RESEARCH AND DOCTORAL STUDIES

FACULTy OF SCIENCEUniversity of South Bohemia in České Budějovice

HISTORY AND CHARACTERISTICSOF THE UNIVERSITY OF SOUTH BOHEMIAUSB is a research university focusing mainly on natural sciences, social sciences, and humanities. A signi� cant aspect of the scienti� c research activities is close coopera-tion with the Academy of Sciences of the Czech Republic. The university comprises eight faculties, which are located in the historical centre of the town and on the uni-versity campus on its western edge. The campus also comprises student residences, a Rector’s o� ce and the buildings of the Biology Centre of the Academy of Sciences of the Czech Republic.

Applicants for the Bachelor’s, Master’s, and Doctoral degrees may choose from 229 majors with a range of further specializa-

tions. The study of 24 majors is conducted in English and 3 in German. All faculties and institutes provide PhD study pro-grammes in chosen � elds of study and the majority of them have the right to name professors and associate professors.

FACULTY OF SCIENCEUniversity of South Bohemia in České BudějoviceBranišovská 31, CZ-370 05 České Budějovicewww.prf.jcu.cz

of the Czech Republic.

Applicants for the Bachelor’s, Master’s, and Doctoral degrees may choose from 229 majors with a range of further specializa-

tions. The study of 24 majors is conducted in English and 3 in German. All faculties and institutes provide PhD study pro-grammes in chosen � elds of study and the majority of them have the right to name professors and associate professors.

University of South Bohemia is a state university, founded in 1991. It is located in the regional centre of South Bohemia, the town of České Budějovice (population approx. 100 000), about 150 km south of Prague. The town was established in the thirteenth century as a “King’s town” by the Czech King Přemysl Otakar II at the con� uenceof the rivers Vltava and Malše.

The university participates in the Erasmus exchange programme, Erasmus Mundus, Comenius, Aktion, FM EHP/Norska, Yggdrasil-Research stay in Norway, Leonardo da Vinci, Fulbright Commission, and other programmes concerning international cooperation in research, development, and innovation. In 2007 the first cross-border common study programme, Biological Chemistry, was initiated with the Johannes Kepler University of Linz, Austria.

The preparation of other crossborder programmes is in progress, e.g. with the University of Passau, Germany. The university is the Local Contact Point for the EURAXESSCzech Services Centre: Researchers in Motion, which provides foreign scientists with help and advice in arranging stays in the Czech Republic.

The dormitories hold 2300 places. All rooms (mostly double rooms) are connected to the academc computer network and the Internet. There is a modern cafeteria located on campus which has several branches in the town to cater for students with lectures there. Sports facilities include gyms, an athletics stadium, and basketball, volleyball, and tennis courts.

Basic information aBout the universityThe University of South Bohemia is a public educational and research institution of the university type, with eight faculties offering a selection of tertiary education programmes.

numBer of students: 13.450

total numBer of staff: 1.870

RectoR’s officeBranišovská 31a, CZ-370 05 České Budějovice, Czech Republic

• Professor Libor Grubhoffer (Rector), rektor@jcu.cz

• Professor Miroslav Papáček (Vice-Rector, Education and Student Affairs), prorektor-studium@jcu.cz

• Associate Professor Dagmar Škodová Parmová (Vice-Rector, External and Foreign Relations), prorektor-zahranici@jcu.cz

• Professor Tomáš Polívka (Vice-Rector, Research), prorektor-veda@jcu.cz

• Associate Professor Hana Čížková (Vice-Rector, Development), prorektor-rozvoj@jcu.cz

• Eng. Ivan Hájek (Chancellor), ihajek@jcu.cz

• Eng. Hana Kropáčková (Bursar), hkropack@jcu.cz

• Associate Professor Michal Bauer (Academic Senate), bauer@ff.jcu.cz

2 | 3

faculty of PhilosoPhyDean: Professor Vladimír Papoušek Address: Branišovská 31a, CZ-370 05 České Budějovice, Czech Republichttp://www.ff.jcu.cz

faculty of theology Dean: Associate Professor Tomáš MachulaAddress: Kněžská 8, CZ-370 01 České Budějovice, Czech Republichttp://www.tf.jcu.cz/

faculty of education Dean: Mgr. Michal Vančura Address: Jeronýmova 10, CZ-371 15 České Budějovice, Czech Republichttp://www.pf.jcu.cz/

faculty of economicsDean: Associate Professor Ladislav RolínekAdress: Studentská 13, CZ-370 05České Budějovice, Czech Republichttp://www.ef.jcu.cz/

faculty of health and social studies Dean: Professor Valérie Tóthová Address: Jírovcova 24, CZ-370 04 České Budějovice, Czech Republichttp://www.zsf.jcu.cz/

faculty of agRicultuReDean: Professor Miloslav ŠochAddress: Studentská 13, CZ-370 05České Budějovice, Czech Republichttp://www.zf.jcu.cz/

faculty of fisheRies and PRotection of WateRsDean: Professor Otomar LinhartAddress: Zátiší 728/II, CZ-389 25 Vodňany, Czech Republichttp://www.frov.jcu.cz

faculty of scienceDean: Professor František Vácha Address: Branišovská 31, CZ-370 05 České Budějovice, Czech Republic http://www.prf.jcu.cz/

faculties

Basic information aBout the faculty of scienceThe Faculty of Science is a successor of the Faculty of Biological Sciences founded in 1991. FS offers undergraduate, graduate and post-graduate study in an array of biological disciplines, and since 2007 extended by several other fields of science (chemistry, physics, mathematics, informatics).

The three-year Bachelor’s Programmes supply  students with the basic knowledge necessary either for subsequent Master’s studies or for practical professional employ-ment. Students choose from either the “Introductory Biology Programme” (preparation for further studies in Biology or Biology for future teachers), “Biophysics”, “Chemistry and Chemistry for future teachers“, “Applied math-ematics“, “Mathematic for future teachers“, “Physics and Physics for future teachers“, “Measuring and computer technology“ or from professionally orientated programmes, – “Ecology and Environmental Care”, “Biomedical Laboratory Techniques” or “Applied informatics”. These programmes are conducted in the Czech language only, although the students are required to achieve a knowledge of English sufficient to allow them to study from English textbooks. In addition to the study programmes conducted in Czech, the Faculty of Scienceoffers an elite Bachelor’s programmes of “Biological chem-istry” and “Bioinformatics” running in English. The study programmes is carried out within a bilateral cross-border collaboration between the Johannes Kepler University in Linz (Austria) and the Faculty of Science of the University of South Bohemia in České Budějovice. The programmme “Biological chemistry” represents an alternative exten-sion of modern molecular, cellular and structural biology towards biochemistry, bio-organic chemistry, and biophysics.

The Master’s programmes are open to any student who has successfully finished a Bachelor’s programme in biology or related fields at any university. Applicants are accepted on a competitive basis, depending on their results in the admission examination. They may enter different study fields – “Biological chemistry”, “Biophysics”, “Botany”, “Clinical Biology”, “Ecology”, “Experimental Biology”, “Parasitology”, “Zoology”, “Physics” or “Mathematics for future teachers”. Since 2008 it has also been possible to study individual study programmes in combinations

4

offered for double-major and teacher training courses. Most of these programmes are conducted in Czech only, some also in English and the number of English versions is expected to grow. Students gain more theoretical knowledge in their field of specialization and also produce a diploma thesis which should result in a paper to be published in the appropriate regular international scientific journal. Due to the growing interest in exchange programmes for students (such as Socrates/Erasmus) in Europe or even further afield, the programmes offer foreign students a set of half-year courses with a number of interconnected topics.

The Doctoral level may be of particular interest to foreign students. The Ph.D. study fields are shown in the table, and more details on individual programmes are provided on the pages indicated.

Ph.D. programme

Programme director contact Co-operating institutions Guaranteeing department

Botany Prof. Karel Prach (420)-387772220 prach@prf.jcu.cz

Institute of Botany AS CR Department of Botany

Zoology Assoc. Prof. František Sedláček

(420)-387772258 fsedlac@prf.jcu.cz

Biology Centre of AS CR, Institute of Vertebrate Biology AS CR, Institute of Animal Physiology and Genetics AS CR

Departmnet of Zoology

Entomology Assoc. Prof. Oldřich Nedvěd

(420)-387772253 nedved@prf.jcu.cz

Biology Centre of AS CR Departmnet of Zoology

Ecosystem Biology

Prof. Hana Šantrůčková

(420)-387772361 hasan@prf.jcu.cz

Biology Centre of AS CR Department of Ecosystem Biology

Hydrobiology Prof. Jaroslav Vrba (420)-387775873 jaroslav.vrba@prf.jcu.cz

Biology Centre of AS CR, Institute of Microbiology AS CR

Department of Ecosystem Biology

Molecular and Cell Biology and Genetics

Assoc. Prof. Miroslav Oborník

(420)-387775428 obornik@paru.cas.cz

Biology Centre of AS CR, Institute of Animal Physiology and Genetics AS CR

Department of Genetics and Department of Molecular biology

Parasitology Assoc. Prof. Oleg Ditrich

(420)-387775420 oleg@paru.cas.cz

Biology Centre of AS CR Department of Parasitology

Physiology and Developmental Biology –Animal or Plant Specialization

Prof. Dalibor Kodrík,

Assoc. Prof. Jiří Šantrůček

(420)-387775271 kodrik@entu.cas.cz, (420)-387775527 jsan@umbr.cas.cz

Biology Centre of AS CR, Institute of Microbiology AS CR

Department of Animal Physiology and Department of Plant Physiology

Biophysics Prof. Tomáš Polívka (420) 3807773824 tpolivka@jcu.cz

Biology Centre of AS CR, Global Change Research Centre AS CR

Institute of Physics and Biophysics

Other departments and institutes at FS: Department of Medical Biology, Institute of Chemistry and Biochemistry, Institute of Mathematics and Biomathematics, Institute of Applied informatics

5

dePartment of Botany homepage: http://botanika.prf.jcu.cz/head of the department: Prof. Jan lepše-mail: suspa@prf.jcu.cz

research and education activitiesThe Department of Botany is responsible for the Botany Master‘s and Doctoral programmes. The research covers all fields of botany, including taxonomy and the ecology of plants, and also mycology. The main research topics include:

Plant systematicsThe plant systematics group focuses on the microevolution process (particularly the study of hybridization, polyploid and cryptic speciation), and the ecological differentiation of populations and phylogeography of vascular plants, bryophytes and lichens, using both molecular and conventional methods.

PhycologyPhylogenetic relationships of Cyanobacteria and various groups of algae are studied using a polyphazic approach – combined approach using classical methods of optical microscopy, electron microscopy and moleculardata. Moreover, we focus on the ecological role of algae and Cyanobacteria in extreme environments in tropical and polar biotopes.

Plant ecology and vegetation scienceIn this field the ecology of individuals, populations, and

communities, and vegetation on the landscape scale are studied. Individual working groups investigate the ecology

of hemiparasitic plants and their interactions with their hosts, species coexistence in plant communities and the effects of species diversity and ecological invasions. Special attention is paid to methods of (multivariate) data analysis and modelling. Long term research is devoted to vegetation dynamics, especially succession, and its exploitation in restoration ecology. Research is also focused on linking plant functional traits with

species adaptations in extreme alpine and arctic conditions and plant responses to land use changes in

central European species-rich meadows.

ArcheobotanyThe laboratory of archaeobotany and palaeoecology deals with the

analysis of large scale plant micro and macro remains, for example pollen, seeds, diatoms, charcoal, and wood from archaeological sites as well as natural and seminatural sediments. The laboratory’s research programme is concentrated on the postglacial period in Central Europe.

6 | 7

examPle of resultsPublications:Novák, J., Lisá, L., Pokorný, P. & Kuna, M. (2012) Charcoal analyses as an environmental tool for the

study of Early Medieval sunken houses infills in Roztoky near Prague, Czech Republic. Journal of Archaeological Science 39: 808 – 817.

Šmilauerová, M., Lokvencová, M. & Šmilauer, P. (2012) Fertilization and forb:graminoid ratio affect arbuscularmycorrhiza in seedlings but not adult plants of Plantago lanceolata. Plant and Soil 351:309–324.

Doležal, J., Mašková, Z., Lepš, J., Steinbachová D., de Bello, F., Klimešová, J., Tackenberg, O., Zemek, F.& Květ, J. (2011) Positive long-term effect of mulching on species and functional trait diversity in a nutrient-poor mountain meadow in Central Europe. Agriculture, Ecosystems and Environment 145:10-28.

Holá, E., Kučera, J. & Těšitel, J. (2011) Comparison of gemma production among three Lophozia species during the growing season. Flora 206: 691-768.

Kaštovský, J., Fučíková, K., Hauer, T. & Bohunická, M. (2011) Microvegetation on the top of Mt. Roraima, Venezuela. Fottea 11: 171-186.

Klimešová, J., Doležal, J.& Sammul, M. (2011) Evolutionary and organismic constraints on the relation-ship between spacer length and environmental conditions in clonal plants. Oikos 120: 1110-1120.

Komárek, J., Kaštovský, J. & Jezberová, J. (2011) Phylogenetic and taxonomic delimitation of the cyanobacterial genus Aphanothece and descriptions of  Anathece gen. nov. European Journal of Phycology 46(3): 315-326.

Lepš, J., de Bello, F., Šmilauer, P. & Doležal, J. (2011.) Community trait response to environment: disentangling species turnover vs intraspecific trait variability effects. Ecography 34: 856-863.

Prach, K.& Walker, L. R. (2011) Four opportunities for studies of ecological succession. Trends in Ecol-ogy and Evolution 26: 119-123.

Těšitel, J., Lepš, J., Vráblová, M. & Cameron D.D. (2011) The role of heterotrophic carbon acquisition by the hemiparasitic plant Rhinanthus alectorolophus in seedling establishment in natural communities: a physiological perspective New Phytologist 192: 188-199.

Košnar, J., Košnar, J., Herbstová, M., Macek, P., Rejmánková, E.& Štech, M. (2010) Natural hybridiza-tion in tropical spikerushes of Eleocharis subgenus Limnochloa (Cyperaceae): Evidence from morphology and DNA markers. - American Journal of Botany 97:1229-1240.

Novák, J., Petr, L. & Treml, V. (2010) Late-Holocene human-induced changes to the extent of alpine areas in the East Sudetes, Central Europe. The Holocene 20: 895-905.

Řehounková, K. & Prach, K. (2010) Life-history traits and habitat preferences of colonizing plant spe-cies in long-term spontaneous succession in abandoned gravel-sand pits. – Basic and Applied Ecoogy11: 45-53.

Ph.D. theses:Fibich, P. (2012) The effects of neighbours in plant communities: mathematical and experimental

approaches. Těšitel, J. (2011) Biology of the Root-Parasitic Rhinanthoid Orobanchaceae.Sosnová, M. (2011) Ecological constraints limiting the root-sprouting

ability in wetland plant species. Šoun, J. (2011) Taxonomy of selected groups of the genus

Caloplaca.Štastná, P. (2011) Ecology of Rumex alpinus – a retrospec-

tive studies using annual growth markers on rhi-zomes.

Konvalinková, P. (2010) Spontaneous vegetation succes-sion in mined peatlands.

Stibal, M. (2009) Photoautotrophic microorganisms in the glacial ecosystem of Svalbard, high Arctic.

Ekrt, L. (2009) Diversity, variability and distribution of polyploid groups of ferns in Central Europe.

dePartment of ZooloGy homepage: http://zoo.prf.jcu.cz/ head of the department: dr. Roman fuchs e-mail: fuchs@prf.jcu.cz

research and education activities The Department of Zoology is responsible for the Zoology and Entomology Master’s and Doctoral programmes. The Ph. D. programmes are designed to provide students with a thorough overview of biology, ecology and the evolution of animals, and with a good knowledge of modern zoological methodology. The studies are focused on animal phylogeny, ecology and the behavior of fish, birds, mammals, and insects, and animal population ecology. The main areas of focus are listed below:

Phylogeny of animal taxa Phylogenetic relationships are studied using molecular as well as morphological data within various animal taxa. Based on the results of phylogenetic analyzes various question are addressed, such as the origin and role of sociality, body mass etc.

Ecology of plant-insect interactions in tropical rainforests The study of plant-insect food webs in tropical rainforests focuses on the ecological and evolutionary determinants of biodiversity and community structure. We have established a solid logistical base in Papua New Guinea, providing access to tropical ecosystems.

Behavior and phylogeny of cichlids Ecological studies in fish will be transferred to the new Faculty of Fishery and Conservation of Waters in the near future. It is planned that the study of behavior and phylogeny in cichlids will be concetrated on over the next several years because of the high biodiver-sity anticipated.

Cognitive ethology of birds Passerine birds are tested for their ability to distinguish relevant optic patterns and situ-ations coding information on food quality and availability or predation risk. The acoustic information channel is studied using original or modified playbacks.

Biology and ecology of terrestrial and subterranean rodents We are focused on the main features of adaptation

of Bathyergids to the subterranean environment. Field studies are carried out at the localities of

their origin in East Africa. Abundance and population-genetic structure is observed

in fragmented populations to determine their future fate. In vole populations the role of behavioral traits is analyzed.

examPle of resultsPublications: Konvička, M., Zimmermann, K., Klímová, M., Hůla, V., Fric, Z. (2012) Inverse

link between density and dispersal distance in butterflies: field evi-dence from six co-occurring species. POPULATION ECOLOGY 54: 91-101.

Machač, A., Zrzavý, J., Storch, D. (2012) Range Size Heritability in Carnivora Is Driven by Geographic Constraints. AMERICAN NATURALIST 177: 767-779.

Novotný, V., Miller, S. E., Hrček, J., Baje, L ., Basset, Y., Lewis, O. T., Stewart, A. J. A., Weiblen, G.D. (2012) Insects on Plants: Explaining the Paradox of Low Diversity within Specialist Herbivore Guilds. AMERICAN NATURALIST 179: 351-362.

Piálek, L., Říčan, O., Casciotta, J., Almiron, A., Zrzavý, J. (2012) Multilocus phylogeny of Crenicichla (Teleostei: Cichlidae), with biogeography of the C. lacustris group: Species flocks as a model for sympatric speciation in revers. MOLECULAR PHYLOGENETICS AND EVOLUTION 62: 46-61.

Roy, H. E., Adriaens, T., Isaac, N. J. B., Kenis, M., Onkelinx, T., San Martin, G., Brown, P.M. J., Hautier, L., Poland, R., Roy, D. B.,Comont, R., Eschen, R., Frost, R., Zindel, R., Van Vlaenderen, J., Nedvěd, O., Ravn, H. P. Gregoire, J. C., de Biseau, J. C., Maes, D. (2012) Invasive alien predator causes rapid declines of native European ladybirds. DIVERSITY AND DISTRIBUTIONS 18: 717-725.

Dammann, P., Šumbera, R., Massmann, C., Scherag, A., Burda, H. (2011) Extended Longevity of Reproductives Appears to be Common in Fukomys Mole-Rats (Rodentia, Bathyergidae). PLOS ONE 6: e18757.

Klimeš, P., Janda, M., Ibalim, S., Kua, J., Novotný, V. (2011) Experimental suppression of ants foraging on rainforest vegetation in New Guinea: testing methods for a whole-forest manipulation of insect communities. ECOLOGICAL ENTOMOLOGY 36: 94-103.

Rodrigues, H. G., Marangoni, P., Šumbera, R., Tafforeau, P., Wendelen, W ., Viriot, L. (2011) Continuous dental replacement in a hyper-chisel tooth digging rodent. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 108: 17355-17359.

Groves, C. P., Fernando, P., Robovský, J. (2010) The Sixth Rhino: A Taxonomic Re-Assessment of the Critically Endangered Northern White Rhinoceros. PLOS ONE 5: e9703.

Tvrdíková, K., Fuchs, R. (2010) Tits use amodal completion in predator recognition: a field experiment. ANIMAL COGNITION 13: 609-615.

Dolenská, M., Nedvěd, O., Veselý, P., Tesařová, M., Fuchs, R. (2009) What constitutes optical warning signals of ladybirds (Coleoptera: Coccinellidae) towards bird predators: colour, pattern or general look? BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 98: 234-242.

Spitzer, L., Konvička, M., Beneš, J., Tropek, R., Tuf, I. H., Tufová, J. (2008) Does closure of traditionally managed open woodlands threaten epigeic invertebrates? Effects of coppicing and high deer densities. BIOLOGICAL CONSERVATION 141: 827-837.

Riegert, J., Pešata, M., Janeček, Š., Sedláček, O., Reif, J., Hořák, D., Hrazský, Z., Brom, J., Bartoš, M., Bystřická, D. (2007) Ecological interactions between plants and sunbird species in Bamenda Highlands, North-West Cameroon. OSTRICH 78: 322-322.

Ph.D. Theses:Hrouzková, E. (2012) Vibrational communicatio of subterranean rodents.Jůza, T. (2011) Distribution and density of pelagic 0+ fish in canyon-shaped reservoirs and

effectiveness of their sampling by fry trawls.Klimeš, P. (2011) Diversity and ecology of arboreal ant communities in a tropical lowland forest . Kovačiková, L. (2011) Archeozoology of the Neolithic of Bohemia. Lantová, P. (2011) Causes and consequences of personalities in microtine rodents.Lovy, M. (2011) Ecology and activity of mesic Afrotropic mole-rats.Robovský, J. (2011) Evolution of arvicoline rodents (Mammalia: Cricetidae): phylogenetical

approach.Sroka, P (2011) Systematics of mayflies (Ephemeroptera) of the family Baetidae.Konečná, M. (2010) Personality, social hierarchy and hormones in primates.Veselý, P. (2010) Dangerous prey recognition in avian predators.

8 | 9

dePartment of ecosystem BioloGyhomepage: http://kbe.prf.jcu.cz/ head of the department: Prof. hana Šantrůčkováe-mail: hana.santruckova@prf.jcu.cz

Research and education activities The Department of Ecosystem Biology is responsible for the Environmental Ecology Bachelor’s programme, the Ecosystem Biology Master’s and Doctoral programmes, and the Hydrology Doctoral programme. Within the scope of the Ecosystem Biology programme students can chose one of five specializations: Theoretical Ecology, Conservation Biology, Applied Ecology, Hydrology and Soil Biology. Our faculty is the only one in the Czech Republic that offers a study programme focused on soil biology in the ecosystem context.

The research covers both terrestrial and aquatic ecosystem studies, the catchment–lake approach, the ecology of aquatic and soil organisms, microbial ecology, processes in soil, and aquatic and wetland ecosystems disturbed by human activity. It employs advanced molecular techniques, experiments on model organisms, long-term site-based field observations, mathematical modelling and the use of remote sensing in ecology.

HydrobiologyThe research focuses on carbon and nutrient fluxes, aquatic microbial ecology, biotic interactions within pelagic food webs, and fish ecology, particularly in man-made reservoirs and acidified headwater lakes.

Ecosystem BiologyThe research deals with carbon, nitrogen, and phosphorus fluxes and transformations in wetland, forest, and pasture ecosystems with a focus on plant-soil interactions, primary production, C and nutrient transformations in soil and the composition of soil microbial communities. The experimental data are used in the detection of forest disturbances and their subsequent regeneration using remote sensing. Conservation biology focuses on the ecology and management of endangered species, using orchids as a model group.

examPle of resultsPublications:Prchalová, M., Neal, J,W., Munoz-Hincapie,

M., Juza, T., Říha M., Peterka J., Kubečka J. (2012) Comparison of Gill Nets and Fixed-Frame Trawls for Sampling Threadfin Shad in Tropical Reservoirs. Transactions of The American Fisheries Society 141: 1151-1160.

Čuhel, J., Šimek, M. (2011) Effect of pH on the denitrifying enzyme activity in pasture soils in relation to the intrinsic differences in denitrifier communities. Folia Microbiologica 56: 230-235.

Jersáková, J., Malinová, T., Jeřábková, K., Dötterl, S. (2011) Biological Flora of the British Isles: Pseudorchis albida (L.) Á . & D. Löve. Journal of Ecology 99: 1282-1298.

Jirout, J., Šimek, M., Elhottová, D. (2011) Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle. Soil Biology & Biochemistry 43: 647-656,

Šimek, K., Kasalický, V., Zapomělová, E., Horňák, K. (2011) Alga-Derived Substrates Select for Distinct Betaproteobacterial Lineages and Contribute to Niche Separation in Limnohabitans Strains. Applied and Environmental Microbiology 77: 7307-7315.

Urbanová, Z., Picek, T., Bárta, J. (2011) Effect of peat re-wetting on carbon and nutrient fluxes, greenhouse gas production and diversity of methanogenic archaeal community. Ecological Engineering 37: 1017-1026.

Sirová, D., Borovec, J., Šantrůčková, H., Šantrůček, J., Vrba, J., Adamec, L. (2010) Utricularia carnivory revisited: plants supply photosynthetic carbon to traps. Journal of Experimental Botany 61: 99–103.

Zemanova K., Picek T., Dušek J., Edwards K., Šantrůčková H. (2010) Carbon, nitrogen and phosphorus transformations are related to age of a constructed Wetland. Water, Air, & Soil Pollution 207: 39-48.

Ph.D. theses: Kasalický, V. (2012) Ecophysiological characteristics of key members of Betaproteobacteria in

freshwater bacterioplankton.Říha, M. (2012) Dynamics of fish spatial distribution in reservoirs.Sirová, D. (2012) Hunters or gardeners? Plant-microbe interactions in rootless carnivorous

Utricularia.Ameixa, O.M. (2011) Trends in insect biodiversity in a changing Word.Čuhel, J. (2011) The linkage between denitrification activity, N gas emissions, and the size of the

denitrifier community in pasture soils.Jirout, J. (2011) The impact of outdoor cattle overwintering husbandry on soil fungal community.Kintrová, K. (2010) Modelling the population dynamics and prey-predator interactions in an aphid-

ladybird system.Chroňáková, A. (2009) Diversity of the soil microbial community and its functional aspects in-man

influenced environments. (Ecology)Schödelbauerová I. (2009) Orchid diversity. (EB)Wotavová-Novotná K. (2009) Optimisation of management strategies and revitalisation techniques

for some terrestrial orchid species. (Ecology)

10 | 11

dePartment of Genetics homepage: http://kgn.umbr.cas.cz/head of the department: assoc. Prof. Jindřich Bříza e-mail: briza@umbr.cas.cz

research and education activities The Department of Genetics is responsible for the Experimental Biology Master’s programme (specialization Genetics and Genetic Engineering) and for the Mo-lecular, and Cell Biology, and Genetics Doctoral programmes. Its research activities include the genetic engineering of plants, molecular genetics and the diagnosis of plant viruses, viroids, and phytoplasmas, and the molecular cytogenetics and population genetics of insects.

Genetic engineering of plants Several members of the department have had a long involvement in work on plant trans-genesis . At present we focus on the development of transgenic tissue lines in spruce showing high toxicity towards bark beetle species, new biotechnological approaches to nepovirus GFLV (Grapevine Fanleaf Virus) resistance creation in grapevine rootstock culti-

vars, and human papillomavirus protein production in transgenic crop plants. Molecular genetics and diagnosis of plant pathogenes

The topics of research are the functional genomics of hop, the analysis of plant transcriptional factors in relation to me-

tabolome regulation and the analysis of the mechanism of gene silencing in relation to viroid propagation and

pathogenesis. Research on plant nucleases, namely their function and potential utilization in medicine as an

anticancer agent, is also conducted. Concerning plant pathogenes, the research is focused on the diseases of brassicas, legumes, small fruit and fruit trees that are difficult to diagnose, and the development of molecular diagnostics, including those based on microarrays.

Molecular cytogenetics and evolutionary genetics of insects

The cytogenetic research is focused on the study of the molecular composition and differentiation of

W and Z sex chromosomes in moths and butterflies (Lepidoptera) with an aim to disclose the evolutionary

history of lepidopteran sex chromosomes, understand their role in sex determination, and discover new options

for the development of genetic sexing strains. In evolutionary genetics research is done in two areas, on the molecular evolution

of gene families in Drosophila and on the development of molecular markers that may help to solve taxonomic problems and phylogenetic

questions in aphids of the family Adelgidae.

12 | 13

examPle of resultsPublications:Dufková, P., Macholán, M., Piálek, J. (2011) Inference of selection and

stochastic effects in the house mouse hybrid zone. Evolution 65: 993-1010.  

Novotná, J., Havelka, J., Starý, P., Koutecký, P., Vítková, M. (2011) Karyotype analysis of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae) reveals a large X chromosome with rRNA and histone gene families. Genetica 139: 281-289.

van‘t Hof, A., Edmonds, N., Dalíková, M., Marec, F., Saccheri, I. (2011) Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin. Science 332: 958-960.

Viktorinová, I., Kučerová, L., Böhmová, M., Henry, I., Jindra, M., Doležal, P., Žurovcová, M., Žurovec, M. (2011) Characterization of two closely related alpha-amylase paralogs in the bark beetle, Ips typographus (L.). Archives of Insect Biochemistry and Physiology 77: 179-198.

Bříza, J., Růžičková, N., Niedermeierová, H., Dusbábková, J., Vlasák, J. (2010) Phosphomannose isomerase gene for selection in lettuce (Lactuca sativa L.) transformation. Acta Biochimica Polonica 57: 63-68.

Matoušek, J., Kocábek, T., Patzák, J., Stehlík, J., Füssy, Z., Krofta, K., Heyerick, A., Roldan-Ruiz, I., Maloukh, L., De Keukeleire, D. (2010) Cloning and molecular analysis of HlbZip1 and HlbZip2 transcription factors putatively involved in the regulation of the lupulin metabolome in hop (Humulus lupulus L.). Journal of Agricultural and Food Chemistry 58: 902-912.

Nguyen, P., Sahara, K., Yoshido, A., Marec, F. (2010) Evolutionary dynamics of rDNA clusters on chromosomes of moths and butterflies (Lepidoptera). Genetica 138: 343-354.

PhD. theses:Dufková, P. (2011) Sex chromosomes in the house mouse hybrid zone.Koloniuk, I. (2010) Turnip ringspot virus: differentiation of new species in the Comovirus genus.Fuková, I. (2007) Molecular cytogenetic analysis of the sex chromosome W in Lepidoptera.Lenz, O. (2007) Parallel detection of selected fruit trees viruses by oligonucleotide microarrays. Vítková, M. (2007) Structural and molecular differentiation of sex chromosomes in Lepidoptera.

dePartment of molecular BioloGy homepage: http://kmb.prf.jcu.cz/cs/head of the department: Prof. ivo Šaumane-mail: sauman@entu.cas.cz

research and education activitiesMolecular parasitology Trypanosomes are protists that have found unorthodox solutions to a number of cell processes. We are studying the function of numerous proteins of the mitochondrion of T. brucei, causative agents of the sleeping sickness. We are also involved in the screening of certain chemical compounds that are toxic to these parasites.

Evolutionary protistology We have recently described the phylum Chromerida, a novel group of secondary algae closely related to apicomplexan parasites. Genomes, transcriptomes and proteomes of two of these algae are now being sequenced, and their life cycles, cellular biology, and metabolism are being extensively investigated.

Molecular basis of the insect circadian clock and diurnal rhytmicity Circadian and seasonal (photoperiodic) biological clocks are found in most living organisms and their fundamental properties are highly conserved. The long-term goal of this project is to gain a general understanding of the cellular and molecular mechanisms that underlie circadian rhythmicity in insects.

Molecular neurobiology We want to understand how the human brain works. We are using a combination of linear and non-linear optical phenomena with molecular biology tools, towards the development of techniques that will allow optical monitoring of the electrical and chemical activity of neurons.

Mechanisms of cell fate decisions The worm, Caenorhabditis elegans, offers a unique model in which the differentiation of individual cells can be followed during the development of the animal. We use the tools of RNA interference and modern microscopy to study the molecular signals that determine cellular fate and the formation of distinct organs and tissues.

Insect development Insects are the most numerous and diverse group of animals on Earth. We study the action of juvenile hormones and steroid hormones on metamorphosis, a dramatic developmental transition from crawling larvae to flying adults. We use various insect model species and a broad array of genetic and molecular methods. Fruit fly Drosophila melanogaster as a model for human diseases. Using the powerful genetic tools available via the study of Drosophila as a model, we study the role of adenosine in the regulation of energy metabolism during immune response and the role of the CKIepsilon gene in cancer.

14

Developmental biology and genomics Understanding the molecular mechanisms that direct cell-fate and function using the pre-implantation mouse embryo as model system. We also Investigate cell-to-cell communication via the Notch signaling pathway, using Drosophila genetics and molecular biology techniques.

examPle of resultsPublications:Acestor, N., Zíková, A., Dalley, R.A., Anupama, A.,

Panigrahi, A.K., Stuart, K.D. (2011) Trypanosoma brucei mitochondrial respiratome: composition and organization in procyclic form. Molecular & Cellular Proteomics 10, 1–14.

Allen, A.E., Dupont, C.L., Oborník, M., Horák, A., Numes-Nesi, A., McCrow, J.P., Zheng, H., Johnson, D.A., Hu, H., Fernie, A.R., Bowler, C. (2011) Evolution and metabolism significance of the urea cycle in photosynthetic diatoms. Nature 473, 203-209.

Charles, J.P., Iwema, T., Epa, V.C., Takaki, K., Ryneš, J. and Jindra, M. (2011) Ligand-binding properties of a juvenile hormone receptor, Methoprene-tolerant. Proc. Natl. Acad. Sci. USA 108, 21128-21133.

Kořený, L., Sobotka, R., Janouškovec, J., Keeling, P.J., Oborník, M. (2011) Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites. Plant Cell 23, 3454-3462.

Lazar, J., Bonsae, A., Timr, S., Firestein, S. (2011) Two-photon polarization microscopy reveals protein structure and function, Nature Methods 8, 684-690.

Gray, M.W., Lukeš, J., Archibald, J.M., Keeling, P.J. and Doolittle, W.F. (2010) Irremediable complexity? Science 330, 920-921.

Janouškovec, J., Horák, A., Oborník, M., Lukeš, J. and Keeling, P.J. (2010) A common red algal origin of the apicomplexan, dinoflagellate and heterokont plastids. Proc. Natl. Acad. Sci. USA 107, 10949-10954.

Jedrusik, A., Bruce, A.W., Tan, M.H., Leong, D.E., Skamagki, M., Yao, M. and Zernicka-Goetz, M. (2010). Maternally and zygotically provided Cdx2 have novel and critical roles for the early development of the mouse embryo. Dev. Biol. 344, 66-78.

Kobelková, A., Bajgar, A. and Doležel, D. (2010) Functional molecular analysis of a circadian clock gene timeless promoter from the drosophilid fly Chymomyza costata. J. Biol. Rhythms 25: 399-409.

Žuberová, M., Fencková, M., Šimek, P., Janečková, L., Doležal, T. (2010). Increased extracellular adenosine in adenosine deaminase deficient flies activates a release of energy stores leading to wasting and death. Disease Models & Mechanisms 3: 773-84.

Hajdušková, M, Jindra, M, Herman, M.A. and Asahina, M. (2009) The nuclear receptor NHR-25 cooperates with the Wnt/β-catenin asymmetry pathway to control differentiation

of the T seam cell in C. elegans. J Cell Sci. 122, 3051-3060.Krejčí, A., Bernard, F., Housden, B.E., Collins, S., Bray, S.J. (2009) Direct response to

Notch activation: signaling crosstalk and incoherent logic. Science Signal. 2(55).Zhu, H., Šauman, I., Yuan, Q., Casselman, A., Emery-Le, M., Emery, P. and Reppert,

S.M. (2008) Cryptochromes define a novel circadian clock mechanism in monarch butterflies that may underlie sun compass navigation. PLoS Biol. 6, e4. doi:10.1371/journal.pbio.0060004.

15

dePartment of ParasitoloGyhomepage: http://kpa.prf.jcu.cz/ head of the department: Prof. Václav hypšaemail: vacatko@paru.cas.cz

research and education activities The Department of Parasitology is responsible for the Parasitology Master’s and Doctoral programmes. The research covers structural, ecological, biochemical, phylogenetic, and molecular aspects of parasite biology, and is focused on several dominant areas.

Protist and metazoan parasites associated with fishThe long tradition of fish parasite research is associated with several laboratories of the Institute of Parasitology ASCR. The majority of the topics are connected to Microsporidia, Myxosporidia, Amphizoic amoebae, Cestodes, and Trematodes infecting fish hosts. The research includes various aspects of parasite biology, including morphological/

ultrastructural characterization and the description of new parasite species, elucidation of their life cycles, and evolutionary studies

using the tools of molecular phylogeny.

Medical and veterinary parasitologyThe research deals with organisms causing

opportunistic infections, such as cryptosporidians and microsporidians. It employs natural

and experimental infections to study such parameters as the susceptibility of the hosts, host specificity, and histopathological changes.

Molecular biology of vectorsWithin this research area, the role of various

molecular and cellular factors, such as ixoderins, salivary gland proteins (Salp), or

α2-macrotubulin, in tick immunity and vector capacity is analyzed using the approaches

and techniques of molecular biology. At the ecological/epidemiological level, the strains of tick-

borne encephalitis virus and Borrelia burgdorferi are genetically and immunologically characterized.

Molecular phylogenetics and evolution of parasites Phylogenetic relationships and population structure are studied using

molecular data within various types of parasitic and symbiotic associations. Based on the results of phylogenetic analyzes, various questions of evolutionary parasitology are addressed, such as the role of geography and host specificity in parasite population structure, and coevolutionary patterns between the host and the parasite.

16 | 17

examPle of resultsPublications:Brabec, J., Scholz, T., Králová-Hromadová, I., Bazsalovicsová, E., Olson, P.D. (2012) Substitution

saturation and nuclear paralogs of commonly employed phylogenetic markers in the Caryophyllidea, an unusual group of non-segmented tapeworms (Platyhelminthes).INTERNATIONAL JOURNAL FOR PARASITOLOGY, 42: 259-267 DOI: 10.1016/j.ijpara.2012.01.005.

Ditrich, O., Chrdle, A., Sak, B., Chmelík, V., Kubale, J., Dyková, I., Kváč, M. (2011) Encephalitozoon cuniculi Genotype I as a Causative Agent of Brain Abscess in an Immunocompetent Patient. JOURNAL OF CLINICAL MICROBIOLOGY, 49: 2769-2771 DOI: 10.1128/JCM.00620-11.

Dyková, I., Lorenzo-Morales, J., Kostka, M., Valladares, B., Pecková, H. (2011) Neoparamoeba branchiphila infections in moribund sea urchins Diadema aff. antillarum in Tenerife, Canary Islands, Spain. DISEASES OF AQUATIC ORGANISMS, 95: 225-231 DOI: 10.3354/dao02361.

Husník, F., Chrudimský,T., Hypša, V. (2011) Multiple origins of endosymbiosis within the Enterobacteriaceae (gamma-Proteobacteria): convergence of complex phylogenetic approaches. BMC BIOLOGY, 9: 87 DOI: 10.1186/1741-7007-9-87.

Rudenko, N., Golovchenko, M., Grubhoffer, L., Oliver, J.H. (2011) Borrelia carolinensis sp. nov., a novel species of the Borrelia burgclorferi sensu lato complex isolated from rodents and a tick from the south-eastern USA. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 61: 381-383 DOI: 10.1099/ijs.0.021436-0.

Ph.D. theses:Ash, A. (2012) Diversity of tapeworms (Cestoda) in freshwater fish of India.Brabec, J. (2012) Molecular systematics and evolution of basal cestode lineages. Kvičerová, J. (2012) Phylogeny of coccidia and coevolution with their hosts.Nováková, E. (2012) Molecular phylogeny and genome evolution of insect symbiotic bacteria. Soldánová, M. (2011) Composition and structure of larval trematode communities in model

freshwater pulmonate gastropods in eutrophic environments in Central Europe.Bartošová, P. (2010) Phylogenetic analyses of myxosporeans based on the molecular data. Chmelař, J. (2010) Transcriptomic and functional analysis of salivary proteins from the tick

Ixodes ricinus.

dePartment of animal PhysioloGyhomepage: http://kfz.prf.jcu.cz/head of the department: Prof. dalibor Kodríke-mail: kodrik@entu.cas.cz

research and education activitiesThe Department of Animal Physiology is responsible for the Experimental Biology Master‘s programme and the Physiology and Developmental Biology Doctoral programme. The research covers structural, ecological, biochemical, and molecular aspects of animal physiology, and is focused on several dominant areas.

Insect stress hormonesAn anti-stress reaction in insects is controlled by adipokinetic neuropetides. This project deals with the detailed molecular, biochemical and physiological characterisation of the hormones to contribute to a better understanding of their function and evolution.

Study of diapauseDiapausing insects cease to develop, rely on accumulated energy resources, and suppress their metabolism. The molecular and biochemical correlates of diapause, including the function of biological clock genes and their products, are under study. The practical aspects of insect imaginal diapause are studied on the beetle Ips typhographus model.

Study of insect silkInsect silk is a natural source of a number of interesting proteins for practical application. Natural or recombinant silk proteins are studied in several lepidopteran and trichopteran models, and their utilization in practice is considered.

Physiological roles of adenosine in DrosophilaAdenosine has multiple signalling roles in neurotransmission, ischemia, and immune response. This project examines the involvement of extracellular adenosine in the physiology and energy metabolism of Drosophila as a suitable model for such investigations.

Anaerobic metabolism of fishSeveral animals can survive

a shortage of oxygen in their environs by using

alternative biochemical pathways. The

anaerobic lipid metabolism of

fish is studied on Carassius

model.

examPle of resultsPublications:Kodrík, D., Vinokurov, K., Tomčala, A., Socha, R. (2012) The effect of adipokinetic hormone on midgut

characteristics in Pyrrhocoris apterus L. (Heteroptera). Journal of Insect Physiology 58: 194-204.Krishnan, N., Kodrík, D. (2012) Endocrine control of oxidative stress in insects. In: Farooqui T. and

Farooqui A.A. (Eds.), Oxidative Stress in Vertebrates and Invertebrates: Molecular Aspects of Oxidative Stress on Cell Signalling, Wiley-Blackwell, New Jersey, ISBN: 978-1-118-14814-3, pp. 261-270.

Košťál, V., Doležal, P., Rozsypal, J., Moravcová, M., Zahradníčková, H., Šimek P. (2011) Physiological and biochemical analysis of overwintering and cold tolerance in two Central European populations of the spruce bark beetle, Ips typographus. Journal of Insect Physiology 57: 1136-1146.

Košťál, V., Korbelová, J., Rozsypal, J., Zahradníčková, H., Cimlová, J., Tomčala, A., Šimek, P. (2011) Long-term cold acclimation extends survival time at 0°C and modifies the metabolomic profiles of the larvae of the fruit fly Drosophila melanogaster. PLoS ONE 6: e25025.

Košťál, V., Zahradníčková, H., Šimek, P. (2011) Hyperprolinemic larvae of the drosophilid fly, Chymomyza costata, survive cryopreservation in liquid nitrogen. Proceedings of the National Academy of Sciences USA 108: 13041-046.

Velki, M., Kodrík, D., Večeřa, J., Hackenberger, B.K., Socha, R. (2011) Oxidative stress elicited by insecticides: a role for the adipokinetic hormone. General and Comparative Endocrinology 172: 77-84.

Collin, M.A., Mita, K., Sehnal, F., Hayashi C.Y. (2010) Molecular evolution of lepidopteran silk proteins: Insights from the ghost moth, Hepialus californicus. Journal of Molecular Evolution 70: 519-529.

Kodrík, D., Bártů, I., Socha, R. (2010) Adipokinetic hormone (Pyrap-AKH) enhances the effect of a pyrethroid insecticide against the firebug Pyrrhocoris apterus. Pest Management Science 66: 425-431.

Pérez-Hedo, M., Pena, R.N., Sehnal, F., Eizaguirre, M. (2010) Gene encoding the prothoracicotropic hormone of a moth is expressed in the brain and gut. General and Comparative Endocrinology 169: 203-209.

Ph.D. theses:Večeřa, J. (2012) The role of insect adipokinetic

hormones in oxidative stress.Bártů, I. (2010) Analysis of lipids mobilized by

adipokinetic hormones in the firebug Pyrrhocoris apterus (Heteroptera: Pyrrhocoridae).

Alquicer, G. (2009) Physiological importance of insect hormones.

Borovanská, M. (2009) Physiological and molecular adaptations during diapause development and overwintering in a heteropteran bug, Pyrrhocoris apterus.

Shaik, H. A. (2009) Little known components of lepidopteran silk.Taranushenko, Y. (2009) Protease and protease inhibitors in the gut and salivary gland of Nauphoeta

cinerea.Tomčala, A. (2009) Characterization of insect lipids by LC/MS methods.

18 | 19

dePartment of exPerimental Plant BioloGyhomepage: http://kebr.prf.jcu.cz/ head of the department: assoc. Prof. Jiří Šantrůčeke-mail: jsan@umbr.cas.cz

research and education activities The Department of Plant Physiology offers study on the Experimental Plant Biology Master’s programme and the Doctoral specialization of Plant Physiology. The research covers environmental plant physiology, biochemistry, and the biophysics of photosynthesis, and is focused to several dominant areas.

Photosynthesis of higher plants, algae and cyanobacteriaPhotosynthesis is a traditional research topic in institutes located in South Bohemia (Třeboň, České Budějovice, Nové Hrady). The regulation of photosynthesis in higher plants, algae, and cyanobacteria is studied on a molecular level, with respect to environmentally important questions of natural variability of temperature, irradiance, and nutrients. For example, recently we obtained important results on the regulation of photosynthesis in diazotrophic cyanobacteria under conditions of projected increased CO2 levels.

Leaf internal limitations to CO2 fixation (mesophyll transport conductance) are studied using gas

exchange, chlorophyll fluorescence and stable isotope mass spectrometry techniques.

Stomatal physiology, plant-atmosphere interactions

Environmental factors controlling stomatal development and patterning in leaf epidermis are studied using gas exchange, thermography, mass spectrometry, and microscopy. In co-operations with crop research institutes water use efficiency and other physiological and biochemical drought resistance traits are screened in barley, wheat,and forage grass cultivars. Transport and structural properties of the cuticle as a leaf water transport

barrier are studied in cooperation with the Institute of Molecular and Cell Botany, University of Bonn.

Stable isotopes fractionation in biosphereFractionation of water isotopes (18O and D) in the soil-

plant-atmosphere continuum and stable carbon isotopes (13C/12C) in leaves and stems (tree rings) is applied in the

assessment of plant growth conditions, hydraulic architecture and in the tracing of geographical origin of plant products and

herbivores (reptiles).

examPle of resultsPublications:Dinamarca, J., Shlyk-Kerner, O., Kaftan, D., Gidekel,

M., Gutierrez, A. and Scherz, A. (2011) Double mutation in photosystem II reaction centers and elevated CO2 grant thermotolerance to mesophilic cyanobacterium. PloS ONE 6 (12) e28389.

Hájek, T., Ballance, S., Limpens, J., Zijlstra, M. & Verhoeven, J.T.A. (2011) Cell-wall polysaccharides play an important role in decay resistance of Sphagnum and actively depressed decomposition in vitro. Biogeochemistry 103: 45–57.

Hisem, D., Hrouzek, P., Tomek, P., Tomšíčková, J., Zapomělová, E., Skácelová, K., Lukešová, A., Kopecký, J. (2011) Cyanobacterial cytotoxicity versus toxicity to brine shrimp Artemia salina. Toxicon 57: 76-83.

Laiho, R., Ojanen, P., Ilomets, M., Hájek, T. & Tuittila, E.-S. (2011) Moss production in a boreal, forestry-drained peatland. Boreal Environment Research 16: 441–449.

Laine, A.M., Juurola, E., Hájek, T. & Tuittila, E.-S. (2011) Sphagnum growth and ecophysiology during mire succession. Oecologia 167: 1115–1125.

Pavlovič, A., Slováková, L‘., Šantrůček, J. (2011) Nutritional benefit from leaf liter utilization in the pitcher plant Nepenthes ampularia. Plant, Cell and Environment, 34: 1865-1873.

Schaufele, R., Šantrůček, J., Schnyder, H. (2011) Dynamic changes of canopy-scale mesophyll conductance to CO2 diffusion of sunflower as affected by CO2 concentration and abscisic acid. Plant, Cell and Environment, 34: 127-136, doi: 10,1111/j.1365-3040.2010.02230.x.

Hájek, T. & Adamec, L. (2010) Photosynthesis and dark respiration of leaves of terrestrial carnivorous plants. Biologia 65: 69–74.

Macková, J., Vašková, M., Macek, P., Hronková, M., Schreiber, L., Šantrůček, J. (2010) Plant response to drought stress simulated by ABA application: changes in chemical composition of cuticular waxes, Environmental and Experimental Botany, doi: 10.1016/j.envexpbot.2010.06.005.

Prudnikova, T., Gavira, J.A., Řezáčová, P., Pineda Molina, E., Hunalová, I., Sviridova, E., Shmidt, V., Kohoutová, J., Kutý, M., Kaftan, D., Vácha, F., Garcia-Ruiz, J.M. and Kutá Smatanová, I. (2010) Toward the crystallization of photosystem II core complex from Pisum sativum L.Crystal Growth & Design 10 (8): 3391-3396.

Vrábl, D., Vašková, M., Hronková, M., Flexas, J., Šantrůček, J. (2009) Mesophyll conductance to CO2 transport estimated by two independent methods: effect of variable CO2 concentration and abscisic acid. Journal of Experimental Botany 60: 2315-2323.

PatentKaftan, D., Lukeš, M., Nedbalová, L. (2012) The photosynthetic microorganism for production of

phospahatidylglycerol and ways to increase the content of phosphatidylglycerol in the said photosynthetic microorganism. CZ2001-705.

Ph.D. thesesReňák, D. (2011) Role of transcription factors in early male gametophyte development of

Arabidopsis.Herbstová, M. (2010) Structure and function of pigment-protein complexes of photosynthetic

microorganisms.Kohoutová, J. (2010) Structural analysis of extrinsic proteins from the oxygen-evolving complex of

photosystem II from higher plants.Macková, J. (2010) The role of plant cuticle in water loss protection.

20 | 21

dePartment of medical BioloGy homepage: http://kme.prf.jcu.czhead of the department: Prof. Jan Kopeckýe-mail: jan@paru.cas.cz

research and education activitiesThe Department of Medical Biology is responsible for the Biomedicine Laboratory Techniques Bachelor’s programme and the Clinical Biology Master’s programme. Students of both programmes work on their diploma theses in physiology, clinical haematology, clinical biochemistry, microbiology, and immunology. Good collaboration exists between the Department of Medical Biology and the Regional Hospital in České Budějovice.

The research done at the department focuses on several different topics including many areas of biomedicine, immunology, enzymology, insect morphology, methods for particle and protein separation, and digital imaging. The department is devoted to the study of molecules, microorganisms, and cells, for the diagnosis and management of illness and for the investigation of the mechanisms and pathogenesis of disease. Areas of biomedical research include haematology, immunology, clinical biochemistry, clinical endocrinology, pharmacology, and other biomedical fields.

In the field of enzymology, magnetic carriers, adsorbents and substrates (e.g., cross-linked erythrocytes and modified Saccharomyces cerevisiae cells) have been developed and prepared for enzyme isolation and characterization. Some proteolytic enzymes and low-molecular-weight organic compounds (e.g., tricyclic drugs) and xenobiotics (e.g., dyes) have been isolated using magnetic adsorbents.

In insect functional morphology the research deals with ultrastructural aspects of the ontogeny of body fat and the glands (tarsal and labial) of two termite species. The ultrastructure and function of various organs in tsetse flies, mites, primitive arthropods etc. have been studied. Another topic focused upon is digital imaging – the application of new technologies and equipment for professional use in entomology (and biology in general).

Immunological research is focused on the immunomodulatory compounds present in tick saliva and their effect on the transmission of important human pathogens such as Borrelia burgdorferi and the tick-borne encephalitis virus. The research is aimed towards the development of anti-tick vaccines reducing transmission of tick-borne pathogens.

Immunomodulatory molecules from tick saliva are prepared, recombined, and their effect on immunocompetent

cells, including cell signalling pathways, is tested. As a research by-product, the anti-asthmatic effect of

tick saliva cystatin was discovered.Attention is also devoted to the interaction

of the tick-borne encephalitis virus with the host and the pathogenesis of the infection.

Important data about the localisation of mutations resulting in a reduction of the pathogenicity of TBE virus were published. Also the role of cytotoxic T lymphocytes in the pathogenesis of TBE was described and immunological processes involved in the breakdown of the blood-brain barrier

during TBE infection were elucidated.

examPle of resultsPublications:Lieskovská, J., Kopecký, J. (2012) Tick saliva suppresses IFN signalling in

dendritic cells upon Borrelia afzelii infection. Parasite Immunol. 34:32-39. Chmelař, J., Oliveira, C.J., Řezáčová, P., Francischetti, I.M., Kovářová, Z., Pejler,

G., Kopáček, P., Ribeiro, J.M., Mareš, M., Kopecký, J., Kotsyfakis, M. (2011) A tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation. Blood 117: 736-744. 

Růžek, D., Salát, J., Singh, S.K., Kopecký, J. (2011) Breakdown of the blood-brain barrier during tick--borne encephalitis in mice is not mediated by CD8+ T-cells. PLoS One, 6(5): e20472. 

Slámová, M., Skallová, A., Páleníková, J., Kopecký, J. (2011) Effect of tick saliva on immune interactions between Borrelia afzelii and murine dendritic cells. Parasite Immunollogy 33:654-660. 

Fialová, A., Cimburek, Z., Iezzi, G., Kopecký, J. (2010) Ixodes ricinus tick saliva modulates tick-borne encephalitis virus infection of dendritic cells. Microbes and Infection 12: 580–585. 

Horká, H., Černá-Kýčková, K., Skallová, A., Kopecký, J. (2009) Tick saliva aff ects both proliferation anddistribution of Borrelia burgdorferi spirochetes in mouse organs and increases transmission ofspirochetes to ticks. Journal of Medical Microbiology 299: 373-380.

Růžek, D., Vancová, M., Tesařová, M., Ahantarig, A., Kopecký, J., Grubhoffer, L. (2009) Morphological changes in human neural cells following tick-borne encephalitis virus infection. Journal of General Virology 90: 1649-1658.

Růžek, D., Salát, J., Palus, M., Gritsun, T.S., Gould, E.A., Dyková, I., Skallová, A., Jelínek, J., Kopecký, J. (2009) CD8+ T-cells mediate immunopathology in tick-borne encephalitis. Virology 384: 1-6.

Horká, H., Kýčková, K., Fišerová, L., Kopecký, J. (2008) Efficiency of experimental infection of Ixodes ricinus ticks with Borrelia burgdorferi spirochetes. International Journal of Medical Microbiology 298 S1: 177-179.

Chmelař, J., Anderson, J.M., Mu, J., Jochim, R.C., Valenzuela, J.G., Kopecký, J. (2008): Insight into the sialome of castor bean tick, Ixodes ricinus. BMC Genomics 9: 233.

Růžek, D., Gritsun, T.S., Forrester, N.L., Gould, E.A., Kopecký, J., Golovchenko, M., Ručenko, N., Grubhoffer, L. (2008) Mutations in the NS2B and NS3 genes aff ect mouse neuroinvasiveness of a Western European fi eld strain of tick-borne encephalitis virus. Virology 374: 249-255.

Skallová, A., Iezzi, G., Ampenberger, F., Kopf, M., Kopecký, J. (2008) Tick saliva inhibits dendritic cellmigration, maturation and function, thus favouring development of Th2 response. Journal of Immunology 180: 6186-6192.

Mgr. theses:Fornbaumová, I. (2012) Study of the anticancer efficacy of the virus Langat.Palus, M. (2012) Role of the host genetic background on the pathogenesis of tick-borne encephalitis.Skladaná, V. (2012) Cord blood – influence of cryopreservation and demographic data of mother and

child on engraftment in the transplantation.Šimonová, Z. (2012) Determination of N-glycome of the tick Ixodes ricinus and Dermacentor

marginatus; analysis of N-glycans in tick tissues and their comparison.Vetišková, V. (2012) Comparison of detection methods of tick-borne pathogens (Borrelia burgdorferi

s.l. and tick-borne encephalitis virus) in Ixodes ricinus tick.Brejchová, L. (2011) Study on mechanisms of sensitivity and resistance to extracellular adenosine in

various Drosophila melanogaster cells in vitro.Eiblová, V. (2011) Possibilities of using nanoparticles of various metals as markers for immunocyto-

chemical labelling in field emission scanning electron microscopy.Gregorová, E. (2011) Effect of vaccination with Ixodes ricinus tick saliva on the transmission of Borrelia

burgdorferi and the host cytokine profile. Korandová, E. (2011) Possibilities of using nanoparticles of various metals as markers for immuno-

cytochemical labelling in the low voltage electron microscope.

22 | 23

institute of chemistry and Biochemistryhomepage: http://uch.prf.jcu.cz/ head of the department: assoc. Prof. Šárka Klementová e-mail: sklement@jcu.cz

research and education activities The Institute of Chemistry and Biochemistry is responsible for the Bachelor‘s and Master‘s programmes in Chemistry and Chemistry for Education. The research covers biochemistry and structural biology, environmental and analytical chemistry, computational chemistry, and interdisciplinary fields such as biophysical chemistry.

Single molecule studies on nucleic acids The study of nucleic acids at the single molecule level in vivo using high-tech spectroscopic methods is a key approach in the understanding of the basic molecular processes taking place in living cells. Single molecule research allows observation of structural changes and the dynamics of many molecular processes that are hindered in the usual heterogeneity of DNA content of a cell.

Single particle analysis in structural biology This research is focused on the structural study of protein complexes by means of electron microscopy and single particle analysis. Using these methods, the structure, organization, and mutual relationship of biologically important macromolecules can be revealed.

Environmental and analytical chemistry The occurrence and interactions of the biologically active compounds in the air, water, soil, and plants, their isolation, concentration, and determination with modern instrumental techniques with an emphasis on the chromatography and its connection with mass spectrometry techniques.The photochemical degradation of resistant pesticides in fresh-water systems, the photoinitiated transformation of humic substances and the photochemical oxidation of biopolymers in relation to the environment Chemical processes in operation in constructed wetlands as part of wastewatertreatment, redox properties of wetland systems and the degradation of surfactants from wastewater.

Computational chemistry Computational chemistry is a complementary method used in chemical and biochemical research that gives researchers a powerful tool to calculate or visualize various scientific problems. Both ab initio and molecular dynamics approaches are employed in the field of protein and nucleic acid research.

24 | 25

examPle of resultsPublications:Kabeláč, M., Kroutil, O., Předota, M., Lankaš, F., Šíp, M. (2012) Influence of a charged graphene surface

on the orientation and conformation of covalently attached oligonucleotides: a molecular dynamics study Physical Chemistry Chemical Physics, 14, pp.4217-4229. 

Klementová, Š. (2012) A Critical View of the Photoinitiated Degradation of Herbicides. In: Herbicides - Properties, Synthesis and Control of Weeds, Mohammed Naguib Abd El-Ghany Hasaneen (Ed.), ISBN: 978-953-307-803-8, InTech, Available from: http://www.intechopen.com/articles/show/title/a-critical-view-of-the-photoinitiated-degradation-of-herbicides.

Tříska, J., Vrchotová, N., Olejníčková, J., Jílek, R., Sotolář, R.  (2012) Separation and identification of highly fluorescent compounds derived from trans-resveratrol in the leaves of Vitis vinifera infected by Plasmopara viticola. Molecules 17: 2773-2783.

Furumaki, Š, Vácha, F., Habuchi, S., Tsukatani, Y., Bryant, D.A., Vácha, M. (2011) Absorption linear dichroism measured directly on a single light-harvesting system: the role of disorder in chlorosomes of green photosynthetic bacteria. JACS 133, 6703–6710.

Gardian, Z., Tichý, J., Vácha, F. (2011) Structure of PSI, PSII and antennae complexes from yellow-green alga Xanthonema debile. Photosynth. Res. 108(1), 25-32.

Rijs, A.M., Kabeláč, M., Abo-Riziq, A., Hobza, P., De Vries, M.S. (2011) Isolated gramicidin peptides probed by IR spectroscopy ChemPhysChem, 12 (10), pp. 1816-1821.  Kabeláč, M. , Zimandl, F., Fessl, T., Chval, Z., Lankaš, F. (2010) A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: Structure and dynamics Physical Chemistry Chemical Physics, 12 (33), pp. 9677-9684. 

Herbstova, M., Litvín, R., Gardian, Z., Komenda, J. and Vácha, F. (2010) Localization of Pcb antenna complexes in photosynthetic prokaryote Prochlorothrix hollandica. Biochim. Biophys. Acta - Bioenergetics, 1797, 89-97.

Klementová, Š., Kříž, D., Kopáček, J., Novák, F. and Porcal, P. (2009) UV photo- initiated changes of humic fluorophores, influence of metal ions. Photochem. Photobiol. Sci., 8, 582 - 586.

Kužel, S., Vydra, J., Tříska, J., Vrchotová, N., Hrubý, M., Cígler, P. (2009) Elicitation of pharmacologically active substances in an intact plant. J. Agricultural Food Chem 57: 7907-7911.

Ph.D. Theses:Litvín, R. (2009). Photochemistry of photosystem II reaction centre: Alternative electron pathways.Gardian, Z. (2009) Electron Microscopy in Structural

Studies of the Photosynthetic Apparatus.Bína, D. (2009) Photosynthetic electron

transport in purple bacteria: An in vivo spectroscopic study.

Herbstová, M. (2010) Structure and function of pigment-protein complexes of photosynthetic microorganisms.

institute of Physics and BioPhysicshomepage: http://ufy.prf.jcu.cz/en head of the institute: assoc. Prof. milan Předota, Ph.d.e-mail: predota@prf.jcu.cz

research and education activities Institute of Physics and Biophysics offers Bachelor‘s, Master‘s and PhD. programmes in Biophysics, Bachelor‘s and Master‘s programs in Teaching of Physics, and Bachelor’s programmes in Physics and Measurement and Information Technology.

Laboratory of Applied Plasma PhysicsResearch is focused on the study of the plasma assisted deposition of nanostructured thin films and nanoparticles formation. Nanostructured materials are important for two main reasons: (i) the size regime 1–100 nm corresponds to the size of important biological molecules such as DNA and especially proteins, and films can be used as biocompatible active coatings, e.g. for implants, and (ii) application in the semiconductor industry which has entered the nanometer regime. The object of the

research is both generated plasma discharge (particle densities, energy distribution, particle fluxes towards the substrate, chemistry etc.)

as well as the characterization of produced films/particles.

Molecular dynamics simulationsMolecular dynamics give detailed molecular-level

understanding of the structure, function, and origin of experimental signals. Research focuses on computer simulations of fluids (water and aqueous solutions), phase equilibria, solid-liquid interface, metal-oxide surfaces, and the interactions of biomolecules with surfaces.

Plasma astrophysics – solar plasma physicsFor decades, the effect of solar coronal heating has

remained one of the unsolved problems of solar plasma physics. Presently, two possible features are believed to

be responsible for this interesting phenomenon – magnetic reconnection and MHD waves. We numerically calculate the MHD

equations describing the plasma dynamics and investigate the plasma waves, e.g. wave trains, magnetoacoustic waves, in solar corona.

Time-resolved spectroscopyResearch is focused on ultrafast excited-state processes, taking place at time scales of femtoseconds to nanoseconds,in a variety of systems, ranging from natural pigments (e.g. carotenoids), synthetic systems aimed at controlling electron and energy transfer reactions, to complex pigment-protein complexes responsible for light-driven reactions in various natural systems.

26 | 27

Automatic recognition of bird individuals by their voicesThe identification of individual birds by ornithologists using ring girdling is invasive and has negative influence on the behavior of particular bird. Using computer voice recognition individual birds can be identified non-invasively via voice recordings and recognition. The project‘s approach is based on the production of individual models using Gaussian Model Mixtures. The examined bird is the Chiffchaff (phylloscopus collybita).

examPle of resultsPublications:Jelínek, P., Karlický, M. (2012) Magnetoacoustic waves in diagnostics of the flare current sheets, Astronomy and Astrophysics 537, A46.Pařez, S. and Předota, M. (2012) Determination of Distance-dependent Viscosity of Mixtures in Parallel Slabs using Non-equilibrium Molecular Dynamics“, Phys. Chem. Chem. Phys. 14, 3640.Chábera, P., Durchan, M., Kerfeld, C.A., Polívka, T. (2011) Excited-state properties of the 16 kDa red carotenoid protein from Arthrospira maxima.Biochim.Biophys.Acta.1807, 30, 2011.Straňák, V., Čada, M., Quaas, M. et al (2009) Physical properties of homogeneous TiO2 films prepared by high power impulse magnetron sputtering as a function of crystallographic phase and nanostructure, J. Phys. D: Appl. Phys. 42, 105204.

institute of mathematics and Biomathematicshomepage: http://umb.prf.jcu.cz/ head of the department: Prof. Vlastimil Křivane-mail: krivan@prf.jcu.cz

research and education activities The Institute is responsible for two Bachelor’s and Master’s Programmes in Mathematics and Applied Mathematics. The current research of the Institute focuses on applied mathematics, differential equations, and geometry. In particular, the institute pursues research in mathematical biology. This research, conducted jointly with the Biology Centre of the Academy of Sciences, focuses on the development and analysis of mathematical models of population and evolutionary ecology with the aim of understanding mechanisms regulating species persistence. Mathematical methodologies based on the game theory, differential and difference equations, stochastic processes, and rule-based computer simulations of interacting individuals are used.

examPle of resultsPublications:Daněček, J., John, O., Stará, J. (2011) Morrey space regularity for weak solutions of Stokes systems with

VMO coefficients, Ann. Mat. Pura Appl. 190 (4): 681-701.Daněček, J., Viszus, E. (2011) $C^{0,\alpha}$ - regularity for vector-valued minimizers of quasilinear

functionals, Nonlinear Analysis T.M.A. 74: 5274-5285.Křivan, V. (2011) On the Gause predator-prey model with

a refuge: A fresh look at the history. Journal of Theoretical Biology 274:67-73.

Berec, L. (2010) Impacts of foraging facilitation among predators on predator-prey dynamics.

Bulletin of Mathematical Biology 72:94-121.

Berec, L., Eisner, J., Krivan, V. (2010) Adaptive foraging does not always

lead to more complex food webs. Journal of Theoretical Biology

266:211-218.Eisner, J., Kučera, M., Recke, L. (2010) Smooth parameter dependence of solutions and contact regions for a Signorini boundary value problem. Nonlinear Analysis, T.M.A. 72: 1358-1378.Eisner, J., Kučera, M., Väth, M. (2010) Bifurcation points for a reaction-diffusion system with two inequalities.

J. Math. Anal. Appl. 265: 176-194.

Kalová, J., Mareš, R. (2010) Crossover Equation and the Vapor Pressure of Supercooled Water. Interna-tional JournaL of Thermophysics  31 (4-5): 756-765.  

Zalabová, L. (2010) Parabolic Symmetric Spaces, Annals of Global Analysis and Geometry. 37 (2): 125-141.

Zalabová, L. (2010) Symmetries of Parabolic Contact Structures, Journal of Geometry and Physics. 60 (11): 1698-1709.

Daněček , J., Viszus , E. (2009) $C^{0,\alpha}$ - regularity for vector-valued minimizers of quasilinear functionals, Nonlinear Differ. Equ. Appl., 16 (2): 189-211.

Křivan, V., Cressman, R. (2009) On evolutionary stability in prey-predator models with fast behavioral dynamics. Evolutionary Ecology Research 11:227-251.

28 | 29

institute of aPPlied informatics homepage: http://uai.prf.jcu.cz head of the department: libor dostálek e-mail: libor.dostalek@prf.jcu.cz

research and education activities The Institute of Applied Informatics (hereafter “UAI”) was established on the 1st of January 2009 as one of several new non-biological study programmes at the Faculty of Science. Since then it has gradually worked on the expansion and improvement of informatics and computer science within the faculty. The study programmes offered by the UAI have proven very popular among prospective students.

Study Programmes and Education Activities At the time of writing the UAI performs education at the Bachelor‘s level. This covers various expert study disciplines such as networks and security, banking or web portal design, and databases. To provide support for certain courses within these study programmes the UAI possesses certified education systems such as the Cisco Networking Academy for networking and security, and the Oracle Academy for databases.

UAI has gained accreditation for the joint cross-border Bachelor‘s and subsequent Master‘s studies of Bioinformatics (in English) along with the Johannes Kepler University in Linz, Austria.

Research Activities The original aim of the UAI was to support the biological research carried out at other departments by helping them to evaluate their data more effectively through the use of information technology. To achieve this goal special equipment with a high computational system performance is necessary, which at present is provided by Grid Computing Our work in the following areas are of interest:• Long term archiving of electronic documents, • Wireless sensor networks and • Managing trust

In addition UAI offers a combined Bachelor‘s study programme such as Informatics for Education, and

Informatics and Archivation.

Cisco Networking Academy UAI also administrates and manages a certified network lab for the Cisco Networking Academy courses. These courses are available for all university students, regardless of their faculty affi liation. The

outcome of passing this course is an internationally recognized certificate, which guarantees the basic

network administration skills of the graduate. The lab consists of diverse routers and switches to provide various

30 | 31

types of network topologies, simulations and experiments. The main advantage of this is the ability to create real environment conditions, therefore the lab is useful in the debuging and traceing of possible problems. In addition the lab also supports students within their informatics-oriented thesis writing.

Oracle Academy UAI also offers Oracle Academy courses. During these courses students are trained in Oracle Server administration, database modelling, and system analysis. After passing the course the student may attain an official Oracle certificate at a special price. The course is supported by Oracle’s official learning materials (PowerPoint Slides, Student’s materials, Software), fully in English.

examPle of results:Publications:Dostálek, L., Kabelová, A. (2006) Understanding TCP/IP: A clear and comprehensive guide to TCP/IP

protocols. 480 pages, 19-0481 1-71-X.

research field stations Researchers and students of the FS take part in several projects carried out at field stations in extreme biological environments, particularly at the polar station on Svalbard and tropical station in Papua New Guinea. The scientific programmes cover various biological fields such as ecology, entomology, algology, and parasitology. A practical course of Tropical ecology in Papua New Guinea is available bi-yearly for ten MSc. Students.

research in PetuniaBukta, svalBard islands

field course of troPical ecoloGy at the BinatanG research center, madanG, PaPua new Guinea

University of South Bohemia is a state university, founded in 1991. It is located in the regional centre of South Bohemia, the town of České Budějovice (population approx. 100 000), about 150 km south of Prague. The town was established in the thirteenth century as a “King’s town” by the Czech King Přemysl Otakar II at the confluence of the rivers Vltava and Malše.

DepartmentsDepartment of Botany Pages 6–7

Department of Zoology Pages 8–9

Department of Ecosystem Biology Pages 10–11

Department of Genetics Pages 12–13

Department of Molecular Biology Pages 14–15

Department of Parasitology Pages 16–17

Department of Animal Physiology Pages 18–19

Department of Experimental Plant Biology Pages 20–21

Department of Medical Biology Pages 22–23

Institute of Chemistry and Biochemistry Pages 24–25

Institute of Physics and Biophysics Pages 26–27

Institute of Mathematics and Biomathematics Pages 28–29

Institute of Applied informatics Pages 30–31

gps 48.976344,14.446954

www.prf.jcu.cz

doctoral2013_obalka_webdoctoral2013_blok_web