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Laboratory of Applied Biochemistry

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Our laboratory focuses on the application of biochemical methods in various scientific fields. We apply biochemical, molecular biological, transcriptomic, genomic, proteomic techniques for the study glycobiology of ticks and tick-borne pathogens, tick-host-pathogen interactions, nanostructured surface functionalization, and the study of fish development.

Research

Laboratory of Applied Biochemistry participated in the C4SYS research infrastructure.

C4SYS is a priority infrastructure project on the national roadmap, and currently builds on close collaboration between the Academy of Sciences (Institute of Nanobiology and Structural Biology, Nove Hrady, Institute of Microbiology, Prague, Global Change Research Center, Brno), the University of South Bohemia and Masaryk University, Brno.

Services offered by the laboratory in the frame of C4SYS can be found here.

Published papers

by the laboratory team members can be found here.

 

Research focus

A) Interaction of tick-borne encephalitis virus with tick and host on the molecular and cellular level.

Tick-borne encephalitis virus is one of the most dangerous tick-transmitted pathogens in Europe and Asia. We aim to better characterize the replication of the tick-borne encephalitis virus, the interaction of viral proteins with host and tick molecules, the regulation of virus replication by the host anti-viral proteins on the molecular level, as well as the effects of viral replication on cellular mechanisms.

https://doi.org/10.1371/journal.pntd.0007745

https://doi.org/10.1016/j.dib.2019.105029

https://doi:10.1016/j.ttbdis.2020.101420

https://doi.org/10.1016/j.csbj.2022.05.052

 

B) Tick research

Fibrinogen-related proteins (FRePs) with lectin activity were studied in the Dermacentor and Rhipicephalus ticks. These proteins participate in the tick innate immune response. All of the proteins were found to be glycosylated and a cross-reaction of anti-FReP antibodies with the tick storage protein Hemelipoglycoprotein (HLGP) was discovered; however, the cross-reactivity is most probably dependent on the epitope similarity as sequence similarity was not found between fibrinogen and FRePs on one hand and HLGP on the other. The hemagglutination activity of Rhipicephalus ticks was inhibited by sialic acid and sialylated glycoproteins, GalNAc, and GlcNAc, suggesting similarity to another FReP from Ornithodoros moubata, the Dorin M protein. (Sterba et al., Parasite Vector 2011)

Mass spectrometric analysis of D. marginatus HLGP N-glycans in a collaborating Novotny laboratory (Indiana University, Bloomington, IN) showed the presence of high-mannose and complex type; paucimannosic type glycans were not observed. Furthermore, lectin-activity of HLGP was studied in collaboration with M. Wimmerova lab (Central European Institute of Technology, Masaryk University, Brno, Czech Republic). The highest binding activity was found for galactose. (Dupejova et al., Parasite Vector 2011).

Sialylated N-glycans were detected in Ixodes and Dermacentor ticks – both N-acetylneuraminic and N-glycosylneuraminic acid (NeuGc) were detected again in collaboration with Prof. Novotny's group in Bloomington, IN. Antibodies against NeuGc were utilized for tracking of sialylated glycans in tick tissues and thus we showed the route of sialylated host glycoproteins from the tick gut through the hemolymph to the salivary glands, where they are in part excreted back into the host. (Vancova et al., J. Insect Physiol. 2012).

Next, we used a combination of sialic acid quantitation and detection of metabolically incorporated sialic acid (Click-iT chemistry) to determine expression of sialylated glycoproteins by the ticks themselves. Using this approach we showed, that majority of sialic acid present in fed female Ixodes ricinus ticks is coming from the host and not the tick itself. This can be one of the immune system evasion strategies employed by ticks (Sterba et al., Carbohydr. Res. 2014).

Recently, we work on the determination of the importance of glycan moieties (NeuAc and NeuGc) for the infection of tick and host cells by the Anaplasma marginale MSP1a in collaboration with Prof. de la Fuente's laboratory (IREC, Universidad de Castilla-La Mancha, Ciudad Real, Spain). While it was previously shown, that Anaplasma infection of tick cells is dependent on the presence of core-fucosylated N-glycans, here we are showing for the first time the importance of sialic acid for the infection of tick cells. The presence of host sialylated molecules in tick tissues and on the surface of tick cells could explain these findings.

Our current knowledge on the tick glycobiology was published recently. https://doi.org/10.1186/s13071-018-3062-7

https://doi.org/10.1186/s13071-019-3460-5.

https://doi.org/10.1038/s41598-020-70330-5

https://doi.org/10.1186/s13071-020-04173-4

Various aspects of gene expression regulation are studied in our laboratory, primarily changes in the gene expression in the various tick life-stages and methyltransferases responsible for DNA and RNA methylation.

https://doi.org/10.1016/j.ttbdis.2019.101348

 

C) Functionalized and nanostructured surfaces, biosensors

Antimicrobial effects on various modified and functionalized materials are studied in collaboration with our colleagues from the Laboratory of Applied Plasma Physics, Department of Physics. Furthermore, biocompatibility of the newly prepared surfaces for the growth of human cells is studied. It is important to mention, that we are entirely changing from the usually used cancer cell lines to primary human cells in this research field to better model the in vivo system.

http://dx.doi.org/10.1002/ppap.201900003

https://doi.org/10.1016/j.matlet.2018.07.082

https://doi.org/10.1016/j.apsusc.2019.07.135

https://doi.org/10.1007/s00216-019-02329-5

https://doi.org/10.1016/j.surfcoat.2020.125805

https://doi.org/10.1021/acsami.1c16930

https://doi.org/10.1021/acs.langmuir.1c01409

 

D) Fish gametes and fertilization

We participate in research oriented on various aspects of gametes development and preservation in collaboration with several laboratories from the Faculty of Fisheries and Water Protection.

https://doi.org/10.1007/s10695-018-0538-5

https://doi.org/10.1016/j.anireprosci.2018.03.025

https://doi.org/10.3390/ani9100753

https://doi.org/10.1111/raq.12355

https://doi.org/10.3390/ijms22115925

https://doi.org/10.3389/fmars.2021.736087

https://doi.org/10.1016/j.theriogenology.2019.02.029

 

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Contacts

Master's in Ecology

Contacts

You can address your questions regarding specific issues to the following e-mails:

Admission, enrollment, any other study-related acts, issue of documents needed for visa

Department of Student Affairs (Jindřiška Trefná)

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Visa assistance

Department of Student Affairs (Kateřina Tomková)

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Content of the study, content of this website.

Board of Master's in Ecology programme (Petr Blažek)

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General support

Erasmus Student Network

  



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Practical information

Master's in Ecology

Practical information

This page provides you with the basic practical information to help you find your way in Czechia:

  • Living costs

    As a former east-block country, the living costs are way lower in Czechia compared to west European countries.

     

    CZK (Kč)

    EUR (€)

    exchange rate

    25 (-24)

    1

    dormitory: 1 bed per month (double room - single room)
    - cost of a bed in a shared student flat is similar

    3450 - 6300

    138 - 252

    lunch in university cafeteria

    80 - 100

    3.2 - 4

    lunch in pub

    175 - 300

    7 - 12

    beer 0.5l in pub
    - beer is disproportionately cheap here, other beverages are more expensive

    35 - 55

    1.4 - 2.2

    bus and train ticket from Prague to České Budějovice (students below 26 years can have 25% student discount)

    (180 -) 240

    (7.2 -) 9.6

    bus ticket within České Budějovice

    20

    0.8

    You can check Numbeo to see quite realistic estimates of the local prices. Note that the prices differ between the centre of a capital and outskirts of countryside town: you will rarely see over-average prices around the university campus.

  • Campus

    Most of the building of the Faculty of Science are located in the campus of the University of South Bohemia and Biology Centre of the Czech Academy of Science.

  • Accommodation

    University dormitories
    link (Czech only, but you can see photos), This email address is being protected from spambots. You need JavaScript enabled to view it., English price list
    Excerpt from price-list (autumn 2024):
    - cheapest: a bed in a double-bed room with bathrooms shared on the whole floor (3450 CZK).
    - apartments: a bed in a double-bed roomwith bathroom shared within apartment(4200 CZK).
    - private: a bed in a single-bed room with private bathroom (6300 CZK)

    Private dormitory Pedagog
    link (Czech)
    Excerpt from price-list (autumn 2024):
    - a bed in a double-bed room with bathroom shared within apartment (6950 CZK)
    - a single-bed room with bathroom shared within apartment (10950 CZK)

    Shared student apartments
    The prices are similar to dormitories ranging from 3500 CZK / bed for the cheapest fully occupied apartments to about 7000 CZK for a single room. Prices over 10000 CZK are considered too expensive, unless you want a whole little apartment just for yourself.

    Accommodation scholarship
    Most students are eligible for accommodation scholarship, which is 540 CZK monthly (2024), paid quarterly. Students are to apply in STAG.

  • Transport

    Schedules of all Czech public transport companies can be easily searched on IDOS portal, which is also in English.

    Individual companies differ in their policy on student discounts, but all of them provide a considerable discount for students under 26 years. Some companies accept ISIC, most companies require a Czech student transport card (issued at any bus or train station), the city buses in České Budějovice issue their own pre-paid student card.

    Due to the location of the town on a flat floodplain, bikes are very common, and bikesharing become very popular in last years. Many students consider buying a second-hand bike for around 2000 CZK.

     

  • Administrative requirements

    Foreign nationals must follow specific rules, which differ upon the country of their origin. Generally, there are much lower requirements for EU citizens than for other nationals. A comprehensive summary of the requirements can be found here. Before arrival, you should contact your Czech consulate regarding visa. After arrival, the International Office of the Faculty or University can help you with the residency issues here.

    All long-stay foreigners (incl. EU) must register at the Foreign Police. Funnily, rarely anyone there speaks English, so you would need a Czech buddy to go there with you...

  • Language

    The language is Czech - a Slavic language partly intelligible for speakers of related languages, but usually quite difficult for other foreigners. The main foreign language is English followed by German and Russian. English is mostly spread among young people, at the universities, in town centres, so you will mostly find your way. At the same time, stories about conductors of international trains or foreign police clerks who cannot say a word in any foreign language are not uncommon... Google Translate makes quite good translations nowadays.

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Students

Master's in Ecology

Students

First enrolment

Please, arrange your residency affairs in time and start gathering all required documents as soon as possible (even before admission). Note that your admission cannot be completed until we receive an appropriately authenticated copy of your Bachelor's certificate. Even a smooth visa procedure takes months, and late delivery of required documents hinders the process.

 

Winter semester

Summer semester

registration of new students

2 – 13 September 2024

12 – 14 February 2025

field trip (optional)

15 – 20 September 2024

  

start of lectures

23 September 2024

17 February 2025
  • Postponed enrolment is allowed in case of prolonged visa procedure, but you are to apply for this in advance (or within 5 days after the set date at the latest), otherwise you would be expelled.
  • The dates for next academic year are announced in April. Before the update is done, you can expect similar dates as in last year.

See all dates in academic calendar.
Most information can be found on the faculty website.
STAG is a University database of courses, their lecturers, schedule, theses etc. You will be provided password to enrol or see your study details, but you can browse almost all parts (except students' details) without login.

Fees
  • Net tuition fee: 500 EUR* per year
  • A few additional minor fees (e.g. 100 CZK for issuing the University ID card etc.)

* The fee for study in foreign language has been recently set at the University level to 3000 EUR per year, but the Faculty of Science will largely compensate it to all students. 2500 EUR reduction is guaranteed to all students fulfilling their study obligations as a scholarship. The dean may decide to waive even larger part of the fee upon request. Students study according to the rules valid at their admission, therefore there is no change in the fee (500 CZK per year) for the current students including students admitted in November 2023.

The main fees are given by the Statutes of the University (Articles 27 and 28).

Scholarships and grants

Scholarships for all students during the whole study:

  • Extraordinary scholarship for support of students of study programmes conducted in English language. 2500 EUR per year will compensate most of the tuition fee to all students fulfilling their study obligations.
  • Accommodation bursary about 540 CZK monthly (~22 EUR) (paid quarterly) is intended to cover part of living costs for all students with permanent residence outside the České Budějovice district. There are a few other conditions (e.g. students whose living costs are already covered by other scholarships are not eligible), but usually all students of this programme receive it.

Premium scholarships for excellent students in the second year of study depending on the achievement in the first year:

  • Students with excellent study results can receive 2,000 CZK monthly (~80 EUR) during their second year. For this, students must reach 60 credits and GPA<1.2 in their first year. This scholarship is awarded automatically.
  • Top 20 students across all BSc. and MSc. programmes of Faculty of Science with excellent study and research results get a bonus of 1,200 - 3,000 CZK monthly (~48 - 120 EUR) for publishing in Impact Factor journals or presenting at a conference while maintaining very good study results (60 credits in last year, GPA<1.5). Apply by 15 October or 10 March.
  • Dean's price for the best Master thesis of 5,000 CZK (~ 200 EUR).

See the provision of the dean for details of the scholarships. The amount of accommodation bursary is updated yearly by the rector.

Applicants from some countries can also apply for a scholarship of Czech Ministry of Education, Youth and Sports. This scholarship is out of our control, see detailed information on the ministry website or contact Czech consulate in your country.

Students' research can be supported by several grant agencies; the most relevant for this study programme is Student Grant Agency (SGA) of the Faculty of Science.

Study plan

You are to enrol for courses before the start of each semester. You need to get min. 120 credits during your study, which implies you should aim at min. 30 credits per semester to finish your study in time. It is usual to enrol a bit more courses in the first semesters to have more time for your thesis in the last semester.

There are two obligatory courses (type A) in this Master's programme: "Master Thesis, Practical Part" for 13 credits (in each semester except the first one when it is facultative-obligatory - type B) and "Ecology Colloquia" for 2 credits (once per year, recommended in 2nd and 4th semester). In addition, you are to enrol any courses to get over the 30 credits per semester. When compiling your study plan, remember that you are to enrol facultative-obligatory courses (type B, "core courses") for min. 53 credits during the whole study. (There was a recent change in the study plan: the old plan until 2021/2022 defined Master Thesis as type A in all four semesters and min 40 credits from B courses, while in the new plan since 2022/2023 the Master Thesis in the first semester was changed to type B and therefore the min number of credits from B courses increased.)

See Study and Examination Regulations of USB and Provision of the Dean for more details.

Enrolment takes place in two steps (see the dates in academic calendar).

  • Electronic enrolment (Jun, Jan) - You select in STAG which courses you would like to attend in the next semester. Courses where too few students enrolled may be cancelled, which is announced in the news on the main faculty website short after the end of enrolment.
  • Confirmation of enrolment (Sep, Feb) - You are to present yourself at the department of study affairs to confirm the list of your courses. You can make minor justified adjustments, e.g. remove or replace courses that were cancelled.
Thesis topic and supervisor

You are to find a supervisor and agree on a topic of your thesis during the first semester. Take your time to browse websites of academic departments of the Faculty of Science (mainly Botany, Zoology, Biology of Ecosystems) and institutes of Biology Centre CAS (mainly Entomology 1, 2, Hydrobiology), or Institute of Botany CAS in Třeboň. Talk to several people. Finally, the supervisor will confirm whether you have successfully passed the course "Master Thesis, Practical Part". Find your supervisor in time, so that you can start working soon and the supervisor is happy to confirm your work.

You need to fill a form for assignment of Master thesis and submit it to the Department of Student Affairs. At the same time, you enrol the obligatory course Master Thesis, Practical Part with a code of the department where your supervisor is based (usually KBO/881, KZO/881 or KBE/881), so that you are registered at the right department.

Links to working groups

University of South Bohemia, Faculty of Science:

Department of Botany

Functional Plant Ecology - Jan Lepš

Restoration Ecology - Karel Prach

Department of Zoology

Centre of Cognitive Ethology - Roman Fuch, Petr Veselý

Department of Biology of Ecosystems

Czech Academy of Science, Biology Centre in České Budějovice:

Institute of Entomology

Department of Ecology - Kateřina Sam

Laboratory of Multitrophic Interactions - Kateřina Sam
Laboratory of Evolutionary Ecology - Martin Volf
Laboratory of Tropical Ecology - Vojtěch Novotný
Laboratory of Experimental Ecology - Jan Hrček
Laboratory of Molecular Ecology and Phylogenetics - Pável Matos-Maraví
Laboratory of Integrative Ecology - Jan Klečka

Department of Biodiversity and Conservation Biology - Lukáš Čížek

Laboratory of Woodland Ecology - Lukáš Čížek
Laboratory of Aquatic Insect Ecology - David Boukal

Institute of Hydrobiology

Institute of Botany in Třeboň

Department of Functional Ecology - Jiří Doležal

Submit your thesis

The thesis is submitted to STAG about 1 month before the end of teaching period of your last semester. Please, check the exact date in the academic calendar in advance. Other requirements (format, mandatory sections...) are described in detail in Provision of the Dean. Your supervisor will advice you not only on the content but also the form of the thesis. You should also see several submitted theses to see examples of the form (freely available in STAG). Hardcopies are not required since 2021. Together with submission of your thesis (on-line in STAG), you are to visit the Department of Student Affairs to apply for the State Final Exam.

End of study

At least three days before the final state exam, you are to come to the Department of study Affairs to check your study results and close your study (make sure in advance that you have got all grades in STAG).

The study ends with state final exam, which has two parts. First, you are to defend your Master thesis at a committee of lecturers. Second, a similar committee of lecturers will examine you at an oral theoretical exam, which has three parts:

  • Fundamentals of Ecology
  • a field of student's choice: Plant Ecology, Animal Ecology or Ecological Statistics
  • Theoretical Background of the Master Thesis Topic and Methodology

The diploma (Master's degree certificate) is handed over the students at a graduation ceremony, which usually takes place about 1.5 months after the final state exam. In case you need to leave Czechia or apply for PhD earlier and/or do not want to take part in the ceremony, ask the Department of Student Affairs when you can pick it up.

Seminars
  • Ecology Seminar - Tuesday 16:20 in B2 - info at Department of Botany
  • Kokomo Seminar - Wednesday 12:00 in seminar room of the Entomology institute - ask Kateřina Sam (This email address is being protected from spambots. You need JavaScript enabled to view it.) to add you in the mailing list (may run online on zoom).
  • Zoology Seminar - Students - Wednesday 13:15 in B3; hosts - Wednesday 15:00 in B3; some students and most hosts present in English, info at Department of Zoology
  • Ecology Colloquia - obligatory course, not scheduled. You are to attend the previous seminars as well as present the plan of your thesis (in 2nd semester) and results of your thesis (in 4th semester).
Non-standard situations

The standard procedures were briefly mentioned above, but you may encounter exceptional situations. Please, always refer to the official documents of the Faculty and University or contact the Department of Student Affairs. Here is just a brief outline:

  • Enrolment: You are to enrol every semester in a standard date. If you missed enrolment, your study would be terminated. You can enrol later but you have to apply for it in time and justify it properly. You may also want to enrol earlier (e.g. in case a field trip overlaps with the standard date of enrolment).
  • Courses: You register for courses at enrolment, but you can make changes later. Changes done within three weeks of the study period are easy (simple email to the Department of Study Affairs). A properly justified application in STAG is required after the third week. You cannot unregister from block courses (e.g. field trips) after the course has finished.
  • Credits: You need to get min. 120 credits during your study, which implies you should aim at min. 30 credits per semester. However, the minimum number of credits per semester is 20, not to get expelled. You are allowed to have less only in case you have already more than 120 credits (typically last semesters of "longer study"), and in case of a special study plan (e.g. in case of serious health reason). Also, remember you must get min. 53 credits from the facultative-obligatory courses (type B).
  • Failed courses: If you fail a course, you do not get the credits. It has no other implications, if you still meet the minimum criteria on the credit gain by other courses, unless you fail an obligatory or facultative-obligatory course (i.e. type A or B) when enrolled for the second time.
  • Length of study: The study takes two years. Most students finish in time, but various life situations may lead to longer study.
    • study longer by <1 year: no application needed, no tuition is paid (just the usual 500 CZK/year fee for study in English). You simply do not register for the final state exam at the end of your second year and regularly enrol for the next semester (at least Master thesis XXX/880 for 0 credits as a placeholder). You keep the student status and you must follow usual study rules.
    • study longer by >1 year: similar to previous point, but you pay an additional tuition fee (approx. 25.000 CZK per semester)
    • suspended study: you can apply to suspend your study for up to two years. During this time, you lose the student status, i.e. you do not need to follow any study rules, as well as you have no advantage related to your residency in this country. After solving your life situation, you can continue in the study. You need to apply for suspension and termination of suspension, usually before start of semester.
  • Pregnancy/maternity: you can apply for a special study plan or you can suspend your study (in that case, your study can be suspended for longer than the usual 2-year limit).

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