilg with Biology Molecular and Biochemistry of Society - CongressoftheCroatian BMB2008 bacterium man M:DnAresistant repairinradiation Rad - A, Lindner M. Petranović D, Averbeck D, Bailone K, Slade Zahradka A, SommerS, Stubica, Croatia,September20-23,2008. petitive D erochromatin structureandfunction:fromre Tribolium Meštrović N: Satellite DNAs in insect models – Croatia, September23-24,2008. therapy.to gene from basicbiology Zadar, Adenoviruses: course, FEMS efficacy. tion transduc- tance tocisplatinandadenovirus Majhen D: Integrin αvβ3: Link between resis- Croatia, September20-23,2008. sequences to epigenetics. DonjaStubica, structure andfunction:fromrepetitiveDnA Exploratory Workshop onHeterochromatin . ESFExploratoryWorkshop onHet n A sequencestoepigenetics.Donja

Deinococcus radiodurans Tyrosineof bac- phosphorylation . COSTgenom- 872-Exploiting Tribolium beetles.ESF . HD-

Her- - - -

65 2008. Report Annual RBI ZMB 66 RBI Annual Report 2008. ZMB . 4 3. 15. 13. 12. 11. 2. 1. CONFERENCES SELECTED ORGANIZED 14. 5. 4.

radiation resistant bacterium.7 radiation ca, Croatia,September20-23,2008,PlohlM. tion. Zadar,24-27, 2008. Croatia,September Participa International with Microbiology of Congress Escherichia coli.FourthCroatian in recAmutantsof chromosome degradation reckless in enzyme RecBCD with cooperate M, Petranović Zahradka D: ExoI and SbcCDnucleases M, Buljubašić K, Zahradka Zahradka K: greb, Croatia,november20-21,2008. Years of Molecular Biology inCroatia.Za- 50 Symposium Scientific genomes. of parts secret DNAs: Satellite M: Plohl N, Meštrović 18-19, 2008. September Croatia, Vukovar, days. Ružička XII. overview. an – products food TotalCroatian D: L, Šamec Valek capacity of content andantioxidant phenol A, S, Belščak T, Martinez Stipčević J, Žegarac Piljac September 17-20,2008. International Participation.Osijek,Croatia, Dn matin structureandfunction:fromrepetitive ESF ExploratoryWorkshop onHeterochro vember 20-21,2008,PlohlM,ZahradkaK. No- Croatia, Zagreb, Symposium. Scientific 50 Years ofBiologyinCroatia- Molecular Zagreb, Croatia,n sium 50 Years ofMolecularBiologyinCroatia. Sympo Scientific (Porifera). sponges – ans metazo simplest of repertoire genetic broad W, Müller reveals genomics Comparative K: Vlahoviček D, Perina H, Ćetković M, Harcet Croatia, May29-31,2008. Opatija, Participation. International with tion Protection Radiation of theCroatian Associa- 1, 2008,Vujaklija D. Croatia, Dubrovnik, August 24-September and Communities. olites: Genomes,Signals Metab - Secondary Summer SchoolMicrobial ber 23-24,2008, Ambriović Ristov A. ogy togenetherapy. Zadar, Croatia, Septem- FEMS course, biol from basic Adenoviruses: September 24-27,2008,Vujaklija D. International Participation. th rain oges f irbooy with Microbiology of Congress Croatian A sequencestoepigenetics.DonjaStubi Deinococcus radiodurans ovember 20-21,2008.

Zadar, Croatia, th Symposium – a ------etic stemcelltoimmunocompetentcells. Figure 5.Developmentinthethymusfromcommittedhematopoi- Research articles SELECTED PUbLICATIONS 6. 5. 4. 3. 2. 1. foodchem.2008.07.048). of print:http://dx.doi.org/10.1016/j. ahead frigerated storage.FoodChem 2008(Epub in re- capacity ofdarkfruitjuices antioxidant contentand A. Fluctuationsinthephenolic Piljac-Žegarac J, Valek L, Martinez S, Belščak Cryst GrowthDes2008:8:435. reaction inthepresenceof magnesium ions. enzyme-catalyzed by particles calcite loidal mimetic precipitationof nanostructured col- Bio- B. Salopek-Sondi SD, Škapin I, Sondi Pharmacol 2008:74:298. reactive oxidativespecies.Mol drug induced of elimination by glutathionedependent cells iscaused carcinoma laryngeal human in resistance drug mediated integrin αvβ3 A. kopec S, Fritz G, Osmak M, Ambriović-Ristov Ja- N, V,Mikac Roje D, Majhen A, Brozović 15:1156. type IIsynthase.ChemBiol2008: polyketide of proteinsformingabacterial arrangement P, CrumpMP, PF.J, Long Crosby Proposed J, Wattana-Amorn D,Cullum D, Hranueli lija VujakS, Heidelberger J, Zucko - G, Castaldo 25: 2699. man geneticdiseases.MolBiolEvol2008: hu- with associated genes of origin tionary T,Domazet-Lošo evolu Tautz ancient D. An Hodgkin lymphoma.Blood2008:111: 3296. los andHeliosexpressioninHodgkinnon- M, Džebro S, Dominis M. Aberrant Ikaros, Aio Matulić S, Kapitanović L, Čičin-Šain M, Antica - - 1. inbooks Chapters 8. 7. 2008: http://www.els.net. Satel- Ltd., Chichester & Sons, Wiley (ELS), John Alpha of of LifeSciences lite DnA.In:Encyclopedia Evolution Đ. Ugarković Beetles. PLoSOnE2008a:3:e1594. Transcription of Centromeric SatelliteDnA in Promotes II Pol RNA Đ. Ugarković Ž, Pezer dase III.BiolChem2008:389:163. pepti- the activecenterofhumandipeptidyl in residue tyrosine Functional N, M. Abramić J, Špoljarić B, Šimaga Š, Vujaklija D, Makarević J, Jajčanin Vukelić B, Salopek-Sondi 3. 2. 1. Invited review articles Chem Acta 2008:81:511. the outermembraneofchloroplasts.Croat across translocation lar conceptofprotein molecu The E: Schleiff H, Fulgosi A, Vojta ero)chromatin. Gene2008:409:72. tion of tandem repeatsincentromeric(het- and evolu functionality: structure,genomics and selfishness between DNAs Satellite B: Mantovani N, Meštrović A, Luchetti M, Plohl cancer. SeminCancerBiol2008b:18:123. non-coding RnAand in aneuploidy heterochromatin and of Role Đ. Ugarković Ž, Pezer - -

67 2008. Report Annual RBI ZMB 68 RBI Annual Report 2008. consists ofthefollowinglaboratories: The Division of Molecular Medicine(ZMM) Head: KrešimirPavelić DIVISIONAL ORGANIZATION a a a a a a a a a a a a a a Division ofMolecularMedicine Sanja Kapitanović Laboratory forpersonalizedmedicine, Levanat Laboratory forhereditarycancer, Sonja Žarković Laboratory forOxidativeStress,neven Oliver Vugrek Group for Translational Medicine, Neuropharmacology, DankaPeričić Laboratory ofMolecular Jasminka Pavelić Laboratory ofMolecularOncology, Neuropsychiatry, DoroteaMuck-Šeler Laboratory ofMolecular Tatjana Marotti Laboratory forreactiveradicals, Marijeta Kralj Laboratory ofFunctionalGenomics, and Transplantation, MirkoHadžija Laboratory ofMolecularEndocrinology Bacteriology, MagdalenaGrce Laboratory ofMolecularVirology and Gall-Trošelj Laboratory ofEpigenomics,Koraljka Oncology, JelkaGabrilovac Hematology, Immunologyand Laboratory ofExperimental Krešimir Pavelić Laboratory forSystemsBiomedicine, OVERVIEW OFTHEDIVISION to thestudyofdisease. lence, for research inmolecularapproaches as acentreofexcel- is emerging the Division on -omicsapproaches. tools based As such, phering the molecular basisof disease, and at deci- research aimed tools and diagnostic new diseases, viral and cancer against use velopment ofmoleculartargetedtherapyfor eral strategicprojects. the de- These include methodology,and theeducationofscientistsstudents. scientific of improvement the effects ofdrugsoncellsandlivingorganisms, the explorationofbiochemical and cellular the development and evaluation of new drugs, ease prevention,thereductionofriskfactors, genetic factorsindis of theimpact of ation evalu the through realized are goals These agnosis, treatmentandpreventionofdisease. develop and improve to new strategies for the and di diseases of nature the of knowledge Medicine istoexpandandstrengthenthe The Division is currently developing sev- developing is currently The Division The missionoftheDivisionMolecular http://www.irb.hr/en/str/zmm - - -

69 2008. Report Annual RBI ZMM TOP ACHIEVEMENTS IN bASIC well known phenomenon of spontaneous AND APPLIED RESEARCH regression of Walker 256 carcinoma in rats (Jaganjac et al., 2008). Curcumin’s molecular mechanism ZMM of action in the context of Lipidomics and lipid peroxidation epigenomic modulation using the yeast cell model

In the research on the mechanism of ex- The cellular adaptation to metabolic pression regulation of IGF2 and H19, H19 changes induced by the synthesis of poly- silencing in tumour cells upon curcumin unsaturated fatty acids is associated with treatment was induced, and the IGF2/H19 increased resistance to oxidative stress imprinting, CTCF and IGF2-R loss of hetero- (Čipak et al., 2008). zigosity and presence of H. Pilory in laryngeal squamos carcinomas in humans was Novel potential anticancer analyzed (Novak Kujunđić et al., 2007). compounds

Mechanism of anticancer activity Over 150 newly synthesized compounds, of novel quinoline derivaties such as urea and carbamate derivatives of primaquines, novel ketoprofen amides, using a proteomic approach based on fluoroalkylated pyrimidine derivatives, en- 2DE coupled with a mass spectrometric ediynes, glucosylated and adamantylated mechanistic study, the n-amidino-substi- enkephalin analogues, adamantane substituted benzimidazo-1,2-a-quinoline was ob- tuted crown compounds and many others tained. The quinoline derivative triggered were screened in vitro for potential antitu- transient, p53-independent G2-M arrest in mor activity and the possible mechanisms mutant p53 human colon cancer cells and of action were ascertained for the most ef- succeeding mitotic transition, whereby these fective ones (Kralj et al., 2008; Hranjec et cells underwent cell death probably due to al., 2008). mitotic catastrophe. The antiproliferative effect of the quinoline derivative supports its Antitumor therapy and p21WAF1/CIP1 possible role as an antimetastatic agent in gene colorectal carcinoma (Sedić et al., 2008). The molecular mechanisms underlying Cooperation of antioxidatve cell cycle and cell death were studied using enzyme network cDnA-arrays and qPCR. The p21 can as- sume a dual role in apoptosis in the same In ageing mouse liver and brain, stronger correlative links of antioxidatve enzyme net- cell system depending on the chemothera- works exist in old female mice than in old male peutic agent: its over-expression enhances mice demonstrating one possible reason why apoptosis in cisplatin-treated cells and at- old females are better protected from oxidative tenuates apoptotic signals in methotrexate- stress than males (Sobočanec et al., 2008). treated cells. The observed dual role of p21 was in direct correlation with the modulation Granulocytes in spontaneous of caspase 3 and 7 activation and changes in regression of Walker 256 carcinoma the expression of GADD45a gene (Kraljević Pavelić et al., 2008)

RBI Annual Report 2008. Annual Report 2008. RBI Granulocytes were found to be effective host defence in the early stage of cancer. This finding explained for the first time the

70 The influence of IL-8 and IL-10 on sporadic colon cancer development and progression

IL-10 SNP promoter genotypes were ZMM associated with increased risk of sporadic colon cancer. A significant increase in IL-8 and a decrease in IL-10 mRnA expression in tumour tissue compared with normal mu- cous tissue were observed. Positive IL-10 immunohistochemical reaction was more frequent in well differentiated tumours and IL-8 staining was more frequent in poorly differentiated tumours. These results indicate a possible tumour promoting role of IL-8 and Figure 1. The 4800 Plus MALDI TOF/TOFtm analyser that tumour protective role of IL-10 in sporadic relies on the Matrix-assisted laser desorption/ionization MS. colon cancer (Čačev et al., 2008). rification. Additionally, the molecular weight A novel therapeutic indication in analysis could be performed according to bipolar depression the MS and MS/MS measurements. Peptide and protein identification from complex mix- Six weeks of treatment with low doses tures is performed by using specialized soft- of the antiepileptic drug lamotrigine signifi- ware packages that are directly connected cantly reduced depressed symptoms, and with publicly open databases such as The decreased platelet serotonin concentration Protein Data Bank or SwissProt (Figure 1). in patients with bipolar depression, indicating that lamotrigine possesses an in vivo serotonin-uptake inhibiting property, and this NEW METHODS effect might have contributed to its antide- pressant activity (Šagud et al., 2008). Breast cancer genes BRCA 1and 2

Patents The first screening for the breast cancer genes BRCA 1 and 2 was done in Croatia, Kraljević Pavelić S, Cindrić M, Sedić M, with new sequence variants in BRCA1 and Hock K, Pavelić K. Proteomic profile and pro- BRCA2 genes detected by high-resolution tein detection methods in blood. P2008056A melting analysis in an elderly healthy female population. RBI Annual Report 2008. MODERN FACILITIES, METHODS Analysis of gene expression within AND EQUIPMENT intact mouse embryos

The new Laboratory for systems bio- RNA whole mount in situ hybridization is medicine, which includes the Centre for Pro- a recently introduced method which enables teomics and Mass Spectrometry as well as analysis of gene expression within intact the Centre for Transcriptomics, has been mouse embryos (Korolija M, Ph.D. thesis). established. The Centre for Proteomics and Transcripts of target genes are hybridized Mass Spectrometry offers commercial ser- with digoxigenin-labelled riboprobes and vi- vices which include amino-acid, protein and sualized in situ by an alkaline phosphatase peptide sequencing upon isolation and pu- detection system (Figure 2).

71 of the Standing Committee, European Medi- cal Research Council, ESF. Krešimir Pavelić was appointed as a coordinator of the EU expert group for Stem cell therapy and regenera- tive medicine in European Medical Research ZMM Council, European Science Fundation (ESF). On the meeting of European Medical Re- Figure 2. Fgf 8 expression in the apical ectodermal ridge (AER, search Council in The Royal College of Physi- indicated by arrows) of the developing limb buds of mouse cians in UK, Krešimir Pavelić initiated the revi- embryos at embryonic day 9.5 (a) and embryonic day 11.5 (b). talization of the project EuroSTELLS. Krešimir Genotyping assays for Human Pavelić is Editor of the Journal of Oncology papillomavirus (HPV) types and Central European Journal of Biology. Nela Pivac was appointed as a member of Although there are more than 100 Human the Regional CInP (Congress Internationalle papillomavirus (HPV) types, only the high-risk neuro-Psychopharmacologicum) Committee (oncogenic) types cause cervical precancer for Southern and Eastern Europe. and cancer (Figure 3). Due to the large num- Sonja Levanat was appointed as a Council ber of HPV types, 4 genotyping assays were member of European Association for Cancer evaluated on a wide spectrum of less preva- Research (EACR). lent HPV types indicating that the use of only Magdalena Grce was appointed as a del- one assay in epidemiological and clinical stud- egate from RBI and a member of the Board ies might lead to biased conclusions (Sabol et of Directors of the European Cervical Cancer al., 2008). In addition, a novel HPV type 16 Association (ECCA). variant with 63-nucleotides duplication in the E1 region was found. This particular variant DOMESTIC FUNCTIONS found in 11% cervical specimens of 429 HPV 16 positive Croatian women show reduced Krešimir Pavelić is president of the Na- oncogenicity, which is particularly interesting tional Scientific Council, president of the for the prediction of disease progression. Governing Board of the Institute for Medical Research, Member of the Governing Board, Agency for Science and High Education, Ministry of Sciences, Education and Sports, and Dean in Department of Biotechnology at the university of Rijeka. Tatjana Marotti was re-appointed as a member of the Board of Governers of Ruđer Bošković Institute. Figure 3. Distribution of Human Papilloma Virus (HPV) types in Croatia. AWARDS INTERNATIONAL FUNCTIONS FameLab 2008 award to Marko Košiček Krešimir Pavelić was appointed in No- vember as a Secretary General of the Euro- Marko Košiček (Figure 4) received both pean Molecular Biology Conference (EMBC) the Croatian and International FameLab and ex officio member of the EMBO Council. 2008 awards organized by the Festival of RBI Annual Report 2008. Annual Report 2008. RBI Until November he was vice-president of the Science and the British council for the best EMBC. Krešimir Pavelić is also member of scientific presentation. FameLab, originally the EMBC Strategic Working Party, Member

72 a UK talent competition, was established in pany. This Company has started the heredi- 2005 and aims to find the best new talents in tary breast cancer genetic testing, using a science communication. sophisticated method developed in the Divi- sion of Molecular Medicine at Rudjer Bos-

Annual award for young researchers kovic Institute, led by Sonja Levanat and her ZMM in biomedicine group. Genetic testing can reveal if person has a gene mutation associated with possi- Ana Šarić received the Annual award for ble breast and ovarian cancer development. young researchers in biomedicine from the This testing analyzes BRCA1 and BRCA2 Society of university Teachers, Scholars and genes, which are often mutated in hereditary Other Scientists – Zagreb for the year 2007. breast and ovarian cancer. She was awarded for the excellent paper: Šarić et al., published in Neuroscience.

Figure 5. Rudjer-Medikol Diagnostics Ltd.

PROJECTS Figure 4. Marko Košiček Projects supported by the Ministry Award of the Croatian Academy of of Sciences, Education and Sports Science and Arts and The Zagreb Fair 1. Molecular characteristics of the myo-fibroblasts in the Dupuytren’s disease, Krešimir Pavelić Award of the Croatian Academy of Sci- 2. Role of membrane peptidases on tumour and normal cells, Jelka Gabrilovac ence and Arts and The Zagreb Fair to Insti- 3. Epigenetic and Immunomodulatory Changes tute Ruđer Bošković, the editor-in-chief An- in Malignant Head and neck Tumours, Ko- dreja Ambriović Ristov, and editors Anamaria raljka Gall Trošelj Brozović, Branka Bruvo Mađarić, Helena 4. Aberrant DNA methylation in HPV associated

Ćetković, Maja Herak Bosnar, Dubravka lesions, Magdalena Grce RBI Annual Report 2008. Hranilović, Silva Katušić Hećimović, Neven- 5. Obtaining the structures like Langerhans is- ka Meštrović Radan; Snježana Mihaljević, lets from mouse stem cells, Mirko Hadžija Neda Slade and Dušica Vujaklija for the best 6. The role of nm23 genes in oral squamous cell publishing achievement: Methods in Molecu- carcinoma, Maja Herak Bosnar lar Biology. 7. Molecular genetics and pharmacogenetics of gastrointestinal tumours, Sanja Kapitanović 8. The mechanism(s) of cholesterol action in Al- Spin Off Company zheimer’s disease, Silva Katušić Hećimović 9. The role of different cell death responses to The spin off company, Ruđer-Medikol Di- DnA-damage treatment, Marijeta Kralj agnostics Ltd. (Figure 5), was established 10. Signal transduction in tumours: Hh-Gli interac- by Rudjer Innovations as its daughter com- tions and therapeutic potential, Sonja Levanat

73 11. Cytochrome P450 monooxigenase and tu- 6. Cellular sites of dual y-secretase cleavage mour appearance in ageing and oxidative (Silva Katušić Hećimović, Bilateral project stress, Tatjana Marotti with Germany, co-investigators: Harald Stein- 12. Immunopathogenesis of human recurrent her- er, Sven Lammich) pes simplex virus infection, Zorica Mikloška 7. Hereditary Breast Cancer predisposition in ZMM 13. Pharmacogenomics and proteomics of sero- Croatia and Hungary’, (Croatian Hungarian tonergic and catecholaminergic system, Dor- Intergovernmental S&T Cooperation Pro- otea Muck-Šeler gramme 2007-2008, Sonja Levanat, Croatia, 14. Gene therapy of tumours by modulating the Edith Olah, Hungary) molecules of immune system, Jasminka 8. Integrating and Strengthening Genomic Re- Pavelić search in South East Europe (InTEGERS) 15. Stress, GABA-A receptors and mechanisms FP7-REGPOT-2007-1 (Fran Borovečki, of action of neuropsychoactive drugs, Danka members of Coordination Committee: Dor- Peričić otea Muck-Šeler, Nela Pivac) 16. Molecular basis and treatment of psychiatric 9. Frontotemporal dementias and motor neu- and stress related disorders, nela Pivac ron disease (Rajka Liščić, Bilateral Coopera- 17. New approaches in the treatment of malig- tion with Slovenia; co-investigators: Dorotea nant diseases, Marko Radačić Muck-Šeler, Nela Pivac) 18. The role of p53/p73 protein network in soft tis- 10. Genetic testing of monogenetic diseases: sue sarcoma, neda Slade cystic fibrosis, non-sindromic deafness, Rett 19. Molecular characterisation of S-adenosyl- syndrome, (Clinical Hospital Split, Children’s homocysteine deficiency in humans, Oliver Hospital Zagreb, Jasminka Pavelić) Vugrek 11. Genetic factors as markers of suicide (nela 20. Lipids, free radicals and their second messen- Pivac, Bilateral Cooperation with Slovenia; gers in integrative oncology, Neven Žarković co-investigator: Dorotea Muck-Šeler) 12. The role of p73 in cell cycle control (Bilateral Programs supported by the Ministry collaboration with France, Cogito, Neda Slade) of Science, Education and Sports 13. Development of vaccine agains herpes geni- talis (Croatian Fund for development and em- 1. Integrative genomics and proteomics in can- ployment, Zorka Mikloška) cer research. Krešimir Pavelić 14. COST (European Cooperation in the field of 2. Pharmacogenomics, proteomics and psy- Scientific and Technical Research) Action B35 chophysiology of neuropsychiatric disorders, “Lipid Peroxidation Associated Disorders” in Dorotea Muck-Šeler the Domain Biomedicine and Molecular Bio- sciences, Action Chair Neven Žarković Research, developmental and 15. Effects of the lipid peroxidation product 4-hy- international projects droxynonenal on primary hepatocytes, (Cro- atian-Austrian Science Technology Coopera- 1. Development of drugs for treatment of Dupuy- tion Program, Neven Žarković) tren disease, (Croatian Fund for development 16. Support of human bone growth in vitro by and employment. Krešimir Pavelić). bioactive glass and 4-hydroxynonenal, (Aus- 2. Toxicological in vivo studies of Lectranal trian national Bank Jubileums Fond Research (MILSING Corp, Mirko Hadžija) Grant, Renate Wildburger (LKH Graz) and 3. Therapeutic effects of mushroom extracts, Neven Žarković) (HITRA, Mislav Jurin) 17. novel, genuine assays for lipid peroxidation 4. The role of cholesterol in Alzheimer’s disease analyses in experimental oncology, (Bilat- (Alison Goate, nIH - Fogarty International Re- eral project on scientific and technological research Collaboration Award, USA, co-investi- search collaboration with France – COGITO, gator: Silva Katušić Hećimović) Neven Žarković) 5. The mechanism(s) of cholesterol action in Al- 18. Modifying drug resistance by oxidative stress

RBI Annual Report 2008. Annual Report 2008. RBI zheimer’s disease (Silva Katušić Hećimović, and antioxidants (Bilateral Hungarian – Croa- Bilateral project with USA, co-investigator: Ali- tian Scientific and Technological Collaboration son Goate) project, Neven Žarković)

74 SELECTED ORGANIZED Congress-2008, Shanghai, China, June 12- CONFERENCES 17, 2008. 7. Grdiša M. Delivery of specific targeted drugs 1. Čretnik M. Organisation of International Sum- into the cells by TAT-technology. EHRLICH mer School Hottest Topics in Protein Re- II – 2nd World Conference on Magic Bullets, ZMM search, MedILS, Split, Croatia, July 19-26, nurnberg, Germany, October 3-5, 2008. 2008. 8. Kralj M: Adenoviruses for gene therapy of 2. Čretnik M. Asistent on EMBO Course EMBO cancer. International Workshop organized Course on ubiquitin and SuMO, MedILS, by Croatian Microbiological Society Adenovi- Split, Croatia, September 12-19, 2008. ruses: Basic biology to gene therapy. Zadar, 3. Pivac N, Muck-Šeler D. Third Croatian Con- September, 23-24, 2008. gress on the Stress Related Disorders with in- 9. Kralj M: Adenoviruses-mediated p53 or p21 ternational participation: therapy of the stress waf1/cip1 gene transfer and its impact on can- related disorders, Rabac, Croatia, June 5-7, cer therapy. International Workshop orga- 2008. nized by Croatian Microbiological Society 4. Pivac n. European Pharmacological Society Adenoviruses: Basic biology to gene therapy. (EPHAR) 2008, Manchester, united Kingdom, Zadar, September, 23-24, 2008. July 13-17, 2008. 10. Levanat S: Evasive role of Hh-Gli pathway in 5. Pivac N, Muck-Šeler D. Fourth Croatian Con- cancer genetics (with an introduction on the gress of Alzheimer’s disease with internation- state of cancer genetics research in Croa- tia). Yale School of Medicine, Department of al participation, Rovinj, Croatia, October 8-11, Genetics Clinical Rounds, New Haven, CT, 2008. uSA; June 16, 2008. SELECTED LECTURES 11. Levanat S: Molecular diagnostics of inherited breast cancers. 3rd Slovenian Congress of Clinical Chemistry with international partici- 1. Balog T, Sobočanec S, Šverko V, Krolo M, pation and 18th International Symposium of Ročić B, Marotti M, Marotti T. The influence Slovenian Association for Clinical Chemistry of season on oxidant-antioxidant status in and Croatian Society of medical Biochemists. trained and sedentary subjects. 4th Interna- Ljubljana, Slovenia; november 13-15, 2008. tional Conference on Health, Fitness & Active 12. Levanat S: Role of genetics in early breast Living, Athens, Greece, May 8-11, 2008. cancer detection. Croatian Academy for Sci- 2. Grce M. Cervical Cancer Prevention in Croa- ence and Art (HAZu), September 25, 2008. tia. HPV in Human Pathology, Prague, Check 13. Mück-Šeler D, Nedić G, Pivac N, Babić A, Republic, May 1-3, 2008. Grubišić-Ilić M, Kozarić-Kovačić D: Serotoner- 3. Grce M. Cervical Cancer Screening in Europe: gic receptors type 2A in posttraumatic stress th The Status Quo. 9 International Workshop of disorder. 3rd Croatian Symposium on Stres Lower Genital Tract Pathology - HPV-Related Related Disorders with International Partici- Disease in the Vaccine Era: Time to Retire? pation. The Therapy of Stress Related Disor- Viareggio, Italy, May 22-24, 2008. ders, Rabac, Croatia, June 5-7, 2008. 4. Grce M. HPV DNA Testing for Cervical Can-

14. Mück-Šeler D, Mustapić M, Mimica N, Pivac N, RBI Annual Report 2008. th cer Screening. 7 International Symposium Presečki P, Folnegović-Šmalc V: Dopamine- on Molecular Diagnostics, Graz, Austria, May beta-hydroxylase in Alzheimer’s disease. 4th 22-24, 2008. Croatian Congress on Alzheimer’s Disease 5. Grce M. Cervical Cancer Screening Pro- with International Participation, Rovinj, Croa- gramme: Follow-up and Integrating the Ser- tia, October 8-11, 2008. vices of other Healthcare Professionals. 15. Pavelić J: Gene therapy. Who decides for a Consensus Congress on Cervical Cancer fetus? 4th South-East European Bioethical th Prevention in Bulgaria and 14 national Con- Forum, Rijeka-Opatija, Croatia, September ference of Gynaecological Oncology, nesse- 3-8, 2008. bar, Bulgaria, September 18-21, 2008. 16. Pivac N, Nedić G, Mustapić M, Muck-Šeler D, 6. Grdiša M. Specific drug delivery by TAT- Grubišić-Ilić M, Kozarić-Kovačić D. Biological technology. BIT Life Sciences’ World Cancer and genetic markers and suicidal behaviour

75 in posttraumatic stress disorder. 3rd Croa- seen from the –omics point of view. 38th An- tian Symposium on Stress Related Disorders nual meeting of European Environmental Mu- with International Participation. The Therapy tagen Society (EEMS) Cavtat, Croatia, Sep- of Stress Related Disorders, Rabac, Croatia, tember 21-25, 2008. June 5-7, 2008. 27. Pavelić K.: Presentation of the ESF-EMRC ZMM 17. Pivac N, Nedić G, Deželjin M, Mustapić M, Science Policy Briefing on stem cell research. Mimica N, Muck-Šeler D, Folnegović-Šmalc European Science Foundation, European V. Catechol-o-methyl-transferase val158/met Medical Research Council. Paris, France, Oc- polymorphism in Alzheimer’s Disease. 4th tober 13, 2008. Croatian Congress on Alzheimer’s Disease with International Participation, Rovinj, Croa- SELECTED PUbLICATIONS tia, October 8-11, 2008. 18. Pivac N, Nedić G, Mustapić M, Muck-Šeler Research articles D, Kozarić-Kovačić D. Biological background and pharmacotherapy of psychotic posttrau- 1. Antica M, Čičin-Šain L, Kapitanović S, Matulić matic stress disorder. Third Regional CInP M, Džebro S, Dominis M. Aberrant ikaros, aio- Congress, Bratislava, Slovakia, november los and helios expression in Hodgkin and non- 27-30, 2008. Hodgkin lymphoma. Blood 2008: 6: 3296. 19. Žarković N: Development and Validation of 2. Čačev T, Radošević S, Križanac Š, New Technologies for Faster Analysis, Bio- Kapitanović S. Influence of interleukin-8 analysis in Clinical Research, Post Confer- and interleukin-10 on sporadic colon cancer ence Workshop, Olympia Conference Centre, development and progression. Carcinogen- London, uK, February 22, 2008. esis 2008: 29:1572. 20. Žarković N: ELISAs in LPO detection, Free 3. Čipak A, Jaganjac M, Tehlivets O, Kohlwein Radicals and nutrition: basic mechanisms and SD, Žarković N: Adaptation to oxidative stress clinical applications, SFRR Europe & COST induced by polyunsaturated fatty acids in B35 Action, Berlin, Germany, July 5-9, 2008. yeast. Biochim. Biophys. Acta Mol. Cell Biol 21. Žarković N: Lipid Peroxidation Associated Dis- Lipids 2008:178: 283. eases, COST Outreach Activity for Early Stage 4. Grbeša I, Marinković M, Ivkić M, Krušlin B, Researchers in connection with Euro Science Novak Kujundžić R, Pegan B, Bogdanović O, Open Forum, Barcelona, Spain, July 19, 2008. Bedeković V, Gall Trošelj K. Loss of imprint- 22. Žarković N: The Relevance of Immunochemis- ing of IGF2 and H19, loss of heterozygosity try of 4-Hydroxy-2-nonenal for Evaluation of its of IGF2R and CTCF, and Helicobacter pylori Biological Activities, Lipid Peroxidation 2008, infection in laryngeal squamous cell carcino- Karuizawa, Japan, October 15-17, 2008. ma. J Mol Med JMM 2008: 86: 1057. 23. Pavelić K.: The role of integrative genom- 5. Hranjec M, Piantanida I, Kralj M, Šuman,L, ics/proteomics in the detection and treat- Pavelić K, Karminski-Zamola G. Novel ment of metastatic breast cancer. 5th Con- amidino-substituted thienyl- and furyl-vinyl- ference on Experimental and Translational benzimidazole derivatives and their pho- Oncology. Kranjska Gora, Slovenia, March tochemical conversion into corresponding 26-30, 2008. diaza-cyclopenta[c]fluorenes. Synthesis, in- 24. Pavelić K, Varela-Nieto I.: Stem cells and tis- teractions with DNA and RNA and antitumor sue engineering. European Medical Research evaluation. J Med Chem 2008: 51: 4899. Council Forward Look. EMRC 52nd Plenary 6. Jaganjac M, Poljak-Blaži M, Žarković K, meeting. The Royal College of Physicians. Joerg Schaur R, Žarković N. The involve- London, uK, April 22-23, 2008. ment of granulocytes in spontaneous regres- 25. Pavelic K.: Improved navigation and precise sion of Walker 256 carcinoma. Cancer Let drug delivery (contributed talk). HotnanoTop- 2008: 260: 180. ics. Nanostructured bio-interfaces. Portorož, 7. Kraljević Pavelić S, Čačev T, Kralj M. A dual role of p21waf1/cip1 gene in apoptosis of HEp-2 RBI Annual Report 2008. Annual Report 2008. RBI Slovenia, May 26-30, 2008. 26. Pavelić K.: Casting light on molecular events treated with cisplatin or methotrexate. Cancer underlying metastasis of cancer: what can be Gene Ther. 2008: 15: 576.

76 8. Novak Kujundžić R, Grbeša I, Ivkić M, Katdare Chapters in books M, Gall Trošelj K. Curcumin downregulates H19 gene transcription in tumor cells. J Cell 1. Borović Šunjić S, Šunjić I, Wildburger R, Biochem 2008: 104: 1781. Mittelbach M, Waeg G, Žarković N: Lipid 9. Sabol I, Salakova M, Smahelova J, Pawlita M, peroxidation end product as a modulator of Schmitt M, Gasperov NM, Grce M, Tachezy R. cell growth. In: Cell Growth Processes: New ZMM Evaluation of different techniques for identifi- Research. nova Science Publishers, Inc. cation of human papillomavirus types of low Hayashi T (Ed) New York, 2008: 187 prevalence. J Clin Microbiol 2008: 46 :1606. 2. Pivac N, Kozarić-Kovačić D, Nedić G, 10. Sedić M, Poznić M, Gehring P, Scott M, Mustapić M, Stipčević T, Nenadić-Šviglin K, Schlapbach R, Hranjec M, Karminski-Zamola Grubišić-Ilić M, Mück-Šeler D. Neurobiology G, Pavelić K, Kraljević Pavelić S. Differential of Suicidal Behaviour. In: Wounds of War: antiproliferative mechanisms of novel deriva- Lowering Suicide Risk in Returning Troops. tive of benzimidazol-1,2-a-quinoline in colon nATO Science through peace and security cancer cells depending on their p53 status. – Editor: Wiederhold, Brenda K. IOS Press Mol Cancer Ther 2008: 7: 2121. Amsterdam, 2008, pp 3-22. 11. Sobočanec S, Balog T, Kušić B, Šverko V, 3. Sobočanec S, Šarić A, Korolija M, Marjanović Šarić A, Marotti T. Differential response to lipid M, Kralj M, Knežević J, Čretnik M, Balog T, peroxidation in male and female mice with Šverko V, Kušić B, Marotti T. Native propolis age: correlation of antioxidant enzymes matin vivo: On the oxidative/antioxidative effect ters. Biogerontology 2008: 9: 335. and the mechanism of action. In: Scientific 12. Šagud M, Pivac N, Nedić G, Mihaljević Peleš Evidence of the use of Propolis in Ethnomed- A, Kramarić M, Jakovljević M, Muck Šeler D. icine- Editor:Transworld Research Network The effect of lamotrigine on platelet serotonin Fort P.O., Kerala, India, 2008, pp 121-131. concentration in patients with bipolar depression. Letter to the editors. Psychopharmacol- books ogy 2008: 4: 683. 1. Boranić M et al. (Balog T, Čurić G, Gabrilo- Review articles vac J, Gregurek R, Koršić M, Lauc G, Marotti T, Martin Kleiner I, Pivac N, Muck-Šeler D, 1. Bošnjak H., Pavelic K., Kraljevic Pavelic S.: Sabioncello A, Stojević Z, Trkulja V) Psycho- Towards preventive medicine. High-through- neuroendocrinology: interaction of immune, put methods from molecular biology are nervous and endocrine systems (Psihoneu- about to change daily clinical practice. EMBO roimunologija: povezanost imunosustava Rep 2008: 9: 1056. sa živčanim i endokrinim sustavom). Editor: Krznarić Vohalski G. Školska knjiga dd. Za- 2. Grce M, Davies P. Human papillomavirus greb, 2008, pp 1-277. testing for primary cervical cancer screening. 2. Pivac N, Kozarić-Kovačić D, Mustapić M, Expert Rev Mol Diagn 2008: 8: 599. Deželjin M, Nenadić-Šviglin K, Muck-Šeler D. 3. Kralj M, Tušek-Božić Lj, Frkanec L. Biomedical Peripheral biological markers in alcoholism. Potentials of Crown Ethers: Prospective Antitu- Editor: Pivac N. New York, Nova Publishers, mor Agents. ChemMedChem. 2008: 3: 1478. RBI Annual Report 2008. 2008, pp 1-93. 4. Levanat S, Čretnik M, Musani V. Hh-Gli sig- 3. Duraković Z, Žarković N: Biology of aging naling pathway functions and its therapeutic and geriatry (Biologija starenja i gerijatrija) potential in cancer , Croatica Chemica Acta In: Vrhovec B et al., Internal Medicine (In- 2008: 81: 1. terna medicina), Editor: Vrhovec B, Naklada 5. Šagud M, Mihaljević-Peleš A, Pivac N, Ljevak, Zagreb, pp 69-77. Muck-Šeler D, Šimunović I, Jakovljević M: Genetics of schizophrenia in the context of integrative psychiatry. Psychiatria Danubina 2008: 20: 364.

77 78 RBI Annual Report 2008. laboratories: Research (ZIMO) consists of the following The Divisionof Marine andEnvironmental Head: Tarzan Legović DIVISIONAL ORGANIZATION a a a a a a a a a a a a Environmental Research Division ofMarineand

Molecular ecotoxicology, Tvrtko Smital organisms, Emin Teskeredžić Aquaculture andpathologyofaquatic Raspor Biological effects ofmetals,Biserka Radioecology, DelkoBarišić Marijan Ahel biogeochemistry oforganiccompounds, Analytical chemistryand imaging, Vesna Svetličić Bioelectrochemistry andsurface Goran Kniewald Inorganic environmentalgeochemistry, Colloid geochemistry, IvanSondi Lovrić Physical chemistryoftraces,Milivoj Kozarac Aquatic physicalchemistry, Zlatica Kuzmić Satellite oceanography, Milivoj modelling, Tarzan Legović Informatics andenvironmental OVERVIEW OFTHEDIVISION in 4 rdae col wr coordinated, were schools graduate 4 tion, addi In organized. were conferences 5 and held were lectures invited 5 published, were vourable reportsinternationally, three books Current Contents,onepatent received fa- by indexed in journals papers scientific 53 whole world. to the benefit of our country and, indeed, the optimum andhence of theenvironment management the for needed base knowledge the in increase an toward directed is search control. their processes,statesand The re- plied researchof environmental systems, to strive for excellence infundamentalandap- is which division, the of mission overall technology.to the Eachprojectcontributed nano- to down oceanography satellite from marine andenvironmentalscience,ranging in topics of range wide a spanned projects and outsideclients. and Education These Sport tracted bytheMinistryofSciences, on morethan50researchprojectscon- h rsac rsls ee ulse in published were results research The worked scientists division 2008, During http://www.irb.hr/en/str/zimo -

79 2008. Report Annual RBI ZIMO 2 B.Sc, 2 M.Sc. and 4 Ph.D. theses were on the crystal growth of initially formed nano- defended, under the mentorship of Division crystallites of calcite and subsequent ag- scientists. Finally, 18 undergraduate and 63 gregation processes of these particles that post-graduate courses were given at univer- govern the formation of submicron size and sities in Croatia and abroad. nanostructured hierarchical structures of col- ZIMO loidal carbonates. This finding is relevant in understanding the mechanism of formation of complex natural hybrid materials, found in bioinorganic structures generated through nanoparticle assemblies (Sondi et al., 2008).

A novel approach in the determination of trace metal – natural organic matter interactions

An adapted protocol for the electrochemical characterization of the metal ion - natu- Figure 1. Single quadrupole GC/MS system installed in the Labo- ral organic matter (nOM) interaction is pro- ratory for Biogeochemistry of Organic Compounds. posed and tested. A realistic speciation of metal ions in the particular natural water, TOP ACHIEVEMENTS derived from the calculated complexing parameters is obtained (Loius et al., 2008). Overfishing of predatory benthic fishes in the Adriatic Sea confirmed Passive samplers for metals applied as a new tool It has been shown that most of the predatory benthic fish stocks in the Adriatic Sea Passive samplers, DGTs (diffusive gradi- have been overfished. Observed changes ents in thin films), were applied in the Sava between populations of Chondrichthyes and River water (Croatia) as a new tool for the Osteichthyes are in agreement with the Volt- assessment of the labile metal concentra- erra principle down to the extinction of preda- tions. Increased concentrations of Co, Cr, tors. By using the Gause competition model Mn and Fe were found at the location down- under the intensive fishery, it is shown that stream of the municipal sewage outlet, in- an initially dominant competitor may become dicating a detrimental effect of the pollution marginal, in agreement with existing data. point source on surface water quality (Dra- These alarming results indicate the need for gun et al., 2008). a new approach to the management of the multispecies fisheries (Legović, 2008). The evidence of self-purification of the Krka River A novel biomimetic nano-scale aggregation route This study provides the first survey of trace metal content in the Krka River using A novel, bio-inspired precipitation strat- ‘clean’ methods and techniques of sampling, egy, determined as biomimetic nano-scale handling and analysis. Concentrations of Zn, aggregation route, in formation of nanostruc- Cd, Pb and Cu measured in the water of the

RBI Annual Report 2008. Annual Report 2008. RBI tured submicron-size colloidal particles of Krka River are amongst the lowest reported carbonates was described. It involves simul- in the literature for freshwater systems (Cuk- taneous inhibitory effect of magnesium ions rov et al., 2008).

80 Anchialine cave-waters – evidence nism of the biogeochemistry of metal ions. for sustained localised oxidation of Complexation of copper ions in bulk precipi- iodide to iodate tation was measured using differential pulse anodic stripping voltammetry (DPASV). The Anchialine caves provide unusual environ- precipitation samples were collected pe- ZIMO mental conditions due to lack of light, relative- riodically during one year in the mainland ly long seawater residence time, hypoxia, and area of Croatia (Zagreb) and at the Adriatic an exacerbated role of bacteria in the food- coast (Šibenik). The complexation of cop- web. The caves in Croatia provide interesting per ions ranges from 0.010 and 1.4 µ M. iodine chemistry with iodide oxidation in bot- The highest capacity was measured in April tom waters, iodate reduction and iodide re- 2003 in a rainwater sample from the Šibenik mineralization in mid-water, at the halocline. area (Plavšić et al., 2008). Anchialine caves offer an opportunity to improve the understanding of the biogeochemi- Accumulation mechanism for metal cal mechanisms operating generally with io- chalcogenide nanoparticles at Hg dine in marine systems (Žic et al., 2008). electrodes

Total mercury in core sediments in Mercury electrodes preconcentrate metal the bay of bengal, India chalcogenide nanoparticles, enabling their detection at submicromolar concentrations The concentration of total mercury in core by adsorptive cathodic stripping voltamme- sediments (<63 μm) of Sunderban mangrove try. A multistep mechanism was proposed wetland, the Bay of Bengal varies from 9.8 to with polydisperse copper sulphide (Cu S) 535.1 ppb (ngg-1). Based on Igeo and RE-L x nanoparticles. Particles obey the Schulze- (150 ppb) it is concluded that sediments are Hardy rule at various electrolyte strengths unpolluted. Two statistical methods were applied to determine Hg anomalies at post mon- and, consequently, accumulation rates are soon and in pre monsoon period. Results will strongly sensitive to electrolyte concentra- be useful in future sediment quality studies tions (Krznarić et al., 2008). (Kwokal et al., 2008). . Fish cells can develop the multi- Magnetic susceptibility of coal drug/multixenobiotic resistance combustion products in sediments phenotype similar to mammalian tumour cells Coal slag and ash, obtained from burning coal in a textile factory in Duga Resa (Croa- tia), have been discharged directly into the

Mrežnica River for 110 years. The effects RBI Annual Report 2008. have spread almost to Karlovac, 50 km down- stream from the source. Cluster analysis of R-modality indicates that low-field magnetic susceptibility (MS) is linked to B, Mo, na and U (Frančišković-Bilinski, 2008).

Study of organic complexation in atmospheric precipitation

Organic complexation in atmospheric Figure 2. TECAN Infinite M200 system installed in the Laboratory precipitation is an important control mecha- for Molecular Ecotoxicology.

81 It is demonstrated that fish PLHC-1/ PATENT dox cells highly express P-glycoprotein (ABCB1) mediated multidrug resistance, Hršak D, Havriluk M. Mixed bacte- exhibiting similar cross-resistance pheno- rial culture for atrazine degradation, WO type to structurally different xenobiotics as

ZIMO 2007/0966681 A1. The patent application the one described in mammalian cells. This obtained excellent international search re- finding affirms the PLHC-1 cell line as an port and entered into national phases in Eu, important model for studying the develop- uSA, India, China, Canada and Australia. ment of basic resistance mechanisms to different chemicals in aquatic organisms (Žaja New equipment et al., 2008). TECAN Infinite M200 modular monochro- Fish health status in relation to mator-based microplate detection system water quality with fluorescence, absorbance and luminescence detection modes is being used for de- Freshwater fish are monitored on a reg- termination of intracellular accumulation or ef- ular basis in several Croatian rivers (Sava, flux of model compounds in a variety of (eco) Kupa, Dobra, Mrežnica, Zrmanja, Krka toxicologically relevant bioassays (Smital T). and Sutla). Investigations of biochemical GC/MS system with EI, positive and nega- parameters, resorption of nutrients, oc- tive CI, Agilent 7890A Series GC and 5975B currence of bacterial, viral and parasitic inert XL MSD is being used for the determi- diseases as well as the aquaculture tech- nation of specific organic contaminants in nology and cultured fish diet have been various environmental matrices (Ahel M). carried out. Since water quality is the main ultra performance Liquid Chromatog- factor affecting aquaculture, fish could be raphy/Quadrupole-Time-of-Flight Mass used as probes of the water quality. In addi- Spectrometry (uPLC/Q-ToF), Waters tion, our goal is to detect the impact of wild uPLC/Q-ToF Premier is being used for the populations as a reservoir of pathogens determination of polar environmental pollut- (Kapetanović et al., 2008). ants. The major advantage is the capability of the instrument to measure mass accurate- Occurrence and fate of ly, which provides the basis for identification pharmaceuticals in wastewaters of unknown contaminants in complex envi- and natural waters ronmental matrices (Terzić S).

A comprehensive reconnaissance of over seventy individual contaminants in Croatian municipal wastewaters was performed, including some prominent classes of emerging contaminants such as pharmaceuticals and personal care products, surfactants and their degradation products, plasticizers, pesticides, insect repellents, and flame retardants. Due to the rather poor wastewater management practices, most of the contaminants present in wastewaters

RBI Annual Report 2008. Annual Report 2008. RBI reach ambient waters and may represent a significant environmental concern (Terzić et Figure 3. Biominetic formation of nanoscale colloidal carbonates al., 2008). in the Laboratory for colloid geochemistry.

82 The Beckman Coulter LS 13320 is the 3. Electroactive films for ecologically acceptable most versatile multi-wavelength laser diffrac- conversion and energy storage, Višnja Hor- tion particle size analyzer available today. De- vat- Radošević pending on applications and requirements, it 4. Biogeochemistry of metals in sedimentary produces reliable results on particle sizing for systems and soils in Croatia, Goran Kniewald 5. Nature of organic matter, interactions with mi- ZIMO aqueous and non-aqueous samples and dry cro constituents and surfaces in the environ- powders in the range from 20 nm to 2 mm ment, Zlatica Kozarac (Sondi I). 6. Mathematical modelling of circulation and remote sensing of boundary processes, Milivoj EDUCATION Kuzmić 7. Ecological modelling for sustainable manage- Four graduate school studies were coor- ment of resources, Tarzan Legović dinated by the Division members. This in- 8. Elektroanalitical research of microcrystal and cludes: studies on Biophysics with the Uni- traces in dissolved substances, Milivoj Lovrić versity of Split, Environmental Management 9. Interactions of trace metal species in aquatic and Oceanography with the University of environment, Ivanka Pižeta Zagreb, and Environmental Protection and 10. Metal-induced cellular changes in aquatic or- Nature Conservation with the University J.J. ganisms, Biserka Raspor Strossmayer in Osijek. 11. nformation systems on environmental quality and risk, Ivica Ružić HONOURS AND AWARDS 12. Ecotoxicological significance of ABC transport proteins in aquatic organisms, Tvrtko Smital Mirčeski V, Komorsky-Lovrić Š, and Lovrić 13. nanoparticles in biogeochemical processes in M were awarded Macedonian State Award the environment, Ivan Sondi “Goce Delčev”, 2008, for the book “Square- 14. Surface forces on atomic scale applied in Wave Voltammetry. Theory and Application”, marine science and nanotechnology, Vesna Springer, Berlin, 2007. Svetličić Sondi I was awarded The Croatian Acad- 15. Pathology of aquatic organisms in relation to pollution and aquaculture, Emin Teskeredžić emy of Sciences and Arts prize for the high- 16. Networked Economy, Z. Skočir and Jadranka est scientific achievement in natural scienc- Pečar-Ilić es in Croatia. Sondi I was awarded The Scientific Ex- Program supported by the Ministry cellence Award, from the Croatian Ministry of of Sciences, Education and Sports Sciences, Education and Sports for the highly cited article published in Journal of Colloid 1. Biogeochemical processes and environmen- and Interface Science (2004) 275, 177-182. tal risk, Marijan Ahel RBI Annual Report 2008. PROJECTS AND PROGRAMS Selected research, developmental and international projects Research projects supported by the Ministry of Sciences, Education 1. A complex study of marine organic matter and Sports characterization in seas of the European coastal zone, Blaženka Gašparović (Bilateral 1. Organic compounds as molecular markers collaboration with Alfred Wegener Inst Polar of anthropogenic impact to the environment, & Marine Res, Bremerhaven, Germany). Marijan Ahel 2. AFM study of the crystallization of synthe- 2. Radionuclides and trace elements in environ- sized zeolites, Vesna Svetličić (Bilateral Co- mental systems, Delko Barišić

83 operation, Eötvös Loránd university, Buda- 15. Impact of fish farms on marine ecosystems pest, Hungary) of the Adriatic Sea, Goran Kniewald (Croa- 3. Biogeochemical processes in anoxic envi- tian-Slovenian bilateral cooperation) ronments: electrochemistry as an alternative 16. Marine science and coastal management tool for trace metals and sulphur determina- in the Adriatic Western Balkan, An education, Irena Ciglenečki-Jušić (Bilateral collab- tion and research network, Božena Ćosović, ZIMO oration with Eötvös Loránd University, Buda- (Norwegian cooperation programme on re- pest, Hungary) search and higher education) 4. Characterization of river sediment contami- 17. Mechanism of mucilage formation in the nation from humid tropical Hugli River, India Northern Adriatic Sea, Vera Žutić (Bilateral and temperate rivers of Croatia in terms of Cooperation with NSF, USA, Scripps Institu- geochemical and mineralogical data based tion of Oceanography) on weathering, Halka Bilinski (Indian-Croa- 18. Monitoring of freshwater fisheries in 2008, tian bilateral cooperation) Group D – fisheries area Sava; River Sutla, 5. Comparative study between the anthropo- Emin Teskeredžić (Ministry of Agriculture, genically impacted coastal area of Shanghai Fisheries and Rural Development) (China) and the pristine environment of the 19. novel physical chemical techniques to char- Krka river estuary (Croatia), Goran Kniewald acterize the sea surface microlayer, Zlatica (Bilateral cooperation with East China Nor- Kozarac (UK Royal Society) mal unicersity, Shanghai, China) 20. On line toxicity sensors based on modifica- 6. Developmental program for expert basis and tion of membrane organisation, Blaženka studies in freshwater fisheries in 2008, Group Gašparović (NATO, Science for peace and A – fisheries area Kupa, Emin Teskeredžić security programme) (project financed by the Ministry of Agricul- 21. Radiological monitoring around nuclear ture, Fisheries and Rural Development) Power Plant Krško, Željko Grahek (Krško 7. Direct determination of arsenic species in nPP, Slovenia) natural ecosystems by electrochemistry and 22. Radiological Monitoring of Danube River, Del- modelling of its speciation, Dario Omanović ko Barišić (Croatian Waters Management) (ECO-nET, French-Croatian-Bosnian coop- 23. Reference Laboratory, Božena Ćosović, eration project) Dubravka Hršak, Zlatica Kozarac, Biserka 8. Ecosystem Approach for Sustainable Aqua- Raspor (Project funded through the Minis- culture, Tarzan Legović (EU-FP6). try of Regional Development, Forestry and 9. Assessment of hazardous chemical contami- Water Management, Water Management nation in the Sava River basin, Marijan Ahel Directorate) and Tvrtko Smital (nATO Science for Piece) 24. Regular research of radioactivity in marine 10. Electrochemical characterization of marine indicator organisms, Delko Barišić (State of- polysaccharides, Marta Plavšić (Deutsche fice for radiation protection) Forschungsgemeinschaft) 25. Research of biological and physico-chem- 11. Environmental impact assessment of the Man- ical parameters in the Vrana Lake, Emin dalina marine, Neven Cukrov, Željko Kwokal, Teskeredžić (potable water reservoir, island Tarzan Legović (NCP Nautic Centre Prgin) Cres). 12. Environmental impact assessment of the min- eral fertilizer factory in Vukovar, Tarzan Legović ORGANIZED CONFERENCES and B. Hackenberger (Adriatica Dunav) 13. Evaluation of contamination of stream sedi- 1. 1st Regional Symposium on Electrochemistry ments in lithologically different drainage for South-East Europe (RSE-SEE), May 4-8, basins, using advanced geomathematical 2008. Crveni otok, Rovinj, Croatia, Horvat- methods, Stanislav Frančišković-Bilinski Radošević, V. (Austrian-Croatian bilateral cooperation) 2. 7th Symposium of Croatian Radiation Protec- 14. Highly specific determination of illicit drugs in tion Association May 29-31, 2008, Opatija,

RBI Annual Report 2008. Annual Report 2008. RBI municipal wastewater as a basis for the as- Croatia, Grahek, Ž. and Barišić, D. sessment of the drug abuse trends in the City 3. Second Annual Meeting in Albania of the of Zagreb, Senka Terzić (City of Zagreb) Project "Marine science and coastal man-

84 agement in the Adriatic, Western Balkan. An 5. Kuzmić, M. Exploring the Adriatic Bora-in- education and research network", Durresi, duced motions: Observations & Modelling, Albania, September 29 – October 3, 2008, DZLR, Oberpfaffenhofen, Wessling, Germa- Ćosović, B. and Wassman, P. ny, november 11, 2008. 4. First Regional Symposium on Electrochem-

istry of South-East Europe, Rovinj, Croatia, SELECTED PUbLICATIONS ZIMO May 4-8, 2008. Ivošević DeNardis N. rd 5. 3 Christmas Biophysics Workshop: Orga- books nized Molecular Systems, Donja Stubica, Croatia, December 15-16 2008, Svetličić, V. 1. Komarov S. and Legović T. (Eds.) The fifth European Ecological Modelling Conference, INVITED LECTURES Ecological Modelling, Elsevier, pp. 1-177, 212, 2008. 1. Ahel, M. Surfactants and surfactant metab- 2. Barišić, D., Grahek, Ž., Krajcar Bronić, I. and olites in wastewaters and ambient waters, Miljanić, S. (Eds) Proceedings of the 7th Sym- International Conference on Environmental posium of Croatian Radiation Protection As- Research and Mitigation of Water Pollution in sociation. RBI, Zagreb, Croatia. 2008. Romania and in the Lower Danube Region, 3. Deza, M. and Dutour Sikirić, M. Geometry of Bucharest, Romania, September 3-5 2008. Graphs, Polycycles and Two-faced Maps, Se- 2. Svetličić, V. Mucilage phenomenon at the na- ries: Encyclopaedia of Mathematics and its Ap- noscale. Faculty of natural Sciences, univer- plications no. 119, ISBn-13: 9780521873079, sity of Split, October 7 2008. Cambridge university Press, 2008. 3. Ciglenečki, I., Bura-Nakić, E., Carić, M., Kršinić, F., Viličić, D., Burić, Z., Ćosović, B. Scientific papers Seasonal variation of oxic-anoxic conditions in the small, seawater lake (Rogoznica Lake, 1. Cukrov N, Cmuk P, Mlakar M, Omanović D. East Adriatic Coast) related to the global cli- th Spatial distribution of trace metals in the Krka mate changes. Regional Process of the 5 River, Croatia. An example of the self-purifi- World Water : Water in the Mediterranean cation. Chemosphere 2008: 72: 1559. Basin, near East university, Lefkosa, TRnC, 2. Dragun Z, Raspor B, Roje V. The labile metal October 8-10, 2008. concentrations in Sava River water assessed 4. Legović, T. Future of marine resources man- th by diffusive gradients in thin films. Chem agement. Regional process of the 5 World Speciation Bioavailability 2008: 20: 33. Water Forum: Water in the Mediterranean 3. Frančišković-Bilinski S. Detection of geo- Basin near East university, Lefkosa, TRnC, chemical anomalies in stream sediments of October 8-10, 2008. the upper Sava River drainage basin (Slove- nia, Croatia). Fresenius Environmental Bul- letin 2008: 17: 188. 4. Gašparović B, Frka S, Kozarac Z, Nelson A. A method for characterization of sea surface RBI Annual Report 2008. microlayer based on monolayer properties in presence and absence of phospholipids. Anal Chim Acta 2008: 620: 64. 5. Kapetanović D, Vardić I, Kurtović B, Valić D, Teskeredžić E. Detection of the causative agent of furunculosis, Aeromonas salmoni- cida in salmonids of the Krka River. Vet Res Commun 2008: 32: 131. 6. Krznarić D, Helz GR, Bura-Nakić E, Jurašin D. Accumulation mechanism for metal chal- Figure 4. Male spawner Brown Trout (Salmo trutta fario) from cogenide nanoparticles at Hg electrodes: Cu “Krčić”, Knin, fish farm. sulphide example. Anal Chem 2008: 80: 742.

85 7. Kwokal Ž, Sarkar SK, Chatterjee M, 13. Udiković Kolić N, Martin-Laurent F, Devers Frančišković-Bilinski S, Bilinski H, Bhat- M, Petrić I, Begonja Kolar A, Hršak D. Ge- tacharya AK, Bhattacharya BD, Aftab A. An netic potential, diversity and activity of an Assessment of Mercury Loading in Core atrazine-degrading community enriched from Sediments of Sunderban Mangrove Wetland, a herbicide factory effluent. J Appl Microbiol India (A Preliminary Report). Bull Environ 2008: 105: 1334. ZIMO Contam Toxicol 2008: 81: 105. 14. Žaja R, Caminada D, Lončar J, Fent K, Smital 8. Legović T. Adriatic Sea: Impact of the demer- T. Development and characterization of P-gly- sal fishery and evidence of the Volterra prin- coprotein 1 (Pgp1 ; ABCB1) mediated doxoru- ciple to the extreme. Ecol modelling 2008: bicin-resistant PLHC-1 hepatoma fish cell line. 212: 68. Toxicol Appl Pharmacol 2008: 227: 207. 9. Louis Y, Cmuk P, Omanović D, Garnier C, 15. Žic V, Truesdale VW, Cukrov N. The distribu- Lenoble V, Mounier S, Pižeta I. Speciation of tion of iodide and iodate in anchialine cave- trace metals in natural waters: The influence waters – evidence for sustained localised of an adsorbed layer of natural organic mat- oxidation of iodide to iodate in marine water, ter (nOM) on voltammetric behaviour of cop- Mar Chem 2008: 112: 168. per. Anal Chim Acta 2008: 606: 37. 10. Plavšić M, Orlović-Leko P, Kozarac Z, Bura- Chapters in books Nakić E, Strmečki S, Ćosović B. Complex- ation of copper ions in atmospheric precipita- 1. Legović, T. Mathematical Ecology. In: Encyclo- tion in Croatia. Atmospheric Res 2008:87:80. pedia of Ecology, Jørgensen, S.E. and Fath, 11. Sondi I, Škapin SD, Salopek-Sondi B. Bio- B.D. (Eds). Elsevier, 2008, pp 2261-2266. mimetic precipitation of nanostructured col- 2. Smital, T. (2008) Acute and Chronic Effects loidal calcite particles by enzyme-catalyzed of Emerging Contaminants. In: The hand- reaction in the presence of magnesium ions. book of environmental chemistry -Emerging Cryst Growth Des 2008: 8: 435. Contaminants from Industrial and Municipal 12. Terzić S, Senta I, Ahel M, Gros M, Petrović Wastewaters. Barcelo, D. & Petrović, M. M, Barcelo D, Muller J, Knepper T, Marti I, (Eds.), Springer-Verlag, Heidelberg, Germa- Ventura F, Jovančić P, Jabučar D. Occur- ny, 2008, pp 105-142. rence and fate of emerging wastewater contaminants in Western Balkan Region. Sci To- tal Environ 2008: 399: 66. RBI Annual Report 2008. Annual Report 2008. RBI

86 TOP ACHIEVEMENTS OVERVIEW OFTHEDIVISION ewe te oij aes wsen Istria, (western waters Rovinj the between collected since1965at 16 stationslocated parameters, oceanographic and biological Adriatic ecosystem northern changes recent inthe Drastic environment. (Interreg) regardingprotectionof the marine purposes andseveralinternationalprojects ing ofthe Adriatic Seaforthegovernment research, theCentreisinvolvedinmonitor- basic than Other column. water the and ties in benthiccommuni- gional scale,especially to re- from subcellular environment marine search isthestudyofprocessesin of thefollowinglaboratories: The CentreforMarineResearchconsists Head: nenadSmodlaka DIVISIONAL ORGANISATION Centre forMarineResearch Historical datasets of physical, chemical The missionoftheCentreforMarineRe- a a a

toxicology, RenatoBatel Danilo Degobbis marine ecosystem, for processes inthe Laboratory Laboratory formarinemolecular systematic, Ana Travizu Laboratory forecologyand genic globalwarming. 20 years, and atleastinparttotheanthropo- last the in weather dry of periods longer by related to climatic fluctuations, characterized The observed changesare probablypartially to the banofindetergents. polyphosphates phosphorus concentration. It was mainly due of the after a2.5foldreduction late eighties the since significantly more increased it and high very is water River Po the in ratio N/P primary productionprocesses.Infact,the fraction inthe of theunused accumulation contribu- riverine tion. This canbeattributedto an enhanced lower its of spite in sea, However, in the increased the nitrateconcentration increased. transparency water chlo- the of rophyll as well as fraction, nano the of thephytoplanktonbiomass,primarily a decrease occurred, causing gated region intheinvesti- concentrations orthosilicate and orthophosphate of reduction significant dis- charge in2005and2007.Consequently, a water River Po low extremely an with correlated mainly was This 2003. since larly particu- one (1972-1997), to theprevious higher intheperiod1998-2007,compared markedly was column water upper the of ity analysed. delta (Italy),havebeen The salin Croatia) and the zone 12 Nm off the Po River a concentration.Concurrently, the http://www.irb.hr/en/str/cim -

87 2008. Report Annual RBI CIM Alkaline phosphatase activity in an almost balanced inorganic n/P ratio for relation to the nutrient status in microbial requirements. the northern Adriatic Caulerpa racemosa: Adaptive

CIM varieties studied by fatty acid composition

Figure 2. C. racemosa meadow along the coast of St. Juraj isle.

Total lipids and fatty acid composition were monitored seasonally in exposed and shel- Figure 1. PO4 (a), DOP (b), DIN (c), and APA (d) distributions at tered Caulerpa racemosa settlements along the surface during 2004. the coast of St. Juraj isle (Vrsar, Croatia). De- spite the proximities of both populations stud- The role of APA in meeting the seasonal ied, which implies a similar level exposure microbial phosphorus requirements in the to seasonal fluctuations, the alga responses northern Adriatic, an area poor in orthophos- were different. Total lipid changes and fatty phate (PO4), was emphasized. From May to acid composition of the related settlements September, in conditions of exhausted PO4, indicated the differences in thalli condition microbes in upper waters induced high APA during summer and, to some extent, differ- (0.41-5.55 μmol L-1 h-1) to obtain phosphorus ent strategies in cold adaptation during win- from the dissolved organic pool. The high- ter. In August the bad condition of thalli at the est APA was found during spring and sum- sheltered site expressed by low unsatura- mer freshets due to the strongly deficient tion (unS/SAT 0.45) resulted from its sexual PO4 versus inorganic nitrogen supply from propagation state, in contrast to the advanced the Po River. During summer months APA condition of vegetative propagation state at was lower, yet still important for phosphorus the exposed site (unS/SAT: 1.1). The poor recycling, although a low Po River nitrogen thalli condition was related to its slower devel- supply resulted in lower microbial biomass opment at the sheltered habitat, having corre- and consequently in lower APA as well. From spondingly a lower biomass. At this site little to October to December APA in upper waters no difference in total lipids was observed with was low (<0.2 μmol L-1 h-1), even during season. During the winter period (min. temp.

RBI Annual Report 2008. Annual Report 2008. RBI large microbial blooms, when PO4 was prob- 7.7 °C) both settlements altered their fatty ably supplied from deeper waters. APA was acid composition by increasing unsaturation generally irrelevant in deeper waters due to (UNS/SAT up to 1.8), but a pronounced win-

88 ter peak in total lipids occurred at the exposed Alien bivalve species in the site. under similar environmental conditions, northern Adriatic Sea C. racemosa developed different strategies in cold adaptation and propagation state as All but one species of the family Pteriidae a consequence of apparently varying impact (Bivalvia, Pterioida) reported so far from the CIM of the hydrodynamism at these two proximate Mediterranean Sea are introduced to the sites. This study suggests the mode in which Mediterranean either via the Suez Channel exposure impacts the growth cycle of C. rac- (Pinctada radiata, Pteria occa), by aquacul- emosa in temperate regions. ture activities (Pinctada margaritifera, P. radiata) or via shipping (Electroma vexillum). Phototrophic pico- and nanoplank- A few specimens of the lessepsian bivalve ton communities in the northern P. radiata were encountered in the northern Adriatic Adriatic offshore waters (silty-sand bottom, 59 m depth). That was the first record of the species in the Croatian part of Adriatic Sea (Doğan and Nerlović, 2008).

Colonization patterns of the date mussel on artificial structures

Figure 3. 2-D diagram of phototrophic pico- and nanoplankton cells. A colonization pattern of the date mussel on limestone breakwater boulders, which Flow cytometric analysis reveals a more have been placed for 19 years along the complete estimation of abundance and bio- dike of the Rovinj Marina, were studied and mass of all major groups of pico- and nano- compared with natural habitats. In distinction phototrophs in this area than has been available until now, allowing thus a better insight into their potential relative importance both as producers and prey. The first records ofPro- chlorococcus were obtained. Synechococ- cus were the most abundant phototrophs in the area, occasionally matched in number by previously rarely studied phototrophic picoeukaryotes. In terms of biomass, the latter usually comprised more than 50 % of the phototrophic pico-biomass, sometimes up to 90 %. The under-researched phototrophic RBI Annual Report 2008. picoeukaryotes thus seem to be much more important for this ecosystem than was previously thought, while preliminary results on the presence of Prochlorococcus indicate their minor importance in this hydrologically and biologically dynamic area. Estimations of the contribution of each size fraction in the total phototrophic biomass (pico-, nano- and micro-) reveal higher portions of pico- and Figure 4. Date mussels’ boreholes on a breakwater boulder of the marina of Rovinj. In sheltered habitats, 19 years after the placement nano- fraction on average compared to mi- of boulders in the sea, density and total biomass of date mussels cro-fraction. were around 800 individuals m-2 and 3.5 kg m-2 , respectively.

89 from natural habitats, an unexpected high been quantified in detail for the first time for colonization rate and growth of date mussels the northern Adriatic (Ivančić et al., 2008). It was detected on certain unexposed break- has been discovered that alkaline phospha- water boulders so the results could be use- tase plays a vital role in marine microbial CIM ful in predicting the reconstruction of natural communities’ phosphorus recycling in this populations of the date mussel after harvest- orthophosphate-poor area. ing (Devescovi and Iveša, 2008). The effects of hypo-osmotic stress Ecology and distribution of the sponge Aplysina aerophoba in The effects of hypo-osmotic stress on bio- Limski kanal logical parameters in marine molluscs have been employed as a useful tool in pollution Information about sponge distribution pat- assessment. The progressive acclimation of terns and their dependence on light, depth, the mussel Mytilus galloprovincialis to dif- substrate and other factors could be very ferent reduced seawater salinities and its useful for in situ culture and can be utilized to effect on several biochemical markers was improve in vitro maintenance conditions, be- probed and biotests were established. This cause a sustainable growth has not yet been investigation expands understanding of the observed ex situ. An observed decrease of multi-factorial effects of the physical marine abundance and size of A. aerophoba along environment on the specificity of investigat- a depth gradient can be explained with shad- ed biomarkers and biotests, providing insight ing by rocky notches close to the water sur- into the acclimation, adaptive and stress-re- face, by the presence of benthic competi- sponse processes of mussels (Hamer et al., tors (mainly algae) or by high sedimentation 2008). which increases towards the eastern end of the bay (Zucht et al., 2008). Application of the European Union Water Framework Directive Shell biominerals, enzymatic activity and shell matrix proteins A new method for the application of the European Union Water Framework Directive In the last few years, the field of mollus- in the northern Adriatic has been developed. can biomineralization has undergone a tre- Extensive coastal investigations were car- mendous conceptual transformation. Recent ried out to map macroalgae distribution in the advances deal more particularly with the northern Adriatic and to relate their growth structure of shell biominerals at the nano- characteristics with anthropogenic influence scale, and with the identification of an in- and water quality levels (Iveša et al., 2008). creasing number of shell matrix protein components. In this review different aspects of Monitoring the health status of the molluscan shell, from evolutionary and patients from mechanistic viewpoints, are described (Marin et al., 2008). Current research, in collaboration with medical personnel from a local hospital, us- The role of alkaline phosphatase ing surface-confined and bulk powder X-ray diffraction has indicated that renal and uri- The role of alkaline phosphatase in meet- nary biomineralized calculi might not grow

RBI Annual Report 2008. Annual Report 2008. RBI ing the seasonal marine microbial phospho- evenly or have a uniform distribution of rus requirements of the northern Adriatic has constituents. This suggests the preferential

90 inclusion of dominant compounds in the local environment in vivo, and the temporal variance of the dominance of those different compounds may be indicative of the health status of the individual (Lyons et al., 2008). CIM

Figure 6. EROD activity in A) male and B) female Gambusia affinis liver homogenates from ponds, south-western Istrian peninsula. The results are given as a mean values with corresponding standard deviations. The levels of statistical significance (*P < 0.01 and ¤P < 0.05) with a reference site sample (S3 - Bale pond) are indicated.

Figure 5. External morphology of a large human calculus showing non-homogeneous crystal growth and composition.

Mosquitofish as a bioindicator for pesticide pollution

The mosquitofishGambusia affinis, due to Figure 7. DNA integrity in A) male and B) female Gambusia affinis its biological-ecological characteristics and liver homogenates from ponds, south-western Istrian peninsula, due to the biomarker dose-response (MFO Croatia. The results are given as a mean values with correspond- and DnA integrity), is suitable for monitoring ing standard deviations. The levels of statistical significance (*P < of freshwater organochlorine pesticide con- 0.01) with a reference site sample (S3 - Bale pond) are indicated. tamination in general and lindane in particular. The conclusions are based on laboratory family sequences as p63 genes or their ex- experiments with model pesticides and anal- pression isoforms. Our results also indicate ysis of fish living in five Istrian natural ponds p63 as the ancestral gene of the p53 family with different pollution loads. as well as the only gene of the family present in pre-chordate metazoan species.

Analysis of the p63 gene in mollusc RBI Annual Report 2008. Marine pollutants and hypoosmotic Two partial cDNA sequences and one par- conditions cause stress in the tial genomic sequence, all originating from mussel Mytilus galloprovinciali two different p63 alleles were found in one Mytilus galloprovincialis individual. The exon/ The level of acid Dnase activity in the he- intron architecture, DnA and deduced protein mocytes and digestive gland of the mussel sequences were analyzed and compared to Mytilus galloprovincialis changed after expo- p53, p63 and p73 sequences from other or- sure to detergent, gasoline and copper salt, ganisms. The analysis showed our cDNA seas well as to unknown environmental mix- quences code for the TAp63γ isoform of p63 ture at selected sampling sites. Field inves- protein and identified all other molluscan p53 tigations indicated that the digestive gland

91 is a suitable tissue for discrimination of pol- cell cycle and genome size analysis of five luted areas from mariculture areas. Seawa- marine invertebrates with flow cytometry. ter salinity variation (hypoosmotic stress) in Flow cytometry analysis was also introduced the marine environment can affect all investi- as fast and easy to the performed method CIM gated parameters (DnA integrity, p38- MAPK for determination of micronuclei in mussels activation, metallothionein induction, oxygen treated with model pollutants. consumption rate and condition index). New equipment

Dcode system for Denaturating gradient gel electrophoresis (DGGE) is used for characterization of bacterial population structure and dynamics. The method can rapidly provide a characterization of community diversity and composition, and shifts in population can be readily demonstrated. The Rigaku Ultima IV multipurpose X-ray, a fully-equipped state-of-the-art diffractom- Figure 8. Negative DNA integrity SSF×(−1) values measured in gill eter, includes both parafocusing and parallel homogenates of mussels acclimated to different SW salinities during beam geometries, SAXS and WAXS abilities high (summer) and low (winter) seawater temperatures. The results as well as micro area diffraction and accepts are presented in mean values of 4 or 5 gills (each derived from a both solid and liquid-based samples. The single mussel) samples with the corresponding standard deviations. new X-ray diffraction facilities have already Statistically significant differences (P < 0.05) between mussels subjected to SW of 37 and lower salinities in the winter (*) and summer attracted numerous external scientists to es- (¤), and between mussels acclimated to same salinity in winter and tablish scientific collaborations. summer (↔) season are indicated. EDUCATION

The Centre is involved in the organisation of Marine Sciences Studies (undergraduate) at the Juraj Dobrila university in Pula. This is the first time that university courses are performed at our department. The majority of courses are organized by Centre’s scientists. Post-graduate courses were given at the Za- greb, Osijek and Dubrovnik universities.

Figure 9. Similarity analysis of total mussel gills proteins after 1D PROJECTS SDS-PAGE separation: Lim mariculture, mussels subjected finally to 37, 28, 18.5, and 11 salinity during a 14-day acclimation in summer. Differently expressed proteins are indicated by dashed lines. Projects supported by the Ministry A similarity analysis from the acclimation expression protein profiles of Sciences, Education and Sport was performed using an UDGMA algorithm. 1. Impact of pollution on programmed biosyn- Application of flow cytometry in thesis in marine invertebrates, Renato Batel marine environmental research 2. Ecotoxic effects of contamination on marine organisms, nevenka Bihari RBI Annual Report 2008. Annual Report 2008. RBI 3. Biomineralization processes in marine or- For the first time, the genome sizes of ganisms, Davorin Medaković sea mouse and spiny crab were detected by

92 4. Structure and physiology of microbial com- 7. Implementation of the water quality monitor- munities in northern Adriatic fronts, Mirjana ing in the western Istrian coastal sea (north- najdek ern Adriatic) (WICOS), Tamara Đakovac (IN- 5. Mechanism of long-term changes in the TERREG-CARDS/PHARE 2008-2009)

northern Adriatic ecosystem, Robert Precali 8. Proteomique des Mollusques et Biominer- CIM 6. Biodiversity of benthic communities in the Adri- alisation, ProMoBio, F. Marin, D. Kotrošan, atic: natural and human impacts, Ana Travizi Davor Medaković (Egide ECO-NET, France, 2008-2010) Programs supported by the Ministry 9. Carboanhydrase - Gehalt / Aktivität und of Sciences, Education and Sports Biomineralisation in Mittelmeermuscheln und Schwämmen, Hans C. Schröder, Bojan Ham- 1. natural and anthropogenic impacts on the er (Internationales Büro des Bundesministe- Adriatic Sea ecosystem, Renato Batel rium fur Bildung un Forschung – BMBF, MOE 2. Croatian national monitoring programme 08/R55, 2008-2009) Systematic research of the Adriatic Sea as a 10. Development of a Sensor for Marine Biotox- base for sustainable development of the Re- ins, Daniel M. Lyons (Royal Society of Chem- public of Croatia (Project “Adriatic”), nenad istry uK, SensBioTox IRG-4-2008) Smodlaka SELECTED INVITED LECTURES Research, developmental and 1. Devescovi M. Impatto delle mucillaggini sul international projects macrobentos della costa istriana. Corso di Studio in Scienze Ambientali Marine ed 1. Schwaemme aus Rovinj (Kroatien)-Extract- Oceanografia, org. Universita di Bologna in bereitstellung und Marikultur, Project: Mole- Ravenna, Rovinj, 18 June 2008. kulare Biotechnologie und Wirkstoffe mariner 2. Jaklin A. north Adriatic macrobenthos, Corso Schwaemme sowie Schwamm-assoziierter di Studio in Scienze Ambientali Marine ed Mikroorganismen, Renato Batel, Werner E.G. Oceanografia, org. Universita di Bologna in Müller (Croatian German scientific project) Ravenna, Rovinj, 18 June 2008. 2. Biocapital, Marie Curie Research Training 3. Travizi A. Meiofauna as a tool for environ- Network, Renato Batel, Werner E.G. Müller mental quality assessment, Corso di Studio (Eu-FP6, 2005-2008) in Scienze Ambientali Marine ed Oceano- 3. Realization of an integrated monitoring sys- grafia, org. Universita di Bologna in Raven- tem of the quality of the Adriatic Sea, with na, Rovinj, 19 June 2008. particular regard to eutrophication and mu- 4. Iveša Lj, Devescovi M. Assessment of the cilage phenomena (REQuISITE), Danilo ecological status of north-eastern Adriatic Degobbis (Eu InTERREG IIIA, 2004-2006, coastal waters (Istria, Croatia) using macroal- extension 2007-2008) gal assemblages for the European union Wa- 4. Integrated system for monitoring and fore- ter Framework Directive, Workshop Biological casting of meteorological and water condi- Assessment, Coastal waters, European Union tions parameters in the Adriatic Sea (ADRI- Twinning Project Implementing of the Water RBI Annual Report 2008. AMET), Danilo Degobbis (Eu InTERREG Framework Directive in Croatia “Biological as- IIIA, 2004-2008) sessment of transitional and Coastal waters”, 5. Anossie attuali nel nord Adriatico, registra- workshop, Trogir, 30 June 2008. zione nei sedimenti in epoca storica, influ- 5. Travizi A. Implementing the Water Frame- enza sulle risorse di pesca e bentoniche. work Directive in Croatia: Macroinverte- Modellizzazione e previsione (ANOCSIA), brates, Croatian approach, European union Robert Precali (Ministero dell’Istruzione, Twinning Project Implementing of the Water dell’Università e della Ricerca della Repub- Framework Directive in Croatia “Biological blica Italiana, 2004-2008) assessment of transitional and Coastal wa- 6. Monitoring of the marine coastal current of ters”, workshop, Trogir, 30 June 2008. the north Adriatic (nASCuM), nenad Smod- 6. Mičić M, Gobić Medica K, Medica M, Lazar laka (2007-2008) B. Flow cytometric analysis of loggerhead

93 turtle (Caretta caretta) peripheral blood cells 2. Fafanđel M, Bihari N, Smodlaka M, Ravlić S. from north Adriatic Sea, Third Mediterranean Hemocytes/ coelomocytes DNA content in five Conference on Marine Turtles, Yasmine Ham- marine invertebrates: cell cycles and genome mamet, Tunisia, 20-23 October 2008. sizes. Biologia 2008: 63: 730.

CIM 7. Medaković D. X-ray diffraction methods in 3. Hamer B, Jakšić Ž, Pavičić-Hamer D, Perić L, biological, ecological and medical research, Medaković D, Ivanković D, Pavičić J, Zilber- Međunarodni Forum Bosna, Centar za prirod- berg C, Schröder HC, Müller WEG, Smodlaka no naslijeđe, Sarajevo, Bosnia and Herzegovi- N, Batel R. Effect of hypoosmotic stress by low na, 18 november 2008. salinity acclimation of Mediterranean mussel 8. Medaković D. Apoxyomenos, Application of X- Mytilus galloprovincialis on biological param- ray diffraction and spectroscopic methods in eters used for pollution assessment. Aquatic archaeology and museology, Zemaljski muzej toxicology 2008: 89: 137. Bosne i Hercegovine, Sarajevo, Bosnia and 4. Iveša L, Lyons DM, Devescovi M. Assessment Herzegovina, 20 November 2008. of the ecological status of northeastern Adri- atic coastal waters (Istria, Croatia) using mac- SELECTED ORGANIZED roalgal assemblages for the European union CONFERENCES Water Framework Directive. Aquat. Conserv. 2008: DOI: 10.1002/aqc.964. 5. Jakšić Ž, Hamer B, Landeka N, Batel R. West- 1. School of Conservation Biology of the Croa- ern mosquitofish as a bioindicator of exposure tian Biological Society in affiliation with Ruđer to organochlorine compounds. Ecotoxicology Bošković Institute, Centre for Marine Re- & Environmental Safety 2008: 71(2): 426. search, Rovinj, 20-28 June 2008. Hamer B 6. Lucu Č, Pavičić J, Ivanković D, Pavičić-Hamer (Vice Chair), Smodlaka N (Financial director), D, najdek M. Changes in na+/K+-ATPase Pavičić-Hamer D (Organizing committee). activity, unsaturated fatty acids and metallo- thioneins in gills of the shore crab Carcinus SELECTED PUbLICATIONS aestuarii after dilute seawater acclimation. Comparative Biochemistry and Physiology Review articles 2008: 149A: 4: 362. 7. Marie B, Luquet G, Bédouet L, Milet C, Guich- 1. Marin F, Luquet G, Marie B, Medakovic D. ard N, Medaković D, Marin F. Nacre calcifica- Molluscan Shell Proteins: Primary Structure, tion in the freshwater mussel Unio pictorum: Origin, and Evolution. In: Current Topics in De- carbonic anhydrase activity and purification of velopmental Biology, Schatten, P Gerald (ed.). a 95-kDa calcium-binding glycoprotein. Chem- Pittsburgh: Elsevier Science & Technology BioChem 2008: 9 (15): 2515. Books, 2008, pp. 209-276. 8. Vilibić I, Beg Paklar G, Žagar N, Mihanović H, Supić N, Žagar M, Domijan N, Pasarić M. Sum- Scientific papers mer breakout of trapped bottom dense water from the northern Adriatic. Journal of Geophys- 1. Fafanđel M, Bihari N, Perić L, Cenov A. Effect ical Research - Oceans 2008: 113: S1102-1. of marine pollutants on the acid Dnase activ- 9. Zucht, W., Sidri, M., Brümer, F., Jaklin, A., Ham- ity in the hemocytes and digestive gland of the er, B. Ecology and distribution of the sponge mussel Mytilus galloprovincialis. Aquatic Toxi- Aplysina aerophoba (Porifera, Demospongiae) cology 2008: 86: 508. in the Limski kanal (northern Adriatic Sea, Cro- atia). Fresenius Environmental Bulletin 2008: 17(7): 890.

94 rithms, visual interfaces, visual peripherals, rithms, visualinterfaces, visualperipherals, processing, computergraphics, parallelalgo to supportcomputationally basedscience. infrastructure knowledge of generation next ment ofthee-sciencetechnologiesas ondevelop based work, scientific in usage programme istheadvancementofcomputer scientific and researchprogramme. The missionofthis a in engaged actively also is CIR ics andcomputinginfrastructureattheRBI, ordination andmaintenanceoftheinformat Development Scientific Research and OVERVIEW OFTHECENTRE ments: depart- following the of consists (CIC) ing The CentreforInformaticsandComput- Head: KaroljSkala CENTRE ORGANISATION OFTHE and Computing Centre forInformatics The R&D group has experience in signal The R&Dgrouphasexperience insignal In additiontobeingresponsiblefortheco a a a a Đuro Kuzumilović Service andmaintenance, Nikola Pavković Information systems, Davor Davidović ICST researchanddevelopment, Visualisation, KaroljSkala for Optoelectronics and Laboratory - - - - cessing (Sofija,Bulgaria). Hungary), andtheInstituteforParallelPro Technical Slovenia), (Ljubljana, Institute Štefan Jožef Switzerland), (Geneva, CERN with actions tion, CIRhassubstantialcollaborativeinter addi In Services. and Software Technologyfor Platform European a is which Initiative (NESSI), Services and Software Networked European the of member a is Centre The programmes. framework FP7 and 6 FP EU the on based institutions EU 125 with work CIR participatesincontractedcollaborative healthy internationalpresence.Forexample, various domesticprojects,CIRhasavery human-machine interaction. including space, real and virtual in work tive the integrationofuserinterfacesandinterac II project and started with EGEE III through III EGEE with started and project II Unit), finished the work in the EU FP6 EGEE- GridsforEnabling E-science(EGEE) HIGHLIGHTS IN2007 TOP ACHIVEMENTS OR On top of a national scientific program and The CRO-GRIDJRu(JointResearch u niversity Budapest (Budapest, niversity Budapest(Budapest, http://www.irb.hr/en/str/cir - - - - -

95 CIR out 2008. In addition to the existing PARF Digital Research Infrastructure for (Parallel Random Forests classification) and the Arts and Humanities (DARIAH) QRBGS (Quantum Random Bit Generator Service), http://random.irb.hr/ a new service In the last quarter of 2008, the FP7 proj- CIR was introduced: the Protein Database Visu- ect DARIAH began. The initial efforts were alisation Generator (PDVG). mainly focused on building a sustainable web page. The new web page was built on South Eastern European GRid-en- a completely new system and new function- abled e-Infrastructure Development alities were added. We have been testing (SEE-GRID) existing technologies focused on work with SRM protocol and GFAL libraries. In the Eu FP6 SEE-GRID-2 project, as the leader of the Work Package (WP4), CIR actively worked on the collection and sys- tematisation of gained knowledge on Appli- cations Gridification, acting as the editor of a Deliverable to the EC.

Centre for Scientific Visualization (CenVis)

The accomplished goals of the CenVis Eu FP 6 project during this year progress are seen in several large points such as infrastructure development, dissemination actions and regional and national cooperation. We upgraded existing e-Infrastructure with new Figure 1. ICT 2008 Conference in Lyon, ATOMARIUM announced on 3D Display from Holografika and won second prize in “Best processor cluster installation, the establish- Exhibit” Award. ment of a visualization laboratory, selection, evaluation and acquisition of distributed Information Systems development computing and visualization equipment. The and service usage CenVis Informational portal (Vision point) up and running, promotional packages that The Information Systems Department include Grid and Visualization conference continued the efforts to integrate the AAI@ introduced on 31st International Conven- EDU.HR LDAP database with ActiveDirec- tion MIPRO for the purpose of presenting tory database from the Institute’s headquar- the growing development of techniques and ters, aiming to create a unified Single Sign technologies in science. On infrastructure and ensure the basic Ser- CIR, together with the Faculty of Graphi- vices at RBI. cal Arts, a university institution which is Besides maintaining the core infrastruc- perceived as very important in the general ture ICT facilities and services, the Informa- direction of CIR towards Scientific Visu- tion systems department established a new alisation, is working on a Grid Application infrastructure service – OpenVPN, which called VEPPAR (Visual Parallel Processing had entered the testing phase by the end of and Rendering). The first version of this Ap- 2008. We also continued the effort to migrate plication was already used in educational all workstations to the internal network, pro- activities. viding better security for the end-user and the ICT system as a whole. Figure 2 shows

96 the per-month distribution of migrated work- The number of user accounts is slightly stations: increasing, with Figure 6 showing the number of new user accounts added each month. CIR

Figure 2. Number of workstation migrated to internal networks.

The main web-server (www.irb.hr), which provides information to the general public, is Figure 4. Number of resolved tickets. also maintained by the Information systems department. The CMS-driven core engine enables users to develop extended functionality web-applications suc as time-schedule applications etc. Figure 3 shows the per- month distribution of unique visits:

Figure 5. Number of printed pages.

Figure 3. Number of visitors to the RBI web domain.

User support

Our helpdesk is continuing its usage of OTRS ticketing system, which has proven it- self to be an indispensable tool for everyday Figure 6. Number of LDAP user accounts. operations. Figure 4 shows the per-month distribution of resolved issues tracked by OTRS. Project initiatives Printing and teleconferencing services continued to function without any major CIR prepared seven Eu FP7 project pro- problems. Figure 5 shows the statistics of posals for ICT Calls in 2008. In this way, we the public printing service. aim to continue the e-Science program ori-

97 entation and form a project chain on the line brought in from a European Institute for the of e-Infrastructure, distributed computing, purpose of lecturing. parallel applications and scientific visualisation technologies. We also started with Atom- ORGANISATION OF CIR arium project initiatives. This project consists CONFERENCES AND SPORTING of distributed network storage of micro world EVENTS (atoms, genes, proteins etc.) of virtual images that comes from daily rendering on a Grid CIR organized the annual Conference infrastructure and provides search and 2/3D Grid and Visualisation Systems as part of the display in the Atomarium in much the same International Convention MIPRO in Opatija way as planetarium displays planets (macro (http://www.mipro.hr/gvs.htm). world). At the ICT 2008 Conference in Lyon, ATOMARIuM announced on 3D Display PROJECTS AND PROGRAMS from Holografika and won second prize in “Best Exhibit” Award. Projects supported by Ministry of Sciences, Education and Sports New Equipment 1. Scientific Visualisation Methods, Karolj Skala Inside the framework of the Croatian Na- tional Grid Infrastructure CRO NGI a new Programs supported by the Ministry HP blade 96 processor cluster was installed of Sciences, Education and Sports at RBI, for furthering scientific research. During 2008 CIR continued the eScience 1. Distributed Computing and Visualisation programme based on ICST (Information (2007-2012), Karolj Skala Communication Science Technology) on Grid platforms. The Scientific Visualization International EU FP6 projects Laboratory was completed. A number of active network devices were acquired and de- 1. Grid enabled Infrastructure Development, ployed with aim of extending network capac- SEE GRID, Eu F6, 002356, Karolj Skala ity of the RBI core network. These consist of 2. Enabling Grids for E-science-II (EGEE-II), mainly Cisco GB switches. Eu F6, 031688 , Karolj Skala 3. South Eastern European GRid-enabled eIn- frastructure Development 2 (SEE GRID 2) EDUCATIONAL ACTIVITIES Eu FP6, 031775, Karolj Skala 4. Centre for Scientific Visualisation (CenVis), CIR provides 5 undergraduate and 3 Eu FP6, 043947, Karolj Skala graduate courses at Faculty of Electrical 5. Interactive Visual Analysis of Bio-signals – Engineering and computing and Faculty of IVAB, SEE ERA NET, Karolj Skala Graphical Arts at the university of Zagreb. We also hosted the High Performance Com- International EU FP7 projects puting on Grid for Meteorological Applica- tions Workshop, encompassing present 1. Enabling Grids for E-science-III (EGEE-III), Eu FP7, Con. no. 222667, Karolj Skala cluster and grid technologies and the WRF 2. South Eastern European GRid-enabled eIn- prognostic model to wider public with spe- frastructure Development 2 (SEE GRID SCI) cial focus on the meteorological community. Eu FP7, Con. no. 211338, Karolj Skala As part of FP project initiatives, courses and 3. Digital Research Infrastructure for the Arts seminars were held in cooperation with sev- and Humanities, DARIAH Con. no. 211583, eral universities in Zagreb. For the benefit Karolj Skala of training, an experienced researcher was

98 SELECTED PUbLICATIONS

1. Karainova A, Atanassov E, Gurov T, Steva- 2. Kolarić D, Skala K, Dubravić A: Integrated novic R, Skala K: Variance Reduction MCMs System for Forest Fire Early Detection and

with Application in Environmental Studies: Management, Period Biol 2008: 110: 205. CIR Sensitivity Analysis. Applications of Math- ematics in Engineering and Economics. New York: American Institute of Physics, 2008. pp. 549-558.

99 100 OVERVIEW OFTHECENTRE Rijeka and organized a number of scientific of number a organized and Rijeka ofZagreb,Split,Osijek,and universities the at inlecturing to beinvolved continued tre ent was taken out. The scientists of the Cen in highrankingjournalsandapat- published were contributions These chemistry. state chemistry,graph theory, chemical andsolid chemistry,ganometallic photochemistry, bio- valuable contributionsto peptide andor- u Faculty of the of Pharmacy and Biochemistry the at located spectrometer Gemini NMR MHz Varian 300 a and spectrometers NMR MHz 600 and Avance300 Bruker of consists Croatia. Thebasicequipment ofCentre the in nity, industry and institutions governmental commu academic the from researchers and scientists for services performs and research niversity of Zagreb. niversity following laboratories: consistsofthe The Centre Dražen Vikić-Topić) Head: DejanPlavšić(replacementfor CENTRE ORGANIZATION OFTHE Magnetic Resonance Centre forNuclear a a In 2008, the members of the Centre made In 2008,themembersofCentre scientific conducts NMR for Centre The

Moguš-Milanković glasses, Andrea for Laboratory and modelling,DejanPlavšić for nMRspectroscopy Laboratory - - were maintained. Republic Czech the and key,Russia, Brazil, Slovenia, Germany, Hungary,Romania, Tur - Austria, USA, in groups research with tions conferences andcourses. Active collabora- Figure 1. The NMRoperators’ roomwithaviewon7T magnet. http://www.irb.hr/en/nmr

101 nMR TOP ACHIEVEMENTS Correlation between microstructure and electrical Assignation of NMR spectra of new properties of ZrTiO4 ceramics compounds

nMR A series of ZrTiO4 ceramics were pre- Novel β-3-thienyl and β-3-furyl derivatives pared by sintering ball-milled precursor of o-divinylbenzene have been synthesized powders. Ceramics with homogenously and their photochemical behaviour com- dispersed micropores containing both low- pared with 2-thienyl and 2-furyl derivatives. temperature (ordered) and high-temperature Photochemical reactions were monitored (disordered) ZrTiO4 phases were achieved and products were determined by NMR by sintering at 1400°C. The porosity and spectroscopy (Vidaković et al., 2008). the morphology were modified by changing Cadmium(II) complexes of 3-hydroxypico- the sintering time. The impedance spectra linic acid, [CdI(3-OHpic)(3-OHpicH)(H2O)]2, followed the observed changes in the ce- [Cd(3-OHpic)2(H2O)2], and [Cd(3-OHpic)2]n, ramics’ microstructure. The grain boundar- were prepared and characterized by NMR ies’ shape, rather than the grain size, has spectroscopy. In the DMF solution of all the the major influence on the conductivity. The prepared complexes, only the monodentate lowest value for electrical conductivity, 8.1 × mode of 3-OHpicH binding to cadmium(II) 10−10 (Ω•m)−1, was obtained in the ceramics through the carboxylate O atom was deter- sintered at 1400°C for 4 h. This confirms the mined by 1H, 13C, 15n and 113Cd nMR spec- blocking effect of the imperfect grain bound- troscopy (Kukovec et al., 2008). aries; i.e., the defects of the grain bound- A number of derivatives of thymol, car- aries, which were formed during the grain vacrol, and eugenol were synthesized and growth, were followed by an almost com- their structures determined by nMR spec- plete loss of pores (Ličina et al., 2008). troscopy. The obtained derivatives showed remarkably better antioxidative properties according to 1,1-diphenyl-2-picrylhydrazyl and Rancimat assays in comparison with parent compounds and similar antioxidative properties to butylated hydroxytoluene and vitamin C (Mastelić et al., 2008).

Application of methods of discrete mathematics to various chemical problems

It has been shown that topological con- siderations based on the eigenvectors of the Laplacian matrix are able to give reasonable Figure 2. a) Changes of the DC conductivity for ZrTiO4 ceramics shapes of pure carbon nanotube junctions sintered at various temperatures and times, b) SEM images of samples sintered at 1400 °C for 1 h, c) 4 h, d) and 8 h. The insets (Graovac et al., 2008). show HRSEM images. The well known Zagreb and variable Za- greb indices M1 and M2 have been studied Patent and in the case of acyclic molecules unexpected inequalities among these indices have PCT/HR2008/000037, 11989. Kopriva I, been proven (Vukičević and Graovac, 2008). Jerić I, Smrečki V. Method of and system for

102 blind extraction of more than two pure com- burger (Neven Žarković, Andrea Moguš- ponents out of spectroscopic or spectromet- Milanković) ric measurements of only two mixtures by 5. The origin of structural defects and their in- means of sparse component analysis. fluence on macroscopic properties of solar silica glass, Davor Gracin (Andrea Moguš- Milanković), (NFS Croatia, Ruđer Bošković nMR EDUCATION Institute-Lipik Glas d.o.o.)

In 2008, the members of the Centre Contracts with industry taught 5 undergraduate and 9 postgraduate courses at universities in Zagreb, Split, 1. Collaboration contract with PLIVA d.d. Osijek, and Rijeka. 2. Collaboration contract with BELUPO d.d. 3. Collaboration contract with Croatian Institute PROJECTS of Viticulture and Enology 4. Collaboration contract with Lipik Glass d.o.o. Projects supported by the Ministry of Sciences, Education and Sports SELECTED INVITED LECTURES

1. nMR Spectroscopy and Modelling of Bioac- 1. Graovac A. Topological coordinates for car- tive Molecules, Dejan Plavšić bon nanotubes junctions. The First Confer- 2. Modelling of molecules and materials by ence and Workshop on Mathematical Chem- methods of mathematical and computational istry, Tarbiat Modares university, Teheran, chemistry, Ante Graovac. Iran, January 29-31, 2008. 3. Modelling of bioactive molecules and test- 2. Graovac A. On two rather different appli- ing of their properties and activity, nikola cations of directed graphs to chemistry. Štambuk Workshop on Metric Graph Theory and Ap- 4. Influence of structure on electrical properties plications, Isfahan Institute of Technology, of (bioactive) glasses and ceramic, Andrea Isfahan, Iran, February 2-3, 2008. Moguš-Milanković 3. Graovac A, Laszlo I, Pisanski T. Shape analysis of carbon nanotubes junctions. The rd Research, developmental and inter- 23 International Conference MATH/CHEM/ COMP 2008, Verbania, Italy, June 10-13, national projects 2008. 4. Šantić A. Ion dynamics in room temperature 1. Multi-field experimental high resolution NMR ionic liquids - II, complex fluidity measure- studies with applications to bioactive com- ments. Institute of Physical Chemistry, uni- pounds, Vilko Smrečki, (MSES, bilateral col- versity of Műnster, Germany, June 19, 2008. laboration with Austria, WTZ HR 19/2008) 5. Štambuk N. Molecular recognition theory 2. Applications of topological, geometric, alge- and its application in vaccine development braic and combinatorial methods in sciences, and toxicology. BIT Life Sciences 1st World Ante Graovac (MSES, bilateral collaboration Congress of Vaccine, WCV-2008, Foshan, with Slovenia). China, December 1-5, 2008. 3. Investigation of the ion dynamics in ionic liquids by measuring their frequency-dependent mechanical properties, Ana Šantić SELECTED ORGANIZED (Postdoctoral project, nFS Croatia, Institute CONFERENCES AND COURSES of Physical Chemistry, University of Műnster, Germany) 1. Regional Training Course on How to Write 4. Novel method to support bone growth bioac- Competitive Research Proposals for Various tive glass coated with protein/lipid poroxida- Funding Programmes, RER/0/023, IAEA, tion products, nationalbank Jubiläumsfonds Zagreb, Croatia, March18–20, 2008, orga- Grant (Nr. 12611), LKH Graz, Renate Wild- nized by A. Moguš-Milanković.

103 2. The 23rd International Conference on the In- characterization of some novel cadmium(II) terfaces among Mathematics, Chemistry and complexes with 3-hydroxypicolinic acid Computer Sciences, Verbania, Italy, June (3-OHpicH). Crystal and molecular struc- 10-13, 2008., organized by A. Graovac. tures of [CdI(3-OHpic)(3-OHpicH)(H2O)]2, rd 3. The 23 International Course on the Inter- [Cd(3-OHpic)2(H2O)2] and [Cd(3-OHpic)2]n. nMR faces among Mathematics, Chemistry and Polyhedron 2008: 27: 1479. Computer Sciences, Dubrovnik, Croatia, 3. Mastelić J, Jerković I, Blažević I, Poljak- June 16-21, 2008., organized by A. Graovac, Blaži M, Borović S, Ivančić-Baće I, Smrečki D. Vikić-Topić, D. Plavšić. V, Žarković N, Brčić-Kostić K, Vikić-Topić D, 4. The 10th Central European nMR Symposium Müller N. A comparative study on the anti- & The 10th Central European Bruker nMR oxidant and biological activities of carvacrol, users Meeting, Zagreb, Croatia, September thymol and eugenol derivatives. J Agr Food 29-30, 2008, organized by V. Smrečki. Chem 2008: 56: 3989. 4. Graovac A, Laszlo I, Pisanski T. Shape anal- SELECTED PUbLICATIONS ysis of carbon nanotube junctions. MATCH- Commun Math Comput Chem 2008: 60: 917. 1. Vidaković D, Škorić I, Horvat M, Marinić Ž, 5. Vukičević D, Graovac A. Comparing vari- Šindler-Kulyk M. Photobehaviour of 2- and able Zagreb M1 and M2 indices for acyclic 3-heteroaryl substituted o-divinylbenzenes; molecules. MATCH-Commun Math Comput formation of fused 2,3- and 3,2-heteroarene- Chem 2008: 60: 37. benzobicyclo[3.2.1]octadienes and 3-het- 6. Ličina V, Gajović A, Moguš-Milanković A, eroaryl enzobicyclo[2.1.1]hexsenes.Tetrahe- Djerdj I, Tomašić N, Su DS. Correlation be- dron 2008: 64: 3928. tween the microstructure and the electrical 2. Kukovec BM, Popović Z, Pavlović G, properties of ZrTiO4 ceramics. J Am Ceram Vinković M, Vikić-Topić D. Synthesis and Soc 2008: 91: 178.

104 GOALS ANDObJECTIVES ACTIVITIES OVERVIEW OFLIbRARY a priority. becomes redesign sitecompleteweb library and technologies, newest from best the ting get not is site web Library of state present The growing. constantly and daily 3500 than sitewasmore web library ourof visits of ber num average the and users library by well idly changingenvironment. to arap- strategies andtacticalapproaches information technologyexpertsto articulate and researchers, librarians, between ration library functions. strongcollabo This includes of redefinition continuous and library services of development the by followed be scholarly communicationin general should technology.and of theresearch Changes changing landscapedominatedby digital and asapartofthedynamic the RBILibrary rethinking constantly are we sense, this In beginning and endingtheirquestforinformationonline. are Researchers content. tized access tothedigi easy andsimpleonline by characterized is research century ty-first Library In 2008 our virtual entity was recognized was entity virtual our 2008 In twen- early of landscape information The Head ofLibrary:JadrankaStojanovski - - - - protocol (OAI-MHP) are widely accepted. accepted. widely are (OAI-MHP) protocol like theopenarchivesmetadataharvesting Standards affordable. now are repositories and significantly dropped have costs storage online charge, of free and developed well are programmes software Supporting possible. efforts cametogetherto makethisstrategy Many technologytrendsand development ing throughthelicensingofdigitalcontent. publish scholarly modernizing in publishers ly passiveroleofsupportingbigcommercial munication, bothmovingbeyondtheirrelative taking placeinscholarshipandscholarlycom systematic leveragetoacceleratechanges research institutesanduniversitiestoapply allows that strategy new a as emerged ries Figure 1.Librarywebsite. The developmentofinstitutionalreposito http://library.irb.hr - - - -

105 LIB The thinking about digital preservation over time and attention, even the reduced num- the past five years has advanced to the point bers of print publications remained an impor- where the needs are widely recognized and tant part of our collection and will continue to well defined. At RBI Library we started with do so well into the future. In 2008, we sub- LIB digitization of photographic materials in 2008. scribed 90 printed journals as addition to the All digital materials are stored in the institu- electronic version. Lack of stable financing tional repository based on ePrints. and delays in subscription, supported by pub- In 2008 RBI Library focused the efforts lisher’s subscription policies not guaranteeing in building a comprehensive bibliography of continuous access, made subscribed digital RBI papers, together with their citations from content fragile and unreliable. The book col- Web of Science database. It is well known lection amounts to 22,173 volumes, 491 of that scholarly writing is grounded in prior re- which were newly acquired in 2008. search. Citations are demonstrating that RBI publications are referenced and addressed by authorities in the field. Bibliography will provide different bibliometric and sciento- metric analysis necessary for evaluation purposes to improve quality of the research.

COLLECTIONS

Digital collection

The journal acquisition model in 2008 continued to be realized through “big deals” with main world publishers as Elsevier, Springer, Blackwell, Nature Publ. etc., subscribed at the national consortia level directly by the Ministry of Sciences, Education and Sports Figure 2. Library during Open days. (MSES). Beside 20.000 e-journals available to the Croatian academic community, Interlibrary loan RBI subscribed 57 e-journals of the smaller, but not less important publishers. The ac- The RBI Library collection, which repre- cess to the e-journal collection, as to the rel- sents accumulated knowledge, besides being evant bibliographic and full-text databases, a tool that makes research and scholarship was realised mainly through the Centre for possible at RBI, serves scholarly community online databases (http://www.online-baze. in Croatia and abroad. The RBI Library has hr) and in-house developed RBI Library por- a well-established interlibrary loan service tal to e-journals Pero (http://knjiznica.irb.hr/ with other libraries mainly from Croatia, Ger- pero), which became very popular inside the many, united Kingdom and uSA. In 2008, it research community. Over 60 fee and free fulfilled 870 requests for documents made by databases, over 20.000 e-journals and 42 e- RBI staff, and over 495 requests from other books were available to RBI researchers. libraries. Interlibrary loan requests have been handled through online application SEnD de- Printed collection veloped in-house. Through cooperation with numerous libraries we have built and exten- While the organization and accessibility of sive shared collection of greater depth than digital resources accounted for most of our any of the libraries could build alone.

106 SERVICES

The RBI Library web site is the place

where we offer our digital collections and ser- LIB vices. The Library web site is the main access point to the online catalogue and networked resources, carefully selected and organized. In 2008, the Library web site received over 100,000 visits in an average month. The virtual library serves the same diverse population as the physical library, so we organize it to accommodate multiple levels of researcher’s demands. The Library web site is created and maintained by Library staff for the benefit of the entire research community. The Library is working systematically on an extension of the network services made available to users. There were numerous other efforts to give our patrons better tools for accessing information and using the library, requiring less effort from them and allowing much of the basic library staff assistance to be given indirectly. This assistance included: • Library Colloquia (http://knjiznica.irb.hr/ hrv/kolokviji.html) • Library Blog (http://knjiznica.irb.hr/blog) • PERO – e-journals portal (http:// knjiznica.irb.hr/pero) • SEnD - Interlibrary Loan service (http:// send.irb.hr) • CROSBI – Croatian Scientific Bibliography (http://crosbi.znanstvenici.hr) • Who’s Who in Croatian Science (http:// tkojetko.znanstvenici.hr) • HRČAK – portal of Croatian scientific journals (http://hrcak.znanstvenici.hr) • CMS for web sites of Croatian academic and research libraries (http://knjiznice. Figure 3. Library Colloquia. szi.hr) • Centre for online databases (http://www. NEW LIbRARY MANAGEMENT online-baze.hr). SYSTEM

The new Library Management System, which was evaluated and selected by Cro- atian national and university Library for all Croatian higher education and research li-

107 braries, was still not implemented in librar- Faculty of Philosophy, the Faculty of Econom- ies during 2008. The Voyager system was ics and the Faculty of Civil Engineering, from elected to support library functions such 24-25 October 2008, with 200 participants. as acquisition, cataloguing, and interlibrary LIB loan and financed by MSES for all Croatian academic and research libraries. Implemen- tation of Voyager would permit the RBI Li- brary to utilize state-of-the art technology for delivering services. As Voyager was not implemented, a decision was made for migra- tion to the integrated library system KOHA, which is an open source software available to every library and supporting all modules. During 2008, the conversion from unIMARC to MARC21 standard has been done as cus- tomisation of KOHA modules. Figure 5. Librarian’s 2008 conference with information management as a main topic. EDUCATION IT PROJECTS Library staff members are involved in graduate level teaching at university J. J. Stross- In 2008, we continue or activities on the mayer in Osijek and university of Zadar. projects included in the Croatian Scientific As part of the Centre for continuing edu- Portal: Croatian Scientific Bibliography, Who’s cation of librarians we provide several Build- Who in Science in Croatia, HRČAK – portal of ing digital collection courses. Croatian scientific journals, Pair of Compass- es – inventory of the scientific equipment although without the formal contract with MSES and proper financing. The project Centre for online databases was realized through cooperation with the Croatian Academic and Re- search Network (CARNet) and MSES.

SELECTED LECTURES

1. Macan B, Mayer M. Virtual Reference Ser- vice or to Serve Virtual References? RBI Library Experience. LIDA 2008: Education and Training in Digital Libraries & Reference Figure 4. Students (primary school) education. in Digital Environments. Selthofer Josipa, Aparac-Jelušić Tatjana, Krtalić Maja (ed). 2008. 242. CONFERENCE ORGANIZATION 2. Stojanovski J. International visibility of the Croatian scientific output and HRCAK role (in The 8th Annual conference of the Croatian Croatian). CuC 2008: Internet 10.0. Rijeka, Academic and Scientific Libraries 2008 enti- Croatia, 10-12 november 2008. tled “Scientific information management” was 3. Stojanovski J. Science in Croatia. TEMPuS organized by the RBI Library, Croatian Aca- “Capacity Building for Research in Croatia”, demic and Research Network CARNet, the Zadar, Croatia, October 30, 2008.

108 SELECTED PUbLICATIONS

1. Konjević S. Chemical Education Digital Li- support of Croatian scientific journals (in Cro- brary. Chemistry in industry 2008: 57: 323. atian). Chemistry in industry. 2008: 57: 115. 2. Macan B. Detronization of impact factor?! - 4. Mayer M. Depth-First: Walking the Web of LIB appearance of the new, free benchmark SCI- Chemical Information. Chemistry in industry mago Journal Rank (in Croatian). Chemistry 2008: 57: 70. in industry 2008: 57: 262. 5. Mayer M. Interlibrary loan - what, why, how 3. Macan B, Stojanovski J. Analysis of the Minis- and how much (in Croatian)? Chemistry in try of Sciences, education and sports financial industry 2008: 57: 380.

109 110 Rudjer Innovations Ltd.

http://www.r-i.hr

COMPANY ORGANIZATION

Head of Management Board, CEO: Domagoj Oreb Member of Management Board, CFO: Dinko Smolčić Member of Management Board: Božidar Etlinger Business Development Manager: Davorka Moslavac Forjan Business Development Manager: Davor Aničić Business Development Manager: Rudjer Innovations is open to the entire Cro- Lidija Stopfer atian public. Project Analyst: Matea novosel The mission of R-I is to contribute to the development of Croatia as a knowledge society by linking the scientific and research community with enterprises and business- OVERVIEW OF THE COMPANY es and thus through commercialisation of knowledge strengthen the competitiveness Rudjer Innovations (R-I) is a company of Croatia in the global market. specialised in commercialisation of innova- The goal is to establish a cooperation tions and technology transfer. It links science which brings mutual interest, ensuring a win- and technology with economy and industry. win result, with numerous competitive ad- The company is open both to the scien- vantages for both companies and scientists. tific community, including researchers and The activities of R-I include: discovery and innovators, helping them commercialise in- evaluation of intellectual property, protection novations and scientific research results, of intellectual property rights, and assistance and to companies that are willing to apply in selecting and implementing an appropriate the know-how of the scientific community in commercialization model (licensing, estab- their business operations. lishing spin-off companies, joint ventures). Rudjer Innovations Ltd was founded with The company provides consultancy services the full support of the Government and the for technology transfer and business agree- World Bank as a daughter company of the ments, as well as financial support for inno- Ruđer Bošković Institute (RBI). Its aim is to vations and projects. The company aims to promote the cooperation and partnership of help Croatian innovators and scientists and research institutes, universities and innova- to make their knowledge more competitive tor communities with commercial entities. on world markets.

111 TOP ACHEIVEMENTS 1 patent application, and 1 licence. By the end of 2008, it had expanded significantly Portfolio to the point where now it has 7 employees, more than 80 projects (32 from outside RBI), The portfolio of Rudjer Innovations con- 32 patent applications in different protec- tains more than 80 innovations and scientific tion stages with 16 more to come, 7 licence projects in various fields with commercial po- agreements, 1 patent granted and 3 spin-off tential but primarily in chemistry, medicine, companies. The company employees made biology, physics and informatics. Some have contacts with more than 100 companies from already been applied in industry and econo- Croatia and abroad. It is planned to continue my, and others have been prepared for vari- this expansion in 2009 through the establish- ous methods of commercialisation, depend- ment of additional spin-off companies, the ad- ing on the interest and needs of buyers and dition of new innovations to the portfolio and partners. Besides its portfolio of innovations, the intensification of the connection between Rudjer Innovations works on strengthening Croatian science and industry. By doing so, the cooperation between Ruđer Bošković In- the principle aim is to establish RI as a re- stitute and companies from various business gional leader in the area of commercialization areas. RBI’s know-how, professionalism and of science and technology. Other key aims in- multidisciplinary approach in solving prob- clude: becoming the leading organisation for lems of all kinds represent a great potential assessment, protection and commercialisa- for cooperation with companies. tion of intellectual property in Croatia; creating The Rudjer Innovations database of inno- and becoming the central part of a network vations, projects and spin-off companies is of researchers, entrepreneurs, business com- available at a click of the mouse at web page munities, banks and investors whose mutual www.r-i.hr. goal is to ensure optimum commercialisation of intellectual property; and finally, increasing Expansion the number of activities and ensuring funding and support for future research and continu- Rudjer Innovations began its existence ous innovations development as well as ad- in 2006 with a single employee, 1 project, ditional funds for rewarding inventors.

112112

Ruđer Bošković Institute

The Ruđer Bošković Institute (RBI) is the largest Croatian research centre in sciences and science applications. In the multi-disciplinary environment of the Institute more than 500 academic staff and graduate students work on problems in experimental and theoretical physics, chemistry and physics of materials, organic and physical chemistry, biochemistry, molecular biology and medicine, environmental and marine research, electronics, informatics and computer science. Within Croatia, the RBI is a national institution dedicated to research, higher education and provision of support to the academic community, to state and local governments and to technology-based industry. Within the European union, the RBI forms a part of the European Research Area. World- wide, the RBI collaborates with many research institutions and universities upholding the same values and vision.