USE OF MODEL ORGANISMS TO RESOLVE CRUCIAL BIOLOGICAL PROBLEMS ON THE PATH TO INNOVATIONS

Informations projet

MODBIOLIN

N° de convention de subvention: 316304

Projet clôturé

Date de début 1 Octobre 2012

Date de fin 30 Septembre 2015

Financé au titre de

• Specific Programme "Capacities": Research potential of Convergence Regions

Coût total € 3 433 112,00

Contribution de l’UE € 3 062 818,70

Coordonné par

BIOLOGICKE CENTRUM AKADEMIE VID CESKE REPUBLIKY VEREJNA VYZKUMNA INSTITUCE
Czechia

Final Report Summary - MODBIOLIN (USE OF MODEL ORGANISMS TO RESOLVE CRUCIAL BIOLOGICAL PROBLEMS ON THE PATH TO INNOVATIONS)

Executive Summary:
MODBIOLIN project promoted infrastructure building of the Biology Centre of the Academy of Sciences (BCAS), one of the largest research institutions for biological and ecological disciplines in the Czech Republic with important role in the region. BCAS enjoys good international reputation but has not yet reached the productivity of the best EU institutions with similar research profile. By supporting infrastructure development, MODBIOLIN project contributed substantially to narrowing the gap between such top institutions and BCAS. All aspects of infrastructure building were addressed and supported. Specific achievements and their impact on BCAS include: (1) Successful project preparation and management (important experience for future large projects); (2) Organization of scientific meetings as a very efficient and relatively inexpensive way of knowledge exchange and initiation of joint projects and networking; (3) Use of different kinds of mobility to increase know-how exchange (similar activity will be included in future projects; (4) Use of international advertisement of open positions and subsequent hiring of selected researchers to build up new research teams; (5) Upgrading or replacement of obsolete gadgets to provide all researchers with needed instrumental back-up (increase research output has been noted); (6) Acquisition and sharing of expensive instruments increases methodological possibilities and thereby enhances competitiveness of BCAS researches; (7) The purchase of luminiscence microscope boosted investigations of living cells to a qualitatively higher level; (8) A range of knowledge dissemination activities (leaflets, posters, public lectures, “open door” events, promotional video, press conferences, publication on internet portals) has been adopted; (9) MODBIOLIN video will continue to be used for informing stockholders about the purpose of biomedical research on model invertebrates; (10) Established mechanisms of self-evaluation and external evaluation can be modified for general application within BCAS; (11) The e-learning course Technology Transfer Manager-junior promotes awareness of intellectual protection procedures and stimulates interest in innovative research; (12) Socio-economic consequences of MODBIOLIN include promotion of the region, exploitation of BCAS infrastructure for close collaboration with regional research institutions and university, increased research output including innovations, improvement of the gender ratio in BCAS staff, collaboration with regional authorities in the development of the technological park and promotion of the cross-border projects and enhanced interactions with the business sphere.

More than 80 papers were published by MODBIOLIN staff; only examples were provided in section A of part 4.2 of this report.

Project Context and Objectives:
Promotion of infrastructure building of the Biology Centre of the Czech Academy of Sciences (BCAS) was the general goal of MODBIOLIN project. BCAS is one of the largest research institutions for biological and ecological disciplines in the Czech Republic and enjoys good international reputation. However, it has not yet reached the productivity of the best EU institutions with similar research profile. By supporting infrastructure development, MODBIOLIN project contributed substantially to narrowing the gap between such top institutions and BCAS. It has been recognized that all aspects of infrastructure may be improved. The following objectives were set in the project proposal:

• Good project management based on previous BCAS experience, on the example of partnering institutions and advice from the members of international Advisory Board and Steering Committee.

• Knowledge acquirement and ERA building through invitations of excellent researchers to the seminars in BCAS and with the aid of mutual visits between BCAS and partnering institutions. Foster collaborations and networking through the working stays of BCAS researchers in the partnering institutions and vice versa, organization of international scientific meetings and delegation of BCAS researchers to other international meetings.

• Development of human resources in respect to both qualitative and quantitative criteria and building sustainable and coherent research teams capable of critical self-evaluation. International recruiting of new researchers and support of young competent researchers encouraged to organize own research teams. The coherence and sustainability of the teams must continue after project termination.

• Upgrading laboratory equipment to international standards to guarantee that the shortage of basic equipment is not a cause of insufficient research output. Furnishing laboratories of the newcomers with daily used gadgets such as pipettes, shakers, vortexes, simple balances and pH meters, etc. Replacement of old and defective gadgets.

• Improvement of instrumental infrastructure to a level comparable with good research institutes in advanced countries. Analysis of instrument requests to avoid instrument doubling and promote instrument sharing. Organization of tenders as required by the Czech law.

• Knowledge dissemination to the peers, business sphere and general public using several channels: establishment of project web page; distribution of promotional leaflets; poster presentations on fairs; discussions with general public at events such as “Week of science”; press conferences; preparation of promotional video; project promotion via internet.

• Project evaluation focused on project management (with emphasis on the transparency, time-saving efficiency and coherence) and project output (measured by infrastructure improvements and its impact on the number and quality of publications) must include critical self-evaluation as a driving force of further improvements.

• Intellectual property protection is still insufficient in BCAS and will be addressed in the e-learning course Technology Transfer Manager-Junior that will also provide education in the technology transfer mechanisms that will be tested on the example of two inventions.

• The purchase of luminescence microscope will provide qualitative methodological advance in many investigations performed on living cells; the unique instrument allows long-term observation of cells that can be subjected to different treatments.

Project Results:
The enhancement of the BCAS research potential and of its capabilities for innovations was the over-all objective of the MODBIOLIN project. Considerable progress towards this goal has been made through the work described in ten work packages and focused on infrastructure building. The participants of MODBIOLIN agree that the project nearly doubled the scope of infrastructure building normally accomplished in 3 years. It is important that different facets of research infrastructure received attention and support. Through this harmonious development, BCAS has become a valuable and competitive component of ERA contributing to the quality and volume of European research. Major achievements are described in the context of individual work packages. Last section contains descriptions of individual teams that document project impact on infrastructure building.

WP1 Project management
T 1.1 Administration and logistics: Setting up efficient project management was the major goal of the WP1 and was fulfilled. The plan of project realization was approved at the kick of meeting on November 9, 2012. Most members of the Management Committee (MC) and Steering Committee (SC) participated and contributed to the discussion that followed after MC presentations. Project co-ordinator and project manager (both with part-time working effort) were made responsible for direct project management, interactions with MC (MC met in about 2-months intervals and often communicated via e-mail. Members of the Advisory Board (AB) and SC agreed to oversee project management.
T 1.2 Interim and final reports were prepared by the project manager and project co-ordinator with participation of the MC and with input of the AB and SC.
T 1.3 Communication with EC: The project coordinator and project manager frequently consulted the policy project officer and occasionally also the financial project officer about important decisions in the project management. We are grateful for the advices we received. Unfortunately, the communication was hindered by the illness of the initial policy officer and slowed down during summer 2015.
T 1.4 Surveillance of the research ethics: The rules of research ethics were observed throughout the project. New permission to use laboratory animals was issued by the Ministry of Agriculture on May 20, 2014, Accreditation No. 22395/2014-MZE-17214, valid for 5 years.

WP2 Knowledge acquirement
The purpose of WP2 was to enhance qualification of MODBIOLIN researchers through four kinds of mobility:
T 2.1 Invited lectures delivered in BCAS by excellent EU researchers were planned at the rate of 6 speakers every year, with an average stay of 2 days (incl. travel). The plan (9 lectures for each RP) was slightly surpassed because 11 lectures were realized in the 1st and 10 in the 2nd RP.
T 2.2 A quota of 20 months per reporting period was set for the work of MODBIOLIN researchers in EU laboratories (this figure was not included in the person-month tables because all working stays were treated as travel expenditures). Less than planned were used in the 1st but 46.25 months were used in the entire project.
T 2.3 Organization of two workshops in each reporting period was envisaged but the activity was shifted to the 2nd MP; it was justifiably assumed that MODBIOLIN staff would be better prepared for organizing such events and that the meetings in 2015 could provide forum for the formation of consortia for future Horizon2020 projects. Organized meetings included workshops 2nd Chromera Meeting, Methods of Functional Genomics and Molecular Methods in Insect Physiology), and conferences Ticks & Tick Ttransmitted Diseases 2015 and International Conference on Viroids and Viroid-Like RNA (altogether 261 participants).

WP3 Collaboration and ERA building
The activities of WP3 promoted twinning with the partnering institutions and encouraged collaborations within ERA. This was achieved by supporting mutual visits and inviting young members of the partner teams to work for a few months in BCAS. These activities were accomplished in two tasks.
T 3.1 Mutual visits of collaborating researchers between MODBIOLIN teams and advanced EU workplaces with the aim of information exchange and collaboration; 28 outgoing trips and 24 incoming visits were accomplished during project duration.
T 3.2 The working stays of researchers from EU laboratories in the MODBIOLIN laboratories enhanced collaboration, promoted mobility within ERA, and supported research directions in which EU holds important global positions. The stays also contributed to the international academic atmosphere in BCAS, accelerated adoptions of new methods and promoted research supported by the MODBIOLIN infrastructure. The costs of stays in BCAS were treated as travel costs and are therefore not expressed as person/months costs. The stays of foreign researchers in BCAS during project duration amounted to 118.35 person-months, while the plan assumed only 108 person-months.

WP4 Recruitment of experienced researchers
The increase of research potential through the development of human resources was addressed by WP4 that included three following tasks:
T 4.1 The formation of cohesive project staff from the employees of 3 separate BCAS institutes was initiated during project preparation. The staff initially included 14 research teams but 2 of them were dismissed at the start of the 2nd monitoring period because their leaders stayed abroad. Members of these teams joined an existing team but so far not included in MODBIOLIN. Since 5 new teams were formed, there are 18 efficient and sustainable teams at the time of project termination.
T 4.2 The recruitment of experienced researchers was planned to occur in three steps (four researchers in the 1st, four in the 2nd, and two in the 3rd project year. However, the plan could not be observed because some candidates started to work with delays, could get only part-time contracts because of support from other grants, etc.). Eventually we were able to fill 16 positions for very different periods. All newcomers contributed to infrastructure development and most of them represent stable additions to the teams (in five cases they founded new teams.
T 4.3 Recruitment of other researchers: The project plan included recruitment of at least five additional researchers that would be paid from other sources than the budget of MODBIOLIN. The plan was surpassed already in the 1st monitoring period.

WP5 Upgrading basic laboratory equipment
T 5.1 Upgrading basic equipment: Enhancing research potential by equipment upgrading was an important project component. Equipment upgrading included purchase of instruments needed for the teams participating in the MODBIOLIN project from the very beginning as well as for the newly formed teams. Instruments needed daily by the current staff were purchased in the first project year, as fast as the tender procedure permitted. The original budget of WP5 was used up in the 1st MP and was insufficient. The activities of this WP could be executed only by using money originally allotted to other WPs. With this adjustment approved by project officer, we bought basic equipment for 45 245 €, the instruments for laboratory upgrading for 8 427 € and equipment for general laboratory furnishing for 7 286 €. These investments boosted especially the new teams with young and talented staff.

WP6 Acquisition of instruments
The purpose of WP6 was the acquisition of moderately expensive instruments required for the modern research on model organisms. Detailed and careful screen of the needs identified instruments which fell into three categories: (i) available but obsolete, (ii) available with difficulties because of overuse, (iii) unavailable in BCAS. To facilitate tenders, instruments were divided into two categories defined as specific tasks:
T6.1 Purchase of optical instruments: Inverted microscope with filter sets for Ca imaging, Optical fluorescence microscope Olympus BX53, Supermicro-computer, Gradient master and Piston Gradient Fractionator, Fluorescence spectrophotometer with polarization filters, Microplate reader;
T6.2 Purchase of other instruments: Protein liquid chromatograph, Real-time PCR cycler, Behavioral chambers with light regulated system, XF-24 Bioanalyzer including two FluxPacks.

WP7 Knowledge dissemination
Public awareness about the EC support was enhanced through several activities:
T 7.1 Informative web page on MODBIOLIN project explaining the project purpose in Czech and English was created shortly after the GA signature. It is available at www.modbiolin.bc.cas.cz and provides links to promotiomal video, to information on MODBIOLIN workshops and to team annotations published in the internet portal Gate2Biotech.
T 7.2 Press conference was organized shortly after the kick-off meeting but press participation was rather low. Available information indicated that it was common experience. We refrained from organizing press conferences and used internet portal Gate2Biotech (http://www.gate2biotech.com/) for knowledge dissemination and for stimulation of our contacts with the business sphere.
T 7.3 Leaflets and a posters: two leaflets on MODBIOLIN activities have been distributed during whole project duration both nationally and internationally. A poster on MODBIOLIN was displayed at several occasions. About 20 posters prepared by individual researchers for their presentations at international conferences, represented another vehicle of knowledge dissemination.
T 7.4 Film lasting 20 min and composed of four chapters (each on one type of a model organism) is projected in the Czech version in the entrance hall of BCAS and in the English version at international meetings organized by BCAS (https://www.youtube.com/watch?v=H9Km_h6xFGI&index=2&list=UUAoeG6-3Ysjwhr2NtkR5jRg).
T 7.5 Interactions with public occurred most efficiently at the nation-wide events such as “Week of Science” and “Day of Open Doors”.

WP8 Staff coherence and quality control
The integration of research teams into an efficient and sustained staff capable of critical self-evaluation and acceptance of measures for improvements was the goal of WP8. The goal was reached with the aid of several activities: (a) assessment of the project management strategy by the Steering Committee (SC) at the kick-off meeting; (b) self-evaluation of each team every 2nd month with brief oral reports at the MC meetings, (c) evaluation of all project components at general staff assemblies with participation of the Advisory Board (AB) that was the highest quality control body. This work was defined in three tasks:
T 8.1 External evaluation by the AB and the SC with suggestions for improvements
T 8.2 Analysis of the good management practices of the partnering institutions (CNRS Institut de Biologie de l’Ecole Normale Supérieure, Paris; Max Planck Institute for Molecular Cell Biology and Genetics, Dresden; Max Plant Institute for Plant Breeding, Cologne; University of Cambridge - Departments of Biochemistry and Pathology).
T 8.3: Self-evaluation at the level of individual teams with participation of MC. The team leaders presented critical accounts on the team achievements at each. general staff assembly. Participants expressed their opinions on the specific results, general research strategies, and on the team standing in the international context.

WP9 Intellectual property plan and innovation capacity building
BCAS has issued written rules for the protection of intellectual property (authorship rights, patenting of inventions, registration of utility models, etc.). Special regulations concern application and maintenance of both national and international patents, industrial designs and utility designs. The framework for administrative support of the innovative and practically oriented research has been laid down but the interest of staff is still not satisfactory. The activities defined in the tasks and supported by the MODBIOLIN project contribute to a gradual change of this attitude.
T 9.1 The e-learning course Technology Transfer Manager – Junior (TTM-J) was translated from Czech to English (330 standard pages) and installed on the BCAS server. First 11 students registered in May 2015 and graduated in July 2015.
T 9.2 Since no patent applications were submitted during the project, attention was paid to the important utility model “Combinations of primer sets for the detection of genetic polymorphism in the Czech hop cultivars and for cultivars determination”. It was prepared jointly with the Hop Research Institute Co., Žatec, Czech Republic, in 2013, registered by the Czech authorities (No. 25678) in 2014, and commercialized in 2015. MODBIOLIN project supported maintenance of a patent on ferritin (potential vaccination against ticks) that is in BCAS property.
T 9.3: The contacts with business have expanded: BCAS representatives took part in the activities of the CzechBio association, were active in the local Scientific-Technological Park and the South-Bohemian Agency for the Support of Innovative Enterprising, and together with the University of South Bohemia founded a Platform for Biotechnologies. Participation at the EBTNA meeting, which is linked to the European Biotechnology Congress (Lecce, Italy, May 2014), also promoted contacts with the business sphere.

WP10 Qualitative methodological advance
Rapid schooling of several researchers followed immediately by exploitation of the state-of-the-art bioluminescence microscope Olympus LV 200 in 2013 was very significant infrastructure enhancement.

The impact of MODBIOLIN project on team performance

Development of research infrastructure was the purpose and goal of the MODBIOLIN project. Project success can be measured by the improvements of individual infrastructure components or by the enhancement of the research output that reflects such improvements. The descriptions of individual MODBIOLIN teams in the following paragraphs include both approaches. The teams work in the following research areas: A) Regulatory gene cascades, B) Circadian and seasonal rhythms, C) Host-arthropod vector - parasite relationships and D) Plant genome analysis. Teams are numbered within each research area. Five new teams were formed by young talented researchers in the 2nd MP.

A1. Gene cascades in insect sex determination

Infrastructure development with MODBIOLIN support
The team focused on sex determination was formed a decade ago but has been included in the MODBIOLIN project only in 2014 to replace the teams “Modulation of nuclear receptors” and “Flour beetle as a model for development and reproduction” that were terminated. The new team then included the leader František Marec (e-mail: [e-mail]) experienced researchers (Leonela Zusel Carabajal Paladino and Petr Nguyen), a technician (Marie Korchová), three Ph.D. students (Martina Dalíková, Miroslava Sýkorová, Jindra Šíchová) and two undergraduate students (Irena Hladová, Anna Voleníková). In June 2014, we were able to provide salary from the MODBIOLIN budget to the newly recruited researcher Dr. Atsuo Yoshido (Japan). His considerable experience in insect genetics and molecular cytogenetics, and especially in sex chromosome research and gene analysis and mapping, substantially enhanced the team potential. Since January 2015, the team has been strengthened by another young scientist, Dr. Magda Zrzavá, who returned from the maternity leave. Dr. Carabajal Paladino (Argentina), who had grant support until June 30, 2015, had then obtained MODBIOLIN support for the period July-September 2015. Since 1st October 2015, Dr. Yoshido and Dr. Carabajal Paladino are paid from the institutional budget. Both of them significantly strengthen and stabilize the team and both have expressed interest in continuing with the team providing that we will be able to support them from the newly submitted grant projects. Research of the team is mainly funded by grants 14-22765S (given to F. Marec) 14-35819P (given to P. Nguyen) of the Czech Science Foundation. Recently, the team leader F. Marec obtained support from the BINGO-ITN project for four years (1st January 2015 – 31 December 2018), which includes scholarship for one foreign Ph.D. student We have evaluated 29 submitted applications for this position and recruited the best candidate, Mr. Sander Visser, who graduated from the University of Groningen (The Netherlands) this summer and joined the team since August 30, 2015.With the support from MODBIOLIN project the team was also able upgrade basic laboratory equipment. We purchased a Thermomixer Comfort (Eppendorf) for chromosome denaturation and incubation of DNA probes, two Vannas spring scissors and twelve Dumont forceps for dissection of insect tissues, ten Oak Ridge centrifugation tubes, digital laboratory scales, and a benchtop centrifuge Ministar.

Scientific achievements (2014-2015)
We focused on molecular differentiation and evolution of sex chromosomes, and on the identification and mapping of sex-linked genes in several model groups of moths and butterflies (Lepidoptera). Our main achievements can be summarized as follows. (1) We have developed a protocol for two-colour TSA-FISH (i.e. fluoresence in situ hybridization with tyramide amplification of hybridization signals, which is a reliable technique for physical mapping of single-copy genes on insect chromosomes in species, where no genomic tools such as a Bacterial Artificial Chromosome (BAC) library is available (see Carabajal Paladino et al., 2014). (2) We performed a detailed karyotype and molecular cytogenetic analysis of sex chromosomes in three cryptic species of wood white butterflies of the genus Leptidea. Our research revealed considerable karyotype variability with the presence of multiple chromosome rearrangements and a unique sex determination system, based on multiple sex chromosomes, 3-4 Z and 3-4 W chromosomes (see Šíchová et al., 2015). (3) In wild silkmoths, Samia cynthia, we performed crosses between geographic subspecies, S. c. pryeri and S. c. walkeri, which differ in sex chromosome constitution. By means of detailed analysis of their hybrids we showed that the female-specific W (or neo-W) chromosome of S. cynthia ssp. plays no role in sex determination and reproduction, and thus does not contribute to the formation of reproductive barriers between different subspecies (see Yoshido et al., subm. to Heredity).
Examples of publications (2013-2015)
Nguyen P., Sýkorová M., Šíchová J., Kůta V., Dalíková M., Čapková Frydrychová R., Neven L.G. Sahara K., Marec F. (2013) Neo-sex chromosomes and adaptive potential in tortricid pests. Proceedings of the National Academy of Sciences of the United States of America 110: 6931-6936.
Šíchová J., Nguyen P., Dalíková M., Marec F. (2013) Chromosomal evolution in tortricid moths: conserved karyotypes with diverged features. PLoS ONE 8: e64520.
Van't Hof A.E. Nguyen P., Dalíková M., Edmonds N., Marec F., Saccheri I.J. (2013) Linkage map of the peppered moth, Biston betularia (Lepidoptera, Geometridae): a model of industrial melanism. Heredity 110: 283-295.
Yoshido A., Šíchová J., Kubíčková S., Marec F., Sahara K. (2013) Rapid turnover of the W chromosome in geographical populations of wild silkmoths, Samia cynthia ssp. Chromosome Research 21: 149-164.
Carabajal Paladino L.Z. Nguyen P., Šíchová J., Marec F. (2014) Mapping of single-copy genes by TSA-FISH in the codling moth, Cydia pomonella. BMC Genetics 15: S15.
Marec F. (2014) Developmental genetics: Female silkworms have the sex factor. Nature 509: 570-571.
Carabajal Paladino L., Muntaabski I., Lanzavecchia S., Le Bagousse-Pinguet Y., Viscarret M., Juri M., Fueyo-Sánchez L., Papeschi A., Cladera J., Bressa M.J. (2015) Complementary sex determination in the parasitic wasp Diachasmimorpha longicaudata. PLoS ONE 10: e0119619.
Šíchová J., Voleníková A., Dincă V., Nguyen P., Vila R., Sahara K., Marec F. (2015) Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies. BMC Evolutionary Biology 15: 89.
Yoshido A., Marec F., Sahara K. (in press) The fate of W chromosomes in hybrids between wild silkmoths, Samia cynthia ssp.: no role in sex determination and reproduction. Heredity (accepted 17 Nov. 2015).

A2. Regulation of telomeric length in insects

Infrastructure development with MODBIOLIN support
The team includes its leader Radmila Čapková Frydrychová ([e-mail]) and PhD students Michala Korandová and Tomáš Krůček. With the support of MODBIOLIN, the team was able to purchase several pieces of important laboratory equipments – PCR cycler (Biometra), Biohazard box (BioAir), two laboratory centrifuges (Eppendorf), pH meter, stereomicroscope (Arsenal), two sets of laboratory pipettes (Eppendorf) and two laboratory incubators.

Scientific achievements (2014-2015)
The research of the team was focused on telomere homeostasis in Drosophila. Telomeres are considered as a biomarker of aging and a forecaster of longevity, and the short telomeric length seems to be associated with numerous human diseases. The main line of the research followed the associations between telomere biology, environmental stress, oxidative stress level and insect neurohormones. We showed that mild oxidative stress, induced with low doses of the herbicide paraquat, led to stimulation of telomeric activity in Drosophila. Upon mild oxidative treatment, we observed elongation of telomere length and increased transcriptional activity of telomeric elements. Also, we showed that Drosophila lines with long telomeres display a higher resistance against high levels of oxidative stress compared to the lines with short telomeric length. Paraquat treatment, thus, seems to have hormetic effect on Drosophila telomeres.
Recent publications:
Nguyen P., Sýkorová M., Šíchová J., Kůta V., Dalíková M., Čapková Frydrychová R., Neven L.G. Sahara K., Marec F. (2013) Neo-sex chromosomes and adaptive potential in tortricid pests. Proc. Natl. Acad. Sci. US 110: 6931-6936.
Korandová M., Krůček T., Vrbová K., Čapková Frydrychová R. (2014) Distribution of TTAGG-specific telomerase activity in insects. Chromosome Res. 22: 495-503.
Krůček T., Korandová M., Szakosová K., Šerý M., Čapková Frydrychová R. (2015) Effect of low doses of herbicide paraquat on antioxidant defense in Drosophila. Arch. Insect Biochem. Physio. 88: 235–248.
Mason J.M. Randall T.A. Capkova Frydrychova R. (2015) Telomerase lost? Chromosoma. DOI: 10.1007/s00412-015-0528-7
Korandová M., Čapková Frydrychová R. (2015) Telomerase activity and telomere length in Apis mellifera. Chromosoma: (in press).

A3. Interplay between cell signaling and metabolism in Drosophila melanogaster

Development of infrastructure
The team was founded in 2010 and at the start of MODBIOLIN project it included the leader Alena Krejci (e-mail: [e-mail]) one experienced researcher Alexander Bruce, one PhD student Matej Horvath and one master student Vera Slaninova. The team has grown since then. At the moment it consists of three experienced researchers A. Bruce, Raquel Perez Gomez and M. Horvath, two PhD students Vera Slaninova and Zorana Vujin, two master students Pavel Steffal and Dajana Tanasic, four bachelor students Liza Pfleger, Nora Heigleter, Paraskevi Tziortzouda and Aljosa Smajic and a technician Aida Svestkova. D. Tanasic, did her bachelor thesis also in our lab and joined us from August 2015 as a master student. Several other undegraduate students joined the lab for short internships, for example Miriam Staivnicka as part of her Erasmus training program. Research funding is provided by the Ministry of Education, EMBO Installation grant (The interplay between Notch signaling and cellular metabolism) and the Grant Agency of Czech Republic (The role of sirtuins in Notch signaling and Drosophila development), both the latter ones providing funding till the end of 2016. We have close collaborations with the group of Sarah Bray at the University of Cambrigde, the group of Yuri Moshkin at the Erasmus Medical Centre in Rotterdam, the group of Lukas Trantirek in the CEITEC in Brno and the group of Pavel Tomancak in Max Planck in Dresden. We benefited from the Modbiolin project mainly through the purchase of vital instruments (water purification system, microscope, centrifuge and the Seahorse analyzer) but, importantly, also from the mobility funding. We made several stays at the University of Cambridge and Max Planck Institute in Dresden and we were also able to invite several excellent colleagues for short visits of our laboratory. The development of our team would not have been so successful without the Modbiolin support.

Short description of scientific achievements
The fly D. melanogaster has been established as a model to study whole range of human diseases including neurodegenerative disorders, obesity and cancer. We have joined this trend and use Drosophila as a model to study the cross-talk between cellular metabolism and cell signaling in the context of development. The nutritional/ energetic state of a cell has recently emerged as an important regulator of cellular processes. Certain small metabolites can act as direct regulators of signaling, chromatin structure, gene expression and protein translation. We are particularly interested in the NAD+ and NADH levels as potential regulators of cell signaling via Notch receptor. We want to find nodal points of the cross-talk between Notch and metabolic sensing pathways and see whether this crosstalk differs under normal conditions and under conditions of nutritional stress. Our latest data show that Notch promotes the Warburg effect in cancer cells by directly regulating genes involved in metabolism, particularly in glycolysis and the trixarboxylic acid cycle.
Recent publications
Slaninova V, Krafcikova M, Perez-Gomez R, Steffal P, Trantirek L, Bray SJ, Krejci A: Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle. Revisions submitted to Open Biology, 2015.
Pérez-Gómez R, Slováková J, Rives-Quinto N, Krejci A, Carmena A.: A Serrate-Notch-Canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. J. Cell Sci., 2013 .
Terriente-Felix A, Li J, Collins S, Mulligan A, Reekie I, Bernard F, Krejci A, Bray SJ: Notch co-operates with Lozenge/Runx to lock hemocytes into a differentiation programme. Development, 140(4):926-37, 2013.
Housden BE, Fu AQ, Krejci A, Bernard F, Fischer B, Tavare S, Russell S, Bray SJ: Transcriptional Dynamics Elicited by a Short Pulse of Notch Activation Involves Feed-Forward Regulation by E(spl)/Hes Genes. Plos Genetics, 9(1):e1003162, 2013.
Djiane A, Krejci A, Bernard F, Fexova S, Millen K, Bray SJ.: Dissecting the mechanisms of Notch induced hyperplasia. EMBO Journal 32, 60 - 71, 2013.
Krejci A: Metabolic sensors and their interplay with cell signalling and transcription. Review. Biochem Soc Trans., 40(2):311-23, 2012.
Endo K, Karim MR, Taniguchi H, Krejci A, Kinameri E, Siebert M, Ito K., BraySJ, Moore AW: Chromatin modification of Notch targets in olfactory receptor neuron diversification. Nature Neuroscience, 15(2):224-33, 2012.
Bending D, Newland S, Krejcí A, Phillips JM, Bray S, Cooke A.: Epigenetic changes at Il12rb2 and Tbx21 in relation to plasticity behavior of Th17 cells. J. Immunol. 186(6):3373-82, 2011.
Bernard F, Krejci A, Housden B, Adryan B, Bray SJ: Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors. Development 137(16):2633-42, 2010.

A4. Regulation of energy homeostasis in Drosophila melanogaster

Infrastructure development with MODBIOLIN support
The team was organized by its leader Michal Žurovec (email [e-mail]) several years before the start of MODBIOLIN project but research infrastructure of the team has improved dramatically with the project support. First of all we were able to purchase an excellent inverted microscope with fluorescence. This microscope allows us to measure calcium responses in tissue culture cells as well as to perform a number of reporter and survival assays, which we could not do earlier. Our visiting scholars helped us to establish new methods of targeted mutagenesis in Drosophila and several improved methods for clonal analysis. We also enjoyed working stays of foreign scientists in our laboratory. Using MODBIOLIN support, we hosted Dr. Tamas Szlanka, Dr. Erika Viragh, Dr. Agnes Czibula, István Kiss and Dr. Zoltan Hegedus from the Biological Centre MTA in Szeged, Hungary. Thanks to these stays we started very important collaboration that will continue in future years. A paper based on a similar collaboration with a Stockholm University laboratory, was just accepted for publication by the Journal of Innate Immunity. MODBIOLIN also allowed several people from our laboratory to attend conferences and meetings. In addition, our researcher Roman Sidorov could work 3 months in the University of Stockholm (Prof. U. Theopold) and 3 months in the Institute for Genetics CECAD in Cologne (Dr. M. Uhlirova).

Scientific achievements
We characterized Drosophila adenosine receptor and examined its pharmacological profile: We found that Drosophila adenosine receptor protects tumor clones from apoptosis and that adenosine signaling interacts with wts tumor suppressor signaling pathway (references 1, 2); Mechanism of this phenomenon is still not clear but we think that it is connected to energy metabolism of cells. We proved that adenosine deaminases and adenosine transporters are key regulators of energy homeostasis of Drosophila cells (3); Another pathway connected to the energy metabolism, is regulated by Drosophila Imaginal disc growth factors (IDGFs), a small family of chitinase-like proteins which is related to human chit-like proteins involved in arthritis and immunity. We described IDGF3 as a key molecule responsible for hemolymph clotting (4); We made an important progress in reverse genetic methods. Together with Japanese collaborators we established mutagenesis by engineered nucleases in Bombyx mori and Drosophila melanogaster (5); Finally, we also built a small „facility“ for the characterization of physiological mutant phenotypes (6).
Examples of publications
(1) Kucerova L., Broz V., Fleischmannova J., Santruckova J., Sidorov R., Dolezal V., Zurovec M., (2012) Characterization of the Drosophila adenosine receptor: the effect of adenosine analogs on cAMP signaling in Drosophila cells and their utility for in vivo experiments. J. Neurochem. 121: 383-395.
(2) Sidorov R., Kucerova L., Kiss I., Zurovec M. (2015) Mutation in the Drosophila melanogaster adenosine receptor gene selectively decreases the mosaic hyperplastic epithelial outgrowth rates in wts or dco heterozygous flies. Purinergic Signalling 11: 95-105.
(3) Fleischmannova J., Kucerova L., Sandova K., Steinbauerova V., Broz V., Simek P., Zurovec M. (2012) Differential response of Drosophila cell lines to extracellular adenosine. Insect Biochem. Mol. Bio. 42: 321-331.
(4) Kucerova L., Broz V., Arefin B., Maaroufi H. O., Hurychova J., Strnad H., Zurovec M., Theopold U. (accepted) The Drosophila chitinase-like protein IDGF3 is involved in immunity and wound healing. J. Innate Immun.
(5) Sajwan S., Takasu Y., Tamura T., Uchino K., Sezutsu H., Zurovec M. (2013) Efficient disruption of endogenous Bombyx gene by TAL effector nucleases. Insect Biochem Mol. Biol. 43: 17-23.
(6) Kiss B., Szlanka T., Zvara A., Zurovec M., Sery M., Kakas S., Ramasz B., Hegedus Z., Lukacsovich T., Puskas L., Fonagy A., Kiss I. (2013) Selective elimination/RNAi silencing of FMRF-related peptides and their receptors decreases the locomotor activity in Drosophila melanogaster. Gen. Comp. Endocrinol.191: 137-145.

B1. Protein-protein interactions that drive circadian rhythms

Infrastructure development with MODBIOLIN support
MODBIOLIN provided great benefits mainly in improving our research infrastructure. In our group we have purchased locomotor activity monitors for automated activity measurements of small insect species, such as the fruitfly, Drosophila melanogaster, chambers with LED panels with controlled light intensity and color spectrum composition. This infrastructure support, impossible either from current on-going grants or from institutional funding, together with successful grant applications, helped to increase the size of the group remarkably. Currently, the team includes the leader David Dolezel (e-mail: [e-mail]) postdoctoral fellow (J. Kotwica-Rolinska), students (PhD: Olga Bazalová, Jan Provazník, Lenka Chodáková, Bc: Simona Fišerová, František Kitzberger) and two technicians (Jan Martínek, Hanka Vaněčková). In frame of the MODBIOLIN project we were able to start collaboration with group of Rodolfo Costa (University di Padua, Italy), when Dr. Gabriela Mazzotta visited our laboratory and actively participated in reverse genetics experiments and circadian research for 4 months. Dr. Milena Damulewicz (University Krakow, Poland) visited our group for six months and actively participated in immunocytochemistry experiments and training students in microscopy techniques. Eveline Verhulst (Wageningen University, Netherland) joined our team for 1 month and initiated join project connecting the role of sex determination genes with circadian rhythmicity.

Scientific achievements
Circadian biological clocks are found in most living organisms and their fundamental properties are highly conserved in vertebrates and invertebrates. The fruitfly, Drosophila melanogaster served as a premier insect species for the molecular analysis of the circadian rhythms. Because of the functional similarities of the circadian clocks among all metazoans, it was suggested that the molecular mechanisms underlying the clock function would be conserved as well. Surprisingly, we have found striking differences between the molecular regulations of the circadian timing system even among holometabolous insects (references 1, 2). Probably, these differences in circadian clock architecture may be related to different selection pressures, such as insect seasonality (3). To shed some light on functional aspects of some of these modification we have characterized the role of circadian photoreceptor cryptochrome in D. melanogaster (4). Current effort, directly stemming from the MODBIOLIN support, addresses involvement of particular point mutations of circadian genes period and timeless in temperature compensation (Singh, Mazzotta, Martinek and Dolezel, unpublished).
Examples of publications:
(1) A. Kobelkova, R. Zavodska, I. Sauman, O. Bazalova, D. Dolezel, Expression of Clock Genes period and timeless in the Central Nervous System of the Mediterranean Flour Moth, Ephestia kuehniella. J Biol Rhythms, (Jan 29, 2015).
(2) R. Zavodska, S. Fexová, G. von Wowern, G-B. Han, D. Dolezel and I. Sauman, Is the Sex Communication of Two Pyralid Moths, Plodia interpunctella and Ephestia kuehniella, under Circadian Clock Regulation? J Biol Rhythm 27, 206 (Jun, 2012).
(3) D. Dolezel, Photoperiodic time measurement in insects. Curr Opin Insect Sci 7, 98 (Feb 1, 2015).
(4) C. Gentile, H. Sehadova, A. Simoni, C. Chen, R. Stanewsky, Cryptochrome antagonizes synchronization of Drosophila's circadian clock to temperature cycles. Curr Biol 23, 185 (Feb 4, 2013).

B2. Seasonal timing of diapause in insects

Infrastructure development with MODBIOLIN support
At the start of MODBIOLIN project, the team included the leader V. Koštál (e-mail: [e-mail]) experienced researchers Konrad Schottner, M. Hodková and O. Nedvěd (part time contract), research asistant J. Korbelová, technician I.Vacková, PhD students K. Mičulková, J. Rozsypal, P. Šimůnková; H. Kratochvilová; Mgr student T. Urban and Bc student T. Štětina). The team core has not changed but the students did. Three PhD students (K. Mičulková, P. Šimůnková; H. Kratochvílová) interrupted/extended their studies for different reasons (maternal leave, completing the experiments). J. Rozsypal defended his PhD. degree and got a stipend from JSPS to spend one year (2015) at Osaka City University. T. Štětina successfully completed his MSc. degree and moved onto PhD. student position in our lab starting from September 2015. We accepted two new undergraduate students (P. Hůla and V. Francová). In addition, M. Mollaei, a PhD student from the University of Rafsanjan, Iran, is currently staying in our lab for one year. Dr. Rodolphe Poupardin was recruited on 1 February 2014 in frame of MODBIOLIN project. His experience in molecular physiology and bioinformatics substantially enhanced the potential of our team. One paper has already been published with his significant contribution and other publications are on the way. Dr. Poupardin left our team by 30 September 2015 for a position at the University of Veterinary Medicine, Vienna. MODBIOLIN project helped significantly to upgrade our basic laboratory equipment. We were able to purchase a polarizing fluorimeter, which allows analyses of the fluidity and phase changes in artificial membrane vesicles prepared from membrane lipids extracted from variously acclimated insects (one paper). We widely exploit the transcriptional analysis which is performed with the help of newly acquired real time PCR machine (several papers).
After the termination of the MODBIOLIN project, the team of V. Košťál will be funded by the running national grant "Physiology of insect diapause and cold tolerance". We submitted an additional project "Nature of cold injury and its repair in insects" (if successful, funding would start in January 2016.

Scientific achievements (2014-2015)
The insect life-cycle often includes diapause that allows survival during harsh seasons such as temperate winter. We examined molecular and biochemical mechanisms of diapause and associated cold tolerance. We described physiological limits of cold tolerance in several important insect pests including the codling moth, Cydia pomonella and the bark beetle Pityogenes chalcographus. Such knowledge can be implemented in models forecasting population dynamics of these pests. We acquired new data on the seasonal restructuring of biological membranes that represents one of the major mechanisms of cold acclimation. We quantified so far neglected minor lipid components of the membrane (lysophospholipids, sterols and tocopherols) and analyzed the relationships between membrane composition and its biophysical properties such as fluidity. Using D. melanogaster hsp70 null mutant strain, we assessed the contribution of HSP70 and other heat shock proteins to the adaptive complex of cold tolerance. The cold-stimulated expression of hsp70 gene appeared to be particularly important for coping with brief acute exposures to severe cold close to limits of the insect's supercooling capacity. In a detailed RNAseq transcriptomic study, we described the sequence of events associated with very early phases of photoperiodic diapause induction in drosophilid fly, Chymomyza costata. We found that highly complex transcriptional alteration develops already within hours after the change of photoperiodic conditions and includes: silencing of ecdysteroid signalling cascade, downregulation of several general transcription and epigenetic factors, decrease of expression levels in genes coding for cell cycle regulators, deep restructuring of metabolic pathways, and upregulation of pathways linked to detoxification, redox balance and protection against oxidative stress.
Examples of publications (2013-2015)
Rozsypal J., Koštál V., Zahradníčková H., Šimek P. (2013). Overwintering strategy and mechanisms of cold tolerance in the codling moth (Cydia pomonella). PLoS One 8(4): e61745.
Koštál V., Urban T., Řimnáčová L., Berková P., Šimek k P. (2013) Seasonal changes in minor membrane phospholipid classes, sterols and tocopherols in overwintering insect, Pyrrhocoris apterus. J. Insect Physiol. 59, 934-941.
Koštál V., Miklas B., Dolezal P., Rozsypal J., Zahradníčková H. (2014) Physiology of cold tolerance in the bark beetle, Pityogenes chalcographus and its overwintering in spruce stands. J. Insect Physiol. 63, 62-70.
Rozsypal J., Koštál V., Berková P., Zahradníčková H., Šimek P. (2014) Seasonal changes in the composition of storage and membrane lipids in overwintering larvae of the codling moth, Cydia pomonella. J. Thermal Biol. 45, 124-133.
Štětina T., Koštál V., Korbelová J. (2015) The role of inducible Hsp70, and other heat shock proteins, in adaptive complex of cold tolerance of the fruit fly (Drosophila melanogaster). PLoS One 10, e0128976.
Poupardin R., Schöttner K., Korbelová J., Provazník J., Doležel J., Pavlinic D., Beneš V., Koštál V. (2015) Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata. BMC Genomics 16, 720.

B3. Pyrrhocoris apterus - new model for circadian and photoperiodic studies

Infrastructure development with MODBIOLIN support
At the beginning of the MODBIOLIN research project the team consisted of the team leader Ivo Šauman (e-mail: [e-mail]) experienced researcher Radka Závodská, technicians Roman Neužil and Marcela Jungwirthová, and students (PhD: Martin Pivarči, Samarjeet Singh, Adam Bajgar, MSc: Marion Sieber). During the course Adam Bajgar successfully completed his study program (1-3) and was replaced by admitting new student. In frame of the MODBIOLIN project we were able to recruit to our team (and provide a salary from MODBIOLIN budget) a new researcher Hana Sehadová. Her extensive experience with advanced methods of light microscopy (including laser scanning confocal microscopy and in vivo bio-luminescence imaging) in combination with image analysis expertise significantly enhanced the research potential of our team. By virtue of this new team acquisition in frame of the MODBIOLIN we were able to establish a new Laboratory of biological imaging and digital image analysis led by Hana Sehadová. Dr. Sehadová will remain on BC staff after MODBIOLIN project termination supported from the institutional as well as research grant budgets. With the MODBIOLIN funding, we were able to reconstruct and fully equip a new laboratory for Hana Sehadova, which is dedicated for cell and tissue processing for confocal microscopy, bioluminescence imaging, immunocytochemistry, in situ hybridization, and electron microscopy. The new laboratory of Hana Sehadova recently acquired a skillful technician Jitka Pflegerova and two undergraduate students.

Scientific achievements
The linden bug, Pyrrhocoris apterus, served as a model species for insect endocrinology during last five decades, yet no reverse genetic tools were available, and DNA sequences were limited to a few genes cloned by classical approaches, such as PCR. Therefore, we have initiated, in collaboration with GeneCore (EMBL Heidelberg), transcriptome and genome project on this insect species. Functional analyses of genes involved in diapause regulation identified tissue-specific combination of circadian factors and juvenile hormone receptor Methoprene tolerant in the P. apterus gut. A non-periodic, organ-autonomous feedback between Par domain protein 1 and Cryptochrome 2 then orchestrates expression of downstream genes that mark the diapause vs. reproductive states of the gut. These results show that hormonal signaling through Methoprene-tolerant and circadian proteins controls gut-specific gene activity that is independent of circadian oscillations but differs between reproductive and diapausing animals (references 2, 3). A follow up study further confirmed the role of Methoprene tolerant both in reproduction and metamorphosis (1). Our current effort is aiming at identification of all neuropeptide genes and their corresponding receptors (Kotwica-Rolinska et al., in preparation), comparison of diapause and reproduction-specific transcriptomes (Provaznika et al., in preparation) and inventory of circadian genes including functional evaluation of their role in orchestrating daily activities.
Examples of publications:
(1) V. Smykal et al., Juvenile hormone signaling during reproduction and development of the linden bug, Pyrrhocoris apterus. Insect Biochem Mol Biol 45, 69 (Feb, 2014).
(2) A. Bajgar, M. Jindra, D. Dolezel, Autonomous regulation of the insect gut by circadian genes acting downstream of juvenile hormone signaling. Proc Natl Acad Sci U S A 110, 4416 (Mar 12, 2013).
(3) A. Bajgar, D. Dolezel, M. Hodkova, Endocrine regulation of non-circadian behavior of circadian genes in insect gut. J Insect Physiol, (Jun 26, 2013).

C1. Trypanosoma brucei as a suitable model for mitochondrial research

T. brucei is the causative agents of African sleeping sickness, and related flagellates are responsible for a host of other serious diseases of humans and livestock. Full genome sequence of several Trypanosoma species is available and infective stages can be obtained in large amount both in vitro and in vivo. Moreover, it is the only member of the eukaryotic superdomain Excavata that is amenable to the forward and reverse genetics, such as RNAi, overexpression, protein tagging etc. Yet for a number of reasons it still does not belong to the commonly used model systems. We found that T. brucei is a very suitable model for the studies of mitochondrial proteins because: i/ its mitoproteome is available and is as complex as that of higher eukaryotes; ii/ it harbors only single mitochondrion per cell, which can be very efficiently purified; iii/ one stage contains a fully active respiring organelle, while the other stage switches to a dormant mitochondrion; iv/ petite mutants with partially or fully lost mitochondrial DNA are available. We want to exploit the suitability of the active vs. non-active mitochondrion system of T. brucei to study regulation of protein import and expression, to analyze the petite mutants for changes in the mitoproteome and communication of the organelle with the nucleus, and finally, by rescuing knock-downs for various mitochondrial proteins with their human homologs, study the functions and interactions of these proteins.
Infrastructure development with MODBIOLIN support
At the start of the MODBIOLIN project, the Laboratory of Molecular Protistology was led by Prof. Julius Lukeš (e-mail: [e-mail]) and included three post-doctoral researchers (Drs. Eva Horáková, Hassan Hashimi and Drahomíra Novotná), one technician and several bachelor, master and PhD students. The acquisition of MODBIOLIN had a profound impact on the structure and productivity of the laboratory. The scientists supported for 6 months – Ivica Králová-Hromadová and Eva Dobáková, were an excellent choice, as they brought deep knowledge of metabolism, which had positive consequences on a number of projects. With MODBIOLIN support we were able to realize a number of stays abroad and could invite several outstanding researchers, all of which contributed to the lab. The six months stay (2 months in 2013 and 4 month in 2014) of Piya Changmai in the laboratory of Dr. Benoit Vanhollebeke (University of Brussels, Belgium) lead to potentially important discoveries concerning heme metabolism in T. brucei. We have also used the opportunity to invite speakers for short-term stays, such as Dr. Moritz Niemann from the University of Bern.
Just in the last two years four PhD students successfully defended: Piya Changmai (Fe-S cluster synthesis in trypanosomes), currently post-doc at the University of Ostrava, Czech Republic, doing research on human evolution; Lucie Novotná-Ridlon (mitochondrial translation in trypanosomes), currently post-doc at the Salk Institute, La Jolla, USA, doing research on spatio-temporal organization of plasma membrane; Somsuvro Basu
(cytosolic Fe-S cluster assembly in trypanosomes), currently post-doc at Philipps Universitat, Marburg, Germany, where he does research on Fe-S cluster assembly in humans; and Jiří Týč (mitochondrial heat shock and ribosomal proteins in trypanosomes), currently a post-doc at Oxford University, Oxford, U.K. doing research on ultrastructure of trypanosomes and other eukaryotes. Currently, the laboratory has two grants from the Czech Grant Agency (P.I.) a Marie-Curie network grant and a COST grant (as collaborators), recently a grant by Moore Foundations (USA), and its ERC grant is currently in good standing.

Scientific achievements (2014-2015)
The niche lately occupied by our laboratory rests on the interface between molecular dissection of Trypanosoma brucei, a significant human pathogen, phylogenetic studies of monoxenous trypanosomatid parasites, and diversity analyses of diplonemid flagellates. In other words, we want to combine the wide-range of molecular methods established in the laboratory during our two decades-long studies of T. brucei with the identification of new model protists, especially those that are important from the evolutionary or ecological perspective. The laboratory produced a total sum of 70 papers in the course of MODBIOLIN, a production accelerated by the MODBIOLIN award, as can be easily seen from the comparison with previous years. It is also worth mentioning that even with a rather intense production, we are trying to publish in generally highly respected journals, increasing the impact of our work (e.g. our papers were cited about 800x in 2014). As apparent from the titles of attached papers (we have included MODBIOLIN in the acknowledgments of many of them), we are primarily paying attention to the mitochondrion, evolution, diversity, and from the molecular processes to RNA editing, iron-sulfu cluster assembly and heme synthesis. However, we are particularly keen to explore interface between these areas, an approach rarely applied by others.
Examples of publications (2013-2015)
Kozminsky E., Kraeva N., Ishemgulova A., Dobáková E., Lukeš J., Kment P., Yurchenko V., Votýpka J., Maslov D.A. (2015) Host-specificity of monoxenous trypanosomatids: statistical analysis of the distribution and transmission patterns of the parasites from Neotropical Heteroptera. Protist 166, 551-568.
Read L.K. Lukeš J. & Hashimi H. (2015) Trypanosome RNA editing: the complexity of getting U in and taking U out. WIREs RNA 10, 1002 (19 pages)
Horáková E., Changmai P., Paris Z., Salmon D. & Lukeš J. (2015) Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe-S cluster assembly but not heme import into mitochondrion of Trypanosoma brucei. FEBS J. 282, 4157-4175.
Bartošová-Sojková P., Oppenheim R., Soldati-Favre D. & Lukeš J. (2015) Epicellular apicomplexans: parasites „on-the-way-in“. PLoS Pathogens 11, e1005080.
Sunter J.D. Benz C., Andre J., Whipple S., McKean P.G. Gull K., Ginger M.L. & Lukeš J. (2015) Modulation of flagellum attachment zone protein FLAM3 and regulation of the cell shape in T. brucei life cycle transitions. J. Cell Sci. 128, 3117-3130.
Lukeš J., Stensvold C.R. Jirků-Pomajbíková K. & Wegener Parfrey L. (2015) Are human intestinal eukaryotes beneficial or commensals? PLoS Pathogens 11, e1005039
Votýpka J., d’Avila-Levy C.M. Grellier P., Maslov D.A. Lukeš J. & Yurchenko V. (2015) New approaches to systematics of Trypanosomatidae: criteria for taxonomic (re)description. Trends Parasitol. 31, 460-469.
Oborník M. & Lukeš J. (2015) The organellar genomes of Chromera and Vitrella, the phototrophic relatives of apicomplexan parasites. Annu. Rev. Microbiol. 69, 129-144.
Speijer D., Lukeš J. & Eliáš M. (2015) Sex is ubiquitous, ancient, and inherent attribute of eukaryotic life. Proc. Natl. Acad. Sci. USA 112, 8827-8834.
de Vargas C., Audic S., Henry N., Decelle J., Mahé F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J.-M. Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horák A., Jaillon O., Lima Mendez G., Lukeš J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Acinas S.G. Bork P., Bowler C., Gaill F., Gorsky G., Grimsley N., Hingcamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P. & Carsenti E. (2015) Eukaryotic plankton diversity in the sunlit global ocean. Science 348, 1261605.
Flegontov P., Michálek J., Janouškovec J., Lai D.-H. Jirků M., Hajdušková E., Tomčala A., Otto T.D. Keeling P.J. Pain A., Oborník M. & Lukeš J. (2015) Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol. Biol. Evol. 32, 1115-1131.
Týč J., Klingbeil M.M. Lukeš J. (2015) Mitochondrial heat-shock protein machinery Hsp70/Hsp40 is indispensable for proper mitochondrial DNA maintenance and replication. mBio e02425.
Verner Z., Basu S., Benz C., Dixit S., Dobáková E., Faktorová D., Hashimi H., Horáková E., Huang Z., Paris Z., Pena-Diaz P., Ridlon L., Týč J., Wildridge D., Zíková A. & Lukeš J. (2015) Malleable mitochondrion of Trypanosoma brucei. Int. Rev. Cell. Mol. Biol. 315, 73-151.
Lukeš J. & Basu S. (2015) Fe/S protein biogenesis in trypanosomes – a review. Biochim. Biophys. Acta – Mol. Cell. Res. 1853, 1481-1492.
Kraeva N., Ishemgulova A., Lukeš J. & Yurchenko V. (2014) Tet-inducible gene expression system in Leishmania mexicana. Mol. Biochem. Parasitol. 198, 11-13.
Huang Z., Kaltenbrunner S., Šimková E., Staněk D., Lukeš J. & Hashimi, H. (2014) The dynamics of mitochondrial RNA-binding protein complex in Trypanosoma brucei and its petite mutant under optimized immobilization conditions. Eukaryot. Cell 13, 1232-1240.
Basu S., Netz D.J. Haindrich A.C. Herleth N., Lagny T.J. Pierik A.J. Lill R. & Lukeš J. (2014) Cytosolic iron-sulfur protein assembly is functionally conserved and essential in procyclic and bloodstream Trypanosoma brucei. Mol. Microbiol. 93, 897-910.
Grybchuk-Ieremenko A., Losev A., Kostygov A.Y. Lukeš J. & Yurchenko V. (2014) Prevalence of mixed trypanosome infections of freshwater fishes. Folia Parasitol. 61, 495-504.
Lukeš J., Kuchta R., Scholz T. & Pomajbíková K. (2014) (Self-) infections with parasites: re-interpretation for the present. Trends Parasitol. 30, 377-385.
Lukeš J., Skalický T., Týč J., Votýpka J. & Yurchenko V. (2014) Evolution of parasitism in kinetoplastid flagellates. Mol. Biochem. Parasitol. 195, 115-122.
Verner Z., Čermáková P., Škodová I., Kováčová B., Lukeš J. & Horváth A. (2014) Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei. Mol. Biochem. Parasitol. 193, 55-65.
Kovářová J., Horáková E., Changmai P., Vancová M. & Lukeš J. (2014) Mitochondrial and nucleolar localization of cysteine desulfurase Nfs and the scaffold protein Isu in Trypanosoma brucei. Eukaryot. Cell 13, 353-361.
Heger T.J. Edgcomb V.P. Kim E., Lukeš J., Leander B.S. & Yubuki N. (2014) A resurgence in field research is essential to better understand the diversity, ecology and evolution of microbial eukaryotes. J. Euk. Microbiol. 61, 214-223.
Škodová I., Verner Z., Bringaud F., Fabian P., Lukeš J. & Horváth A. (2013) Characterization of two mitochondrial FAD-dependent glycerol-3-phosphate dehydrogenases in Trypanosoma brucei. Eukaryot. Cell 12, 1664-1673.
Ridlon L., Škodová I., Pan S., Lukeš J. & Maslov D.A. (2013) The importance of the 45S ribosomal small subunit-related complex for mitochondrial translation in Trypanosoma brucei. J. Biol. Chem. 288, 32963-32978.
Ammerman M.L. Tomasello D.L. Faktorová D., Kafková L., Hashimi H., Lukeš J. & Read L.K. (2013) A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei. PLoS One 8, e78015.
Votýpka J., Suková E., Kraeva N., Ishemgulova A., Duží I., Lukeš J. & Yurchenko V. (2013) Diversity of trypanosomatids (Kinetoplastea: Trypanosomatidae) parasitizing fleas (Insecta: Siphonaptera) and description of a new genus Blechomonas gen. n. Protist 164, 763-781.
Hashimi H., McDonald L., Stříbrná E. & Lukeš J. (2013) Trypanosome Letm1 protein is essential for mitochondrial potassium homeostasis. J. Biol. Chem. 288, 26914-26925.
Flegontov P., Votýpka J., Skalický T., Logacheva M.D. Penin A.A. Tanifuji G., Onodera N.T. Kondrashov A.S. Volf P., Archibald J.M. & Lukeš J. (2013) Paratrypanosoma is a novel early-branching trypanosomatid. Curr. Biol. 23, 1787-1793.
Changmai P., Horáková E., Long S., Černotíková-Stříbrná E., McDonald L.M. Bontempi E.J. & Lukeš J. (2013) Both human ferredoxins equally efficiently rescue ferredoxin deficiency in Trypanosoma brucei. Mol. Microbiol. 89, 135-151.
Qablan M.A. Oborník M., Petrželková K.J. Sloboda M., Shudiefat M.F. Hořín P., Lukeš J. & Modrý D. (2013) Infections by Babesia caballi and Theileria equi in Jordanian equids: epidemiology and genetic diversity. Parasitology 140, 1096-1103.
Basu S., Leonard J.C. Desai N., Mavridou D.A.I. Tang K.H. Goddard A.D. Ginger M.L. Lukeš J. & Allen J.W.A. (2013) Divergence of Erv1-associated mitochondrial import and export pathways in trypanosomes and anaerobic protists. Eukaryot. Cell 12, 343-355.
Hashimi H., Zimmer S.L. Ammerman M.L. Read L.K. & Lukeš J. (2013) Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol. 29, 91-99.
Maslov D.A. Votýpka J., Yurchenko V. & Lukeš J. (2013) Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed. Trends Parasitol. 29, 43-52.
Vávra J. & Lukeš J. (2013) Microsporidia and „the art of living together”. Adv. Parasitol. 82, 253-319.
Kořený L., Oborník M. & Lukeš J. (2013) Make it, take it or leave it: Heme metabolism of parasites. PLoS Pathogens 9, e1003088.
Verner Z., Škodová I., Poláková S., Ďurišová-Benkovičová V., Horváth A. & Lukeš J. (2013) Alternative NADH dehydrogenace (NDH2): intermembrane-space-facing counterpart of mitochondrial complex I in the procyclic Trypanosoma brucei. Parasitology 140, 328-337.

C2. The role of essential tRNA modifications in parasitic protist Trypanosoma brucei

Infrastructure development with MODBIOLIN support
The Laboratory of RNA Biology of Protists was established in February 2014 in frame of the MODBIOLIN project. At present, the team consists of the team leader Dr. Zdeněk Paris (e-mail: [e-mail]) researcher Jitka Kručinská, PhD student Sneha Kulkarni (since October 2015), and four undergraduate students: Helmut Stanzl, Rebecca Wolkerstorfer, Veronika Běhálková and Kristýna Pospíšilová. In addition, highly experienced researcher Eva Hegedüšová (PhD from Comenius University in Bratislava, Slovakia) will join the lab in February 2016 as a postdoc. This year our group received funding of the Grant Agency of the Czech Republic (grant number 15-21450Y to Z. Paris) to study the role of essential tRNA modifications in trypanosomes. This funding not only guaranties sustainability of the laboratory till the end of 2017 but also allows expanding the team with one research assistant and one graduate student. The MODBIOLIN funding was crucial for the establishment of this laboratory allowing to purchase all necessary pieces of equipment such as incubators, freezers, refrigerators, centrifuges, UV documentation system, microscope and also valuable reagents. Also, other variable expenses associated with starting this group were funded. Thanks to the Modbiolin support, we have also hosted a highly experienced researcher prof. David Rueda from the Imperial Collage London, UK.

Scientific achievements
Our group studies various aspects of RNA biology of protozoan parasite Trypanosoma brucei and related flagellates. In those early evolved unicellular organisms, most genes are regulated post-transcriptionally. Consequently, post-transcriptional processing of RNA becomes of great importance in order to regulate complex life cycles of these pathogens. We are mainly interested in tRNA modifications, nuclear tRNA export and role of the only intron-containing tRNA in trypanosomes. Identification of unique mechanisms of RNA metabolism is our long term goal. We believe this will reveal new drug targets to combat these important parasites.
The main research project in the lab focuses on describing a particular tRNA modification called Queuosine (Q). Q is one of the most complex, but unexplored tRNA modification, found in the first position of the anticodon (wobble base) of several tRNAs. While bacteria can synthetize this modification by 7 enzymatic steps, eukaryotes are fully dependent on their diet or gut microflora to obtain Q. Despite its omnipresence in bacteria and eukaryotes, the function of Q in tRNA is not completely clear. There is a minimal phenotypic effect when queuosine is absent in eukaryotic tRNAs. Interestingly, some studies suggested importance of Q in cancer development. In our project, we take an advantage of the protozoan parasite Trypanosoma brucei and use it as a model for a comprehensive analysis of the tRNA guanine transglycosylase (TGT), an enzyme responsible for Q-tRNA formation in eukaryotes. We employ methods of molecular biology and biochemistry to further explore this unique modification. We hope that this could be eventually exploited in the treatment of diseases caused by trypanosomes.
Examples of publications
Horakova, E., Changmai, P., Paris, Z., Salmon, D., & Lukes, J. (2015). Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe-S cluster assembly but not heme import into the mitochondrion of Trypanosoma brucei. The FEBS Journal.
Sample, P. J., Koreny, L., Paris, Z., Gaston, K. W., Rubio, M. A. T., Fleming, I. M. C., Alfonzo, J. D. (2015). A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. Nucleic Acids Research, 43(8), 4262–4273.
Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z,Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. (2015). Malleable mitochondrion of Trypanosoma brucei. International Review of Cell and Molecular Biology, 315, 73–151.

C3. Drug targets in medically important parasites Leishmania and Trypanosoma

Infrastructure development with MODBIOLIN support
Modbiolin had an enormous impact on the Biology Centre infrastructure including a largely expanded equipment list, established new laboratories and extended collaborative efforts due to short and long stays in EU countries. During the period of 2012-2015 the Laboratory of Functional Biology of Protists consisted of the following members: team leader Alena Zíková (e-mail: [e-mail]); experienced researcher Brian Panicucci; postdoctoral fellows Eva Doleželová and Ondřej Gahura; and students (doctoral: Karolína Šubrtová, Michaela Veselíková, Gergana Taleva; MSc: Hana Váchová, Jan Martínek, Zuzana Kotrbová; bachelor: Michaela Kunzová). During this period of funding, J. Martínek, Z. Kotrbová and H. Váchová successfully completed their MSc degree and moved onto positions in other research labs. Karolína Šubrtová successfully completed her PhD programme and she has accepted a postdoc position at the University of Edinburgh. Moreover, Modbiolin funded two stays of a foreign postdoctoral fellow, Anna Gnipová, who joined our lab for six months during 2014. Her experience in molecular biology and biochemistry substantially enhanced the potential of our team. One publication was released this year with her significant contribution (Gnipova et al., 2015, Eukaryot Cell. 14(3):297-310). A three-week stay of Ondrej Gahura in the laboratory of John E Walker at the Mitochondrial Biology Unit in Cambridge was also supported by Modbiolin; it boosted our long term collaboration with this excellent team. After the termination of the MODBIOLIN project, the remaining team of Dr. A. Zíková (consisting of B. Panicucci, E. Doleželová, O. Gahura, M. Veselíková, G. Taleva and M. Kunzová) will be completely funded by the EMBO Installation grant 1965 (PI A. Zíková) and by the ERC grant (number CZ LL1205, PI A. Zíková).

Scientific achievements (2014-2015)
Subspecies of Trypanosoma brucei cause significant human morbidity and mortality. In many countries, they are recognized as an important threat to public health, but current treatments rely on a handful of drugs with serious limitations due to their toxicity and high cost. The major bottleneck in drug development lies in the identification, validation and characterization of drug targets. Specifically, we are interested in potential chemotheraupetic compounds, which are targeted to the mitochondria and/or are inhibitors of unique and specific biochemical pathways of the parasite. In more details, we focus on 1) T. brucei FoF1- ATPase, which activity can be specifically inhibited by the natural occurring TbIF1 peptide without interfering with the activity of the host’s enzyme. Furthermore, we are exploring several putative potent inhibitors (e.g. bisphosphonates) of the FoF1- ATPase complex; 2) on validation of the Trypanosoma purine salvage pathway as a drug target since we have recently explored potent inhibitors that have been shown to inhibit this pathway in Plasmodium; 3) on characterization of mitochondrial enzymes, which are essential for the infectious stage of the parasite and most likely contribute to the mitochondrial ATP production, a pathway thought to be absent from this parasite. A unique contribution of these enzymes to the parasite’s fitness makes them an excellent drug targets worthy to be explored.
Examples of publications:
1) Šubrtová K, Panicucci B, Zíková A. ATPaseTb2, a unique membrane-boundFoF1-ATPase component, is essential in bloodstream and dyskinetoplastic trypanosomes. PLoS Pathog. 2015 Feb 25;11(2):e1004660.
2) Gnipová A, Šubrtová K, Panicucci B, Horváth A, Lukeš J, Zíková A. The ADP/ATP carrier and its relationship to oxidative phosphorylation in ancestral protist Trypanosoma brucei. Eukaryot Cell. 2015 Mar;14(3):297-310.
3) Alkhaldi A, Martinek J, Panicucci B, Dardonville C, Zìkovà A, de Koning H. Trypanocidal action of bisphosphonium salts through a mitochondrial target in bloodstream form Trypanosoma brucei. International Journal for Parasitology: Drugs and Drug Resistance. Accepted.

C4. Chromera velia as a model to study evolution of parasitism in Apicomplexa

Infrastructure development with MODBIOLIN support
MODBIOLIN provided many benefits mainly in improving research infrastructure. In my lab we have purchased high quality optical and fluorescence microscope Olympus and replaced old fume hoods with the functioning new ones. The team included the team leader M. Oborník (e-mail: [e-mail]) research assistant dr. Kateřina Jiroutová, postdoctoral fellows drs. Heather Esson, Zoltan Fussy, Aleš Tomčala (all financed by the Czech Science Foundation, CSF) and Eva Hajdušková (financed from an Operational Program Project) and PhD students Jitka Kručinská, Jaromír Cihlář and Jan Michálek. As mentioned above, the team benefited from the MODBIOLIN project mainly by improving the laboratory equipment. Frankly speaking, without MODBIOLIN we would have no chance to get this equipment and we highly appreciate our involvement in MODBIOLIN. We have obtained additional funding from the Czech Science Foundation for projects concerning the genomics of eustigmatophyte algae (13-33039S) and the search for the origin of exosymbiont in organisms with secondary plastids (15-176435). We have hosted a highly experienced researcher dr. Ansgar Gruber from the University of Konstanz in Germany for a period of three months. Our cooperation continue without EU funding: J. Cihlář and Z. Fussy spent few weeks in A. Gruber lab in 2015.

Scientific achievements
Chromera velia is a novel photosynthetic alveolate that has been isolated from a coral reef in Australia. Phylogenetic analysis revealed that C. velia is the closest known photosynthetic relative to the apicomplexan parasites, such as Plasmodium falciparum or Toxoplasma gondii. This relationship is supported by the detection of several typical morphological features of Apicomplexa, such as cortical alveoli or four membranes surrounding the plastid, in C. velia. In addition to these morphological synapomorphies (1), molecular characters common for Apicomplexa and C. velia were also identified, for instance the use of non-canonical code UGA for tryptophan in plastid encoded proteins (1) and presence of non-canonical heme pathway (2). Since this alga is non-pathogenic, non-toxic and easy and cheap to cultivate, it is a suitable model to study evolution of parasitism in Apicomplexa. We have participated on the sequencing of nuclear genomes both chromerid algae (3), and we also reconstructed unusual respiratory chain of C. velia (4).
Examples of publications:
(1) Moore RB, Oborník M, Janouškovec J, Chrudimský T, Vancová M, Green DH, Wright SW, Davies NW, Bolch CJS, Heimann K, Šlapeta J, Hoegh-Guldberg O, Logsdon JM, Carter DA. (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451, 959-963.
(2) Kořený L, Sobotka R, Janouškovec J, Keeling PJ, Oborník M (2011) Tetrapyrrole synthesis of photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites. Plant Cell 23, 3454-3462.
(3) Woo YH, Ansari H, Otto TD, Klinger C, Kolísko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo C, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast F, Miranda- Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings N, Regelado EP, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey D, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks J, Templeton TJ, Waller RF, Lukeš J, Oborník M & Pain A (2015) . eLife 4, e06974.
(4) Flegontov P, Michálek J, Janouškovec J, Lai H, Jirků M, Hajdušková E, Tomčala A, Otto TD, Keeling PJ, Pain A, Oborník M, Lukeš J (2015) Divergent Mitochondrial Respiratory Chains in Phototrophic Relatives of Apicomplexan Parasites. Molecular Biology and Evolution 32, 1115-1131.

C5. Laboratory of Environmental Genomics

Infrastructure development with MODBIOLIN support
The Laboratory of Environmental Genomics (LEG) was founded directly from the initiative of MODBIOLIN WP4 providing salary for the head of the lab Aleš Horák (e-mail [e-mail]) from March 2013 to September 2015. MODBIOLIN also provided basic research infrastructure, such as inverted and stereo microscopes, PCR cycler, Gel Imaging system and replacement of old fumehood to name the most significant. On the top of that, MODBIOLIN covered long-term stay of A. Horák in the laboratory of Dr. Colomban de Vargas in SBR Roscoff (05-06/14), the stay of Jana Veselá in the laboratory of Dr. Adriana Zingone in The Stazione Zoologica Anton Dohrn of Naples (04/15) and the long-term stay of Dr. Sonja Rueckert from the Edinburgh Naper University in BCAS (08-09/14). MODBIOLIN also funded short-term visits of A. Horák to the Oceanomics kick-off meeting in Paris (02/13) and to the laboratory of prof. Chris Bowler (ENS Paris, 04/15). The attendance of A. Horák at ASLO meeting (Granada, Spain, 02/15) was also supported by MODBIOLIN. The Laboratory of Environmental Genetics currently includes the head A. Horák, Dr. Jana Veselá and the PhD. student Olga Flegontová.

Scientific achievements
We have participated in the analysis of the dataset of planktonic samples collected during the Tara Oceans expedition. We helped to describe diversity and patterns of distribution of mysterious protistan group who rankend third most diverse and sixth most abundant among all eukaryotes of sunlit oceans, called planktonic diplonemids. The partial results were published in Science (de Vargas et al., 2015) and Current Biology (Lukeš, Flegontova, & Horák, 2015). We are preparing a detailed survey for publication. We are also applying the same methodology to the analysis of other protistan clades. We also took part in the functional analysis of the genomes of two algal relatives of apicoplexan parastites, Chromera velia and Vitrella brassicaformis (Woo et al., 2015).
Selected publications
de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahe, F., Logares, R., ... Velayoudon, D. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science, 348(6237), 1261605–1261605. doi:10.1126/science.1261605
Lukeš, J., Flegontova, O., & Horák, A. (2015). Diplonemids. Current Biology, 25(16), R702–R704. doi:10.1016/j.cub.2015.04.052
Woo, Y. H., Ansari, H., Otto, T. D., Klinger, C. M., Kolisko, M., Michálek, J., ... Pain, A. (2015). Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife, 4, 1–41. doi:10.7554/eLife.06974

C6. Sphaerospora as a model for studying parasite transmission in aquatic systems

Infrastructure development with MODBIOLIN support
The team is led by A.S. Holzer (e-mail: [e-mail]) and complemented by the expertise of evolutionary biologists Dr. Ivan Fiala (researcher) and Dr. Pavla Bartošová (postdoctoral scientist). During the course of the project, two postdoctoral scientists, Gema Alama-Bermejo and Ashlie Hartigan, joined the group and established a new line of research that will serve as an important basis for vaccine design for the aquaculture industry. PhD students Alena Kodádková and Sneha Patra (hired in 2012) as well as the technician Hana Pecková were involved in a variety of experiments and assays. While all salaries of this research group were covered from 5 additional grants and projects (Czech Academy of Sciences and Czech Science Foundation), the construction of an aquaculture recirculation system, funded by MODBIOLIN, was essential for a number of applied studies as well as for the maintenance of sphaerosporid proliferative stages in carp blood in vivo. The team also profited from the MODBIOLIN-funded stays at collaborating research centers (Hungarian Academy of Sciences). The team was successful in obtaining funding for the follow-on research by a large Horizon 2020 project (ParaFishControl) of a total of 8,1 Mio Euros (29 partners; 5 years), where A.S.Holzer is the leader for the program “myxozoans in carp”.

Scientific achievements (2014-2015)
Based on our Sphaerospora molnari transcriptome produced with the support of MODBIOLIN in 2013 we have developed a line of research into myxozoan proteolytic enzymes as important candidates for developing specific anti-myxozoan strategies, which are still missing worldwide (no legalized treatment for myxozoans in fish destined to human consumption). The protease household and the expression of proteolytic enzymes in highly proliferative stages of the parasite in carp blood was analysed and we are currently finishing the proteomic characterization of the most important candidates. Over the last years, we have also attempted to develop the first myxozoan in vitro culture system; we have prolonged laboratory culture from 2 to 6 weeks. This has allowed us to perform a number of assays using carp leukocytes of different types in order to estimate host-parasite interaction on a cellular and molecular level. We are trying to further improve culture protocols in order to be able to perform molecular interference assays in near future. In order to better understand the mechanism and function of the rapid motility of S. molnari blood stages in carp, specific antibodies for the highly expressed, aberrant form of S. molnari cytoplasmatic actin were designed, produced and applied for fluorescent and immunogold localization of the motor protein and demonstration of its mode of action. Furthermore, inhibition in vitro assays showed that this motility is used for evading attachment of macrophages and lymphocytes which is essential for the elimination of large numbers of parasites by the immune system of the host. Finally, we investigated the contribution of S. molnari as an etiological agent co-responsible for swim bladder inflammation in common carp and studied the diversity and evolution of members of Sphaerospora sensu stricto. Several publications related to the large-scale studies in 2014 and 2015 are still being completed.
Examples of publications (2013-2015)
Feist SW, Morris DJ, Alama-Bermejo G, Holzer AS (2015) Cellular processes in myxozoans. In: Myxozoan Evolution, Ecology and Development, B. Okamura et al. (Eds.): 139-154.
Holzer AS, Hartigan A, Patra S, Pecková H, Eszterbauer E (2014) Molecular fingerprinting of the myxozoan community in common carp suffering Swim Bladder Inflammation (SBI) identifies multiple etiological agents Parasites & Vectors 7: 398.
Bartošová P, Fiala I, Cinková M, Jirků M, Caffara M, Fioravanti ML, Atkinson SD, Bartholomew JL, Holzer AS (2013) Sphaerospora sensu stricto: Taxonomy, diversity and evolution of a unique lineage of myxosporeans (Myxozoa). Molecular Phylogenetics and Evolution 68: 93-105.
Holzer AS, Bartošová P, Pecková H, Tyml T, Atkinson S, Bartholomew J, Sipos D, Eszterbauer E, Dyková I (2013) Who's who' in renal sphaerosporids (Bivalvulida: Myxozoa) from common carp, Prussian carp and goldfish - molecular identification of cryptic species, blood stages and new members of Sphaerospora sensu stricto. Parasitology 140: 46-60.
Holzer AS, Pecková H, Patra S, Brennan NP, Yanes-Roca C, Main KL (2013) Severe glomerular disease in juvenile grey snapper Lutjanus griseus L. in the Gulf of Mexico caused by the myxozoan Sphaerospora motemarini n. sp. International Journal for Parasitology: Parasites and Wildlife 2: 124-130.

C7. Laboratory of parasitic therapy

Infrastructure development with MODBIOLIN support
The recruitment of team leader Kateřina Jirků-Pomajbíková (e-mail: [e-mail]) as a new MODBIOLIN researcher in October 2013 initiated research on parasitic therapy. She is a veterinarian experienced in in parasitology, particularly of primates, incl. humans. She was soon joined by a technician (Jana Vášová) and three bachelor students (Jiřina Růžková, Zuzana Lhotská, Oldřiška Hložková). This small Laboratory of parasitic therapy was strengthened in July 2015 by accepting the experienced researcher Milan Jirků who was supported partly by the Institute of Parasitology and partly by a grant of the Human Frontier Science Programme (HFSP). His experience in molecular biology and parasitology enhanced research potential of the team. In September 2015, two other pregradual students (Jana Levá, Lucie Řežábková) were admitted. Since termination of the MODBIOLIN project, the leader K. Jirků Pomajbíková is fully funded by the Institute of Parasitology and two other team members (J. Vášová, M. Jirků) get support from the Institute and from the HFSP Young Investigators grant.
To increase the competitiveness of the laboratory, Kateřina has established international collaborations with laboratory for microbial eukaryotes supervised by Laura Wegener-Parfrey in the Department of Zoology, University of British Columbia (Vancouver, Canada) and with laboratory for microbiology and infection control supervised by Christen Rune Stensvold in the Statens Serum Institute (Copenhagen, Denmark). This current collaboration combines the expertise in parasitology, microbial ecology and microbiome analyses - these disciplines are necessary to investigate the potential therapeutic impact of symbionts on host health. Kateřina obtained, as the principal investigator, the HFSP Young Investigators grant in collaboration with Laura Wegener Parfrey (Co-I).
With the aid of MODBIOLIN, the laboratory was equipped with several small devices (thermosblocks, mini-centrifuges, microscopes, vortex, automatic pipettes, -20°C freezers) and two investments (deep-freezing box, and thermos-cycler). The deep-freezing box is shared with two laboratories that also participated in the MODBIOLIN project (Zdeněk Paris, Aleš Horák).

Scientific achievement (Oct 2013 – Sept 2015):
The Laboratory was founded in the wake of the fast growing interest in helminth therapy of immune mediated disorders (IMD) in man. This line of research has brought new insights into the therapy of difficult to treat diseases, such as Crohn’s diseases, ulcerative colitis, allergies and many others, whose incidence in developed countries has sharply increased within last decades. Despite of the great interest, this research is still in an initial phase and there is enough space for the deployment of new research programs. Our laboratory is focused on investigations of the therapeutic use of intestinal symbionts to ameliorate some IMD diseases, especially the Crohn’s disease. Conducted research brings together clinical investigation of helminth therapy with investigation of the gut microbiota, which are usually studied separately. This synergy provides a deeper insight into the biotic interactions in the gut ecosystem that can be leveraged to improved symbiont-based therapies for Crohn’s disease (and other IMDs).
Kateřina has already selected model symbionts, established their cultivations under laboratory conditions, optimized immunological methods for analyses of the mucosal immunity and cytokine gene expressions, and performed experiments with the SPF rat model. Effect of symbiont infections on the immune system and gut microbiome can be analyzed and the animal model used to study induced colitis. We are focused on the symbiotic helminths and protists that appear to be essential for optimal composition of gut microflora. Our first results revealed immunomodulatory effect of the helminth candidate (tapeworm Hymenolepis diminuta) on the host organism and also an increase of bacterial richness in the host microbiome (the next-generation analyses of microbiome were done in collaboration with Laura Wegener-Parfrey. During September 2015, we established the induced colitis model on the rat system corresponding to human Crohn’s disease. We are interested in the validation of the effect of both candidates (helminth and protist) on the induced colitis.
Publications (2013-2015):
Lukeš J, Kuchta R, Scholz T, Pomajbíková K (2014) (Self-) infection with parasites: re-intepretation for the present. Trend. Parasitol 30, 377-385.
Lukeš J., Stensvold C.R. Jirků-Pomajbíková K., Wegener Parfrey L (2015) Are human intestinal eukaryotes beneficial, or commensals? PLoS Pathogens 11, e1005039.

C8. The tick Ixodes ricinus as a model for basic and applied biomedical research

Infrastructure development with MODBIOLIN support
This Modbiolin research area originally included Laboratory of Genomics and Proteomics of Disease Vectors (LGPDV) headed by Dr. Michail Kotsyfakis, Laboratory of Vector Immunology (LIV) headed by Dr. Petr Kopáček and newly established Laboratory of Tick-Transmitted Diseases (LTTD) headed by Dr. Ondřej Hajdušek (see separate paragraph for this laboratory). These laboratories have in common their research focus on ticks as diseases vectors and tick molecular factors that facilitate transmission of the tick-borne pathogens. Due to his frequent stays abroad, the former team leader M. Kotsyfakis was replaced by Petr Kopáček ([e-mail]) in 2014. The support of Modbiolin made it possible to recruit the experienced researcher Dr. Ondřej Hajdušek who equipped LTTD and built an ambitious young team. The remaining tick team consists from two senior scientists (Kotsyfakis, Kopáček), two experienced scientists (Sojka, Šíma), one postdoctoral fellows (Urbanová), four PhD. students (Kotál, Perner, Jalovecká, Hartman), technicians (Grunclová, Loosová, Harcubová, Dědouchová ) and three undergraduate students. Beside personal support, a substantial infrastructural development of the team was achieved by the purchase of expensive instruments from the MODBIOLIN budget, namely microplate fluorescent reader, lyophilizer, protein liquid chromatograph and pipetting robot. The sustainability of the team will be ensured by the Institutional support from the Institute of Parasitology BCAS and by the ongoing and future project from the Czech grant agencies (especially Czech Grant Foundation), and by large international collaborative projects such as USA NIH R01 grant, No. 1R01AI093653-01A1 or EU FP7 project Antidote, No. 602272.

Scientific achievements (2014-2015)
Both LGPDV and LVI teams exploited the new instrumental infrastructure provided in frame of Modbiolin project and the research was focused mainly on the European hard tick Ixodes ricinus, the vector of tick-borne encephalitis virus, Lyme disease. I. ricinus serves as an excellent model organism for the description of arthropod recombinant proteins that may have the potential in drug development and/or serve as targets for establishing of novel methodologies to control tick-borne diseases in Europe. The main scientific achievements were the following:
(i) Systems biology approach based on high-throughput transcriptomic and proteomics studies in Ixodes ricinus salivary glands, midgut and hemocytes allowed to identify a large number of molecules which can be further exploited for rational anti-tick strategies.
(ii) Further in-depth characterization of protease inhibitors from tick saliva (sialostatins, serpin IRS-2) and their role in modulation of the host immune system.
(iii) Focus on innate immune system of ticks revealed the function tick primordial complement system (thioester containing proteins and putative C3 convertases) in the phagocytosis of various microbes by tick hemocytes.
(iv) Systematic research of blood digestion and heme/iron metabolism in ticks resulted in detailed characterization of tick molecules that play a significant role in tick physiology, development and reproduction and that can be candidate antigens for an efficient ‘anti-tick’ vaccine.
Selected publications (2014-2015)
Schwarz, A., Tenzer, S., Hackenberg, M., Erhart, J., Gerhold-Ay, A., Mazur, J., Kuharev, J., Ribeiro, J.M. and Kotsyfakis, M. (2014). A systems level analysis reveals transcriptomic and proteomic complexity in ixodes ricinus midgut and salivary glands during early attachment and feeding. Mol Cell Proteomics 13, 2725-2735.
Kotsyfakis, M., Schwarz, A., Erhart, J., and Ribeiro, J.M. (2015). Tissue- and time-dependent transcription in Ixodes ricinus salivary glands and midguts when blood feeding on the vertebrate host. Sci Rep 5, 9103.
Kotsyfakis, M., Kopacek, P., Franta, Z., Pedra, J.H. and Ribeiro, J.M. (2015). Deep Sequencing Analysis of the Ixodes ricinus Haemocytome. PLoS Negl Trop Dis 9, e0003754.
Urbanova, V., Hartmann, D., Grunclova, L., Sima, R., Flemming, T., Hajdusek, O., and Kopacek, P. (2014). IrFC - An Ixodes ricinus injury-responsive molecule related to Limulus Factor C. Dev Comp Immunol 46, 439-447.
Urbanova, V., Sima, R., Sauman, I., Hajdusek, O., and Kopacek, P. (2015). Thioester-containing proteins of the tick Ixodes ricinus: gene expression, response to microbial challenge and their role in phagocytosis of the yeast Candida albicans. Dev Comp Immunol 48, 55-64.

C9. Tick transmitted diseases

Infrastructure development with MODBIOLIN support (staff, equipment, collaborations, sustainability)
At the start of MODBIOLIN, team leader Ondřej Hajdušek (e-mail: [e-mail]) was recruited (March, 2013) to start the laboratory. The MODBIOLIN project fully covered his salary, but from July 7 2013 O. Hajdusek was paid from the MODBIOLIN only by 60%, because of his support from another source (Czech Science Foundation). Recently, the laboratory includes one researcher, two technicians and four undergraduate students. After the termination of MODBIOLIN project, O. Hajdusek was hired by the Institute of Parasitology that also pays the technicians. The laboratory was equipped partially from the MODBIOLIN budget (ultracentrifuge, light microscope, capillary puller and sharpener, and small laboratory equipment) and is now fully operative. The team implemented laboratory transmission models for Borrelia and Babesia and hereby became an important partner within the European Research Area as documented by participation in the FP7 Project Antidote - http://www.antidote-fp7.org/.

Scientific achievements (2013-2015)
Ticks are blood-feeding ectoparasites transmitting some of the most devastating viral, bacterial, and protozoal diseases known to humans and animals. After mosquitoes, they are the most common vectors of diseases. In the Czech Republic, tick-borne encephalitis (TBE) and Lyme disease are the most frequent and the most important human diseases transmitted by ticks. Although an effective vaccine protecting from TBE is on the market, no human vaccine against Lyme disease is currently available. Beside the human infections, ticks and tick-borne diseases also greatly affect livestock, limiting its production in many areas around the world and causing economical losses reaching billions of US dollars every year.
Lyme disease is an emerging human and animal tick-borne disease of temperate climates with a concurrent distribution spanning North America and Eurasia. Borreliosis in humans affects multiple body systems, producing a range of potential symptoms. Babesiosis is an apicomplexan malaria-like parasite (Piroplasmida) affecting health of many animal species and together with Theileriosis are the main reducing agents of the cattle production in tropical and subtropical regions. Moreover, human babesiosis (e.g. Babesia microti in the USA) increasingly raises public health concern.
Anti-tick vaccines offer an alternative way of protection to the use of acaricides in tropical areas with heavily infested animals. Because the use of acaricides is not always possible, is too expensive, is not effective (resistance), or the treatment contaminates milk and meat products, scientists are forced to find suitable tick antigens that could be used for the vaccine development. Although proper mechanism of the vaccines effect has not been fully understood, it is believed that the antibodies engorged during the tick feeding could bind the antigens on the surface of midgut and block the tick feeding and transmission of pathogens.
Availability of the tick genome sequences and RNA interference (RNAi) in ticks brought a powerful method how to test tick genes for the vaccine candidates. Previously, by using RNAi we have described basic components of iron metabolism in the tick I. ricinus and found crucial protein with a novel function, which we called Ferritin2 (FER2). The use of FER2 for the host immunization against ticks has been patented by our group (PV 2008-402). During the MODBIOLIN project, our laboratory worked on an improvement of FER2 vaccine (chimeric vaccine with other antigens) and continued vaccination trial with animals in the countries of economic interest.
During the last three years our Laboratory of Tick Transmitted Diseases also worked on the characterization of tick genes (e.g. immunity, iron and heme metabolism) and development of the laboratory transmission models. Recently, we possess B. afzelii transmission system, where infected I. ricinus tick nymphs (clean larvae fed on infected mice) are able to infect new naïve mouse. We have also successfully developed a method of RNAi in nymphs (micro-injection of dsRNA by glass capillary) and are now able to test tick genes for their effect on transmission of Borrelia spirochetes from the tick into the host. Similar transmission model for Babesia (B. microti) is currently under development.
In the future, we would like to use our knowledge about the tick manipulations gathered at Institute of Parasitology for several decades including tick rearing, feeding, and physiology. The main goal of the future is an identification of new genes important for the tick feeding and pathogen transmission by using transcriptomics and proteomics methods in order to find new tick antigens directly applicable for a new anti-tick vaccine. The laboratory equipment acquired from the MODBIOLIN budget (ultracentrifuge, light microscope, capillary puller and sharpener, and small laboratory equipment) helped to establish the lab and will allow to perform experiments at the level comparable with the top laboratories in the field.
Examples of publications with MODBIOLIN affiliations (2013-2015)
Ayllon, N., Naranjo, V., Hajdusek, O., Villar, M., Galindo, R. C., Kocan, K. M., ... de la Fuente, J. (2015). Nuclease Tudor-SN Is Involved in Tick dsRNA-Mediated RNA Interference and Feeding but Not in Defense against Flaviviral or Anaplasma phagocytophilum Rickettsial Infection. PloS One, 10(7), e0133038.
Golovchenko, M., Sima, R., Hajdusek, O., Grubhoffer, L., Oliver, J. H. J., & Rudenko, N. (2014). Invasive potential of Borrelia burgdorferi sensu stricto ospC type L strains increases the possible disease risk to humans in the regions of their distribution. Parasites & Vectors, 7, 538.
Hajdusek, O., Sima, R., Ayllon, N., Jalovecka, M., Perner, J., de la Fuente, J., & Kopacek, P. (2013). Interaction of the tick immune system with transmitted pathogens. Frontiers in Cellular and Infection Microbiology, 3, 26.
Urbanova, V., Hartmann, D., Grunclova, L., Sima, R., Flemming, T., Hajdusek, O., & Kopacek, P. (2014). IrFC - An Ixodes ricinus injury-responsive molecule related to Limulus Factor C. Developmental and Comparative Immunology, 46(2), 439–447.
Urbanova, V., Sima, R., Sauman, I., Hajdusek, O., & Kopacek, P. (2015). Thioester-containing proteins of the tick Ixodes ricinus: gene expression, response to microbial challenge and their role in phagocytosis of the yeast Candida albicans. Developmental and Comparative Immunology, 48(1), 55–64.

D1. Exploitation of Arabidopsis genome to improve crop
Infrastructure development with MODBIOLIN support (staff, equipment, collaborations, sustainability)
At the start of MODBIOLIN project the team included the team leader Jaroslav Matoušek (e-mail: [e-mail]) experienced researcher Dr. T. Kocábek, Dr. G. S. Duraisamy, technician ing. L. Orctová and the PhD student K. Siglová. The team enlarged in course of MODBIOLIN project. Dr. Ajay Kumar Mishra was recruited on 12.9.2013 and was paid from the MODBIOLIN budget. Dr. Mishra was involved in three original topics by searching in hop for the homologues of A. thaliana genes in several pathways: 1. Genetic determination of metabolome pathway connected to prenylflavonoid and lupulin production, 2. Study of pospiviroid pathogenesis affecting silencing mechanisms, 3. Biogenesis of anticancerogenic plant nucleases. Financial support was secured from the following additional sources: GA13-03037S project entitled “Combinatorial regulation and network of transcription factors involved in the biosynthesis of medicinal prenylflavonoids in hop (Humulus lupulus L.)” for the years 2013-2017; Czech-Japan joint project financed by the Czech Ministry of Education, Youth and Sports “Concurrent propagation of viroid pathogens infecting hop and fruit trees and analysis of their „combinatorial effects“ (2014 -2016); Alexander von Humboldt Stiftung (FRG), Research Group Linkage project entitled “Pospiviroid-induced degradome: the background for the complex and expansive plant disease" for years 2013-2016. In spring 2015, Dr. Mishra applied as principal investigator to the Czech Science Foundation for a grant on “Genome-wide exploration of miRNA-mediated regulatory network and silencing of endogenous miRNAs: prospect towards improvement of growth, development and secondary metabolite production in Humulus lupulus”. After the termination of MODBIOLIN project, the team of Dr. Matoušek will continue to include experienced researchers Dr. Mishra, Dr. Kocábek and Dr. Duraisamy, the technician ing. L. Orctová and the PhD student K. Siglová (all from the MODBIOLIN staff).

Scientific achievements (2014-2015)
The team of J. Matoušek is working on genetic co-determination of biosynthesis of anticancerogenic prenylflavonoids and bitter acids in the lupulin of hop (Humulus lupulus L.). The major task included characterization of lupulin-specific transcription factors (TFs) and analysis of elements of molecular network influencing this regulation. We selected and isolated several important TFs showing expression in hop lupulin glands based on comparison with A. thaliana master TFs or factors involved in genetic determination of flavonoid biosynthesis or trichome morphogenesis. During last two years we focused on the WRKY oligofamily of hop genes. Activation by lupulin-specific WRKY1 gene is associated with binary complex predicted from combinatorial transient expression assay with WDR1 TF (Matoušek et al., 2013), as well as with activity of some kinases. In addition, level of WRKY1 mRNA is regulated by PTGS. Recently, the group is solving this principal unsolved query regarding the molecular regulatory network. The major achievements also include identification and cloning of proximal promoter elements of important genes of prenylflavonoid pathway and most of cloned TFs. Based on these sequences we are able to predict and assay the basis of the network from combinatorial assays in heterologous systems and in hops using biolistic transient expression systems and hop transformation.
In the work frame of analysis of viroid pathogens we primarily focused to work on the mechanisms of viroid-mediated pathogenesis, viroid propagation and adaptation to new natural and experimental hosts. A wide adaptation potential of PSTVd was found (Matoušek, et al., 2014). The viroid adaptation and linked pathogenesis is very complex process involving interconnected network on different levels of cellular metabolism. In order to study the interaction on RNA level by more complex way, we projected wide degradome analyses using NGS and bioinformatics tools; this work is currently running.
From NGS analyses of small RNAs extracted from diseased hops we characterized the presence of another viroid originated as contaminant from citruses (CVdIV). Currently we found that there is some cross protection between HSVd and CVdIV viroids (unpublished) therefore, the analysis of multiple viroid infections is more complex issue. We found genotype-dependent suppression of tomato transcription factor SANT/HTHMyb (SlMyb) due to viroid pathogenesis. In heterologous system of Nicotiana benthamiana, we observed a SlMyb-associated necrotic effect in agroinfiltrated leaf sectors during ectopic overexpression. SlMyb RNA degradation was significantly stronger in viroid-infected tissues. Necroses induction as well as gene silencing experiments using the SlMyb homologues revealed involvement of this gene in plant growth and flower development (Matoušek et al., 2015).
Examples of publications (2013-2015)
Matoušek, J., Kocábek, T., Patzak, J.: Molecular background and networking putatively involved in regulation of lupulin gland metabolome-Results and prospects. Acta Horticulturae, 1010, 2013, 39-46.
Kocábek, T., Matoušek, J.: Functional and complementation analysis of hop genes in heterologous systems. Acta Horticulturae, 1010, 2013, 77-84.
Matoušek, J., Piernikarczyk, R.J.J. Dědič, P., Mertelík, J., Uhlířová, K., Duraisamy, G.S. Orctová, L., Kloudová, K., Ptáček, J., Steger, G.: Characterization of Potato spindle tuber viroid (PSTVd) incidence and new variants from ornamentals. European Journal of Plant Pathology, 138, 2014, 93-101.
Mishra AK, Duraisamy GS, Týcová A, Matoušek J. Computational exploration of microRNAs from expressed sequence tags of Humulus lupulus, target predictions and expression analysis. Comput Biol Chem, 59, 2015, 131-141.
Matoušek J., Piernikarczyk R.J. Týcová A., Duraisamy G.S. Kocábek T., Steger G. Expression of SANT/HTH Myb mRNA, a plant morphogenesis-regulating transcription factor, changes due to viroid infection. J Plant Physiol, 183, 2015, 85-94.

D2. Plant viromes

Infrastructure development with MODBIOLIN support (staff, equipment, collaborations, sustainability)
The team lead by Igor Koloniuk (e-mail: [e-mail]) was established in April 2014 after the return of Dr. Koloniuk from a stay at the University of Kentucky, USA. MODBIOLIN funding supported him in the period July-September, 2015. During this period he submitted proposal “Implementation of NGS in plant virology – unprecedented capacity with a risk of data overflow” that was approved by the Czech Ministry of Education, Youth and Sports and is funded by the COST Action FA 1407 program from the middle of October 2015, after the termination of MODBIOLIN support. The funding will continue until 2017. Dr. Koloniuk submitted another proposal “Insight into the origin and molecular basis of hypovirulence of the ME711 isolate of Phomopsis longicolla phytopathogenic fungus” to the Czech Science Foundation. It is expected that by January 2016 the team will include 2 experienced researchers, one PhD student and a technician.

Scientific achievements (2014-2015)
Research activity has been focused on novel RNA viruses phylogenetically related to the Fabavirus genus (Secoviridae family) that were identified in the sweet and sour cherry trees. The finding was compelling due to a two reasons: a) It was the first fabavirus identified in a wooden plant species; b) the very first sequence data indicated on extraordinary intra-host variability that was far higher than usual. These results required solid evidences to avoid misinterpretation of NGS data. Further exploration confirmed our initial results and revealed that this virus exists within the host as several groups distinguished by sequence identities. The research part is almost finished and the manuscript is to be submitted by the end of 2015.

Potential Impact:
Infrastructure building of the Biology Centre of the Czech Academy of Sciences (BCAS) was the purpose and goal of MODBIOLIN project. Project realization was a demanding job because different components of research infrastructure ought to be addressed and supported in certain proportions. Positive impact of activities such as staff building, equipment upgrading and collaborations within ERA can already be noticed in the publication output of BCAS but more pronounced enhancement of BCAS research potential is expected to occur after project termination when all infrastructure improvement will be in place. The links established between MODBIOLIN teams will foster investigations on selected model organisms as one of the two dominating research areas of BCAS (ecology is the other one) and thereby contribute to the coherence and profile of the whole institution and its standing in ERA. The concentration of resources on the solution of pressing biological problems is inevitable. Higher BCAS output will have positive influence on other educational and research-oriented institutions in the region. Increasing interest in intellectual protection and technology transfer evokes hope that in a few years project impact will be perceived also in the business sphere. We foresee the following short term and long term benefits of MODBIOLIN project.

Enhancement of the publication output, which is documented at the end of the “Main S & T results” section of this report, is a direct effect of infrastructure improvements that is expected to culminate in a few years. This also applies to the applications for research support: the preparation of proposals will capitalize on the MODBIOLIN experience and recently established contacts within ERA will facilitate formation of project consortia. We expect increased interest of BCAS researchers in the research promoting programs of EU, specifically in the Horizon2020 initiatives. Improved preparation of project proposals combined with higher BCAS competitiveness will enhance positive evaluations of the submitted project applications. The MODBIOLIN experience is also important for BCAS administration that will guarantee smooth and expert management of future successful projects, including efficient use of the provided financial support.

All MODBIOLIN teams have links to the partners in ERA and will continue to collaborate and participate in networking that is a natural platform for the organization of scientific meetings. Small workshops (maximally 50 participants) proved to be a very efficient and relatively inexpensive way of knowledge exchange. The procedure of workshop organization developed in the frame of MODBIOLIN will be applied to future activities of this kind. This can also be said about other kinds of mobility. There has been and will be great interest in the rotation (long-term stays in different laboratories) of young researchers but it is difficult to gain support for this activity. The rotation is closely linked to flexibility and sustainability of the research teams. MODBIOLIN experience with long-term stays and with staff hiring based on international advertisement will affect personnel policy of BCAS and influence decisions in the area of human resources development and staff coherence.

The importance of instrumental infrastructure development for the enhancement of the research potential cannot be overestimated. All teams have daily-use small instruments at their benches and enjoy easy access to the expensive equipment. The leadership of BCAS will certainly try to maintain this favourable situation that makes BCAS staff competitive internationally, but actual situation will depend on the over-all research support. The sharing of instruments is controlled directly within BCAS and is likely to be further improved; there is tendency to establish service laboratories but some of the associated problems have not been resolved (for example, to which extent should researchers performing only a routine service be included as co-authors in the resulting publications and patents?). The researchers from industry and the university teachers will have increasing access to unique instruments. This activity will contribute to the maintenance of BCAS interactions with the university and will enhance interactions with the business sphere.

MODBIOLIN use of several kinds of knowledge dissemination revealed their advantages and disadvantages. Project web page is relatively easy to install and modify and is justifiably the method of choice. Project promoting leaflets may reach audience (e.g. foreign laymen) that is unlikely to search for project webpage in the internet; another leaflets advantage is their easy distribution by miscellaneous means. Presentation of posters at various gatherings and technological fairs offers the possibility of personal contact with the audience. Domestic national public is probably most effectively approached at the publicized nation-wide events such as “Open door”, “Week of science” and “Night of scientists”. Making a promotional video is a more costly but rewarding activity because the video can be distributed in different ways and attracts diverse audience. We have also good experience with the use of the internet portal “Gate2Biotech” that is viewed as an ideal platform for the establishment of contacts with the business sphere. On the other hand, we cannot recommend regional press conferences unless they are linked to some sensation; writing a contribution to a newspaper or providing interviews for the broadcasting and TV stations is more efficient. We have also met low interest in our attempts to organize a larger (more than 10 participants) meeting of NGOs. This evaluation of the means of knowledge dissemination in the region will be helpful to BCAS and other institutions that aim at increasing public awareness about the importance of both basic and applied research.

The set-up of MODBIOLIN management proved successful and is likely to be mimicked in the future projects: part-time engagement of 1 - 2 persons directly responsible for the project management, for interactions with the local Management Committee (MC, composed of leading project researchers), and for communication with the project officers in Brussels. The evaluation of project management associated with advice provided by one or two external bodies such as the Advisory Board and the Steering Committee was also found helpful. Since it is difficult to find meeting dates acceptable for all, electronic communication should be preferred.

The availability of English interactive e-learning course “Technology Transfer Manager-junior (TTM-J) (learning material equivalent to standard 330 pp) is expected to increase education in the ways of intellectual property protection and enhance interest in BCAS research yielding practical innovations. Successful commercialization of the identification of hop cultivars by DNA probes in 2015 demonstrated that generation of practical applications is possible. The negotiations on the commercialization of the patented use of ferritin 2 for the vaccination against ticks reveal complexity of such processes and the need of adequate education.

Long-term MODBIOLIN impacts in the region include improvement of the gender ratio in the staff of BCAS staff and other educational and research institutions, closer interactions with local technological park in all activities stimulating founding of small businesses, and participation in the planning of socio-economic development of the South Bohemia region and adjacent regions Upper Austria and Bavaria.

List of Websites:
www.modbiolin.bc.cas.cz