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Napsáno od Petr Capek dne . Zveřejněno v PRF.

Pokyny pro PhD studenty KBE

Katedra biologie ekosystémů

All pending graduate students (including those on interruption/parental leave, as their original rules may have been changed meanwhile), as well as their supervisors (including those external and potential) should be aware of all the milestones implying by the current Dean’s provision No. 62 (in Czech). Here is an overview of important milestones and duties of PhD students enrolled in both doctoral programmes, i.e. Ecosystem Biology or Hydrobiology.

  1. “No later than two months after the commencement of study, the student is obliged to submit, via the Department of Student Affairs, a proposed ‘Doctoral Study Plan’ to the specialist board of the doctoral study programme …” – We strongly recommend being faster, in particular during winter semesters, when the approval process used to be delayed due to the Christmas season.
  2. “No later than in the second semester of study, enroll for the subject ‘Literature review’ (KBE/806) … it is recommended to submit the review at least one month before the end of the second semester…” (see also Requirements of "Literature review") – However, we strongly recommend being faster, otherwise you risk a penalty, i.e. reduced stipend since your second year (i.e. from the 13th month until its approval).
  3. “Submit an annual report on the progress … every year by 31 October” – completely and carefully filled!
  4. Be aware of all your duties, such as conference presentations (KBE/907), study stays abroad (FBI/801–803), annual presentations at doctoral conference/seminar (KBE/805), teaching activities, etc.
  5. To receive an assessment in STAG from:
    • KBE/907 (the presentation at an international conference in foreign language) – student has to send a confirmation of his presentation (i.e. a scan from the conference abstract book) to the chair of the specialist board (Jana Jersáková or Jaroslav Vrba) of either doctoral study programme.
    • KBE/800 (Doctor´s Thesis, Practical Part) – the student’s supervisor has to send a confirmative e-mail to either chair of the specialist board of either doctoral study programme or to the secretary of our department (Jana Vrbová) with his/her approval to grant a student with the assessment.
  6. Fulfil most of prerequisites, such as elective courses, English exams (OJZ/940, OJZ/950) followed by state exam (FBI/D1), timely within four years = until the end of your regular study.
  7. Provide proper author’s affiliation (FSc USB) of yourself on all publications intended for your dissertation thesis – otherwise the papers cannot be included into your thesis!
  8. Do not intentionally postpone submitting your dissertation thesis beyond the standard period of study because of writing excessive manuscripts (e.g. for supervisor’s projects). We prefer and strongly encourage all students to finalize his/her dissertation thesis within the standard period, providing he/she can fulfil minimal requirements: i.e. “three publications or papers of which the student is (co)author … a part must have been accepted for publication in a journal attaining in the previous five years an impact factor of at least 0.5 … main author of at least one of the published papers (or papers accepted for publication)…”. If you are in shortage of published or accepted papers, consult the chair of the specialist board.
  9. Last but not least, one should consider the regular deadlines for new PhD applications, consult the Department of Student Affairs for completeness, and follow the instructions of admission proceedings of our department!

Číst dál …Pokyny pro PhD studenty KBE

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Napsáno od Jiří Cehák dne . Zveřejněno v PRF.

D84 - upravující podmínky vedení kvalifikačních prací

Opatření děkana č. D 84
upravující podmínky vedení kvalifikačních prací

ze dne 4. prosince 2017
ve znění ze dne 17. ledna 2022

Článek 1. Vedení kvalifikačních prací

  1. Vedoucím bakalářské a magisterské (diplomové) práce může být osoba s vědeckou hodností Ph.D., CSc., nebo vyšší, případně odborník z praxe s dokončeným magisterským nebo inženýrským vzděláním a pěti lety praxe v oboru.
  2. Kvalifikační práci podle bodu 1 může vést i student v doktorském programu s podmínkou, že současně s vedoucím práce bude ustanoven supervizor, který splňuje kvalifikační předpoklady uvedené v předchozím odstavci. Supervizor poskytuje metodickou podporu vedoucímu práce i bakalantovi či diplomantovi.   
  3. Vedoucí bakalářských a diplomových prací schvaluje a případné supervizory ustanovuje vedoucí katedry. Ustanovení supervizora musí být výslovně uvedeno v zadávacím protokolu kvalifikační práce.
  4. Témata bakalářských a diplomových prací schvaluje vedoucí katedry a garant programu studia.
  5. Vedoucím disertační práce může být profesor, docent, doktor věd nebo jiný významný odborník navržený oborovou radou po schválení děkanem fakulty. Pokud navržený školitel nebyl habilitován nebo nemá titul doktor věd, musí jeho zařazení mezi školitele schválit vědecká rada fakulty. Požadavky na jeho odbornou kvalitu jsou obdobné jako fakultní požadavky na uchazeče o habilitaci. Pokud byl navrhovaný vedoucí již schválen vědeckou radou pro školení doktorandů v jiném programu, schvaluje jeho zařazení mezi školitele daného programu děkan na základě písemného návrhu předsedy oborové rady (garanta programu). Školitele na návrh oborové rady jmenuje děkan. Témata disertačních prací schvaluje oborová rada vedená garantem programu. Pravidla pro disertační práce jsou stanovena Opatřením děkana č. D 62.
  6. Pokud vedoucí práce není zaměstnancem PřF JU, přebírá částečně povinnosti školitele (zejména úkony administrativní povahy) fakultní garant.
  7. Jeden student doktorského studia může vést nejvýše tři kvalifikační práce podle bodu 1.
  8. Jeden akademický pracovník PřF JU může být vedoucím maximálně osmi kvalifikačních prací (v součtu všech diplomových a disertačních). Výjimku z tohoto pravidla může v odůvodněném případě povolit děkan fakulty. Počet vedených bakalářských prací není omezen.

Článek 2. Závěrečná ustanovení

  1. Znění tohoto opatření platné od 4. 12. 2017 se zrušuje.
  2. Toto aktualizované znění nabývá účinnosti dnem vydání.

prof. Ing. Hana Šantrůčková, CSc.
děkanka Přírodovědecké fakulty JU
PRF_cz

PDF ke stažení zde

Číst dál …D84 - upravující podmínky vedení kvalifikačních prací

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Napsáno od František Vácha dne . Zveřejněno v PRF.

Laboratoř spektroskopie jednotlivých molekul

Right now we are looking for motivated students of all levels (Bc, Mgr, PhD)!

Contact information

Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.

Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.Tato e-mailová adresa je chráněna před spamboty. Pro její zobrazení musíte mít povolen Javascript.

Address:
Building C (room 01037) 
Faculty of Science
University of South Bohemia in České Budějovice
Branišovská 1760
370 05 České Budějovice

Phone: 00420387776237
GPS: 48.9772847N, 14.4451364E

Research Interests

Allosteric communication in membrane protein complexes linked to conformational transitions on multiple timescales

- Development of novel mechanistic models of molecular machines behind protein translocation

Motivation:

Allosterically modulated molecular machines mediate many of the key processes in all forms of life. The Sec translocon, a membrane bound protein complex, is the principal route for the efficient transport of heterogeneous polypeptides across or into lipid bilayers. The bacterial translocon consists of two main parts, a cytosolic ATPase SecA and membrane channel SecYEG. Based on our group’s recent findings we propose that the Sec translocon is a novel type of stochastically coupled hybrid molecular machine, where the processive SecA steers the energy landscape of a stochastic SecYEG channel allosterically dependent on nucleotide state. We present a number of research projects to map the full allosteric network regulating different stages of protein translocation in the Sec complex using a combination of mutagenesis, single-molecule and in silico methods.
 

Publications:

• Allen, W. J., et al (2016) Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation, Elife. 5.
• Fessl, T., et al (2018) Dynamic action of the Sec machinery during initiation, protein translocation and termination, Elife. 7.
• Corey, R. A., et al (2019) ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery, Elife. 8. 
• Fessl, T., et al (2020) Dynamics of Membrane Proteins Monitored by Single-Molecule Fluorescence Across Multiple Timescales, Methods in Molecular Biology

 

Studies of G protein signaling at the single molecule level
- Getting insights into non-canonical G protein signaling and development of signaling activity sensors  

Motivation:

The G protein signaling cascade is a major pathway responsible for cellular communication with the external environment. It is present in all eukaryotes from yeast to humans. G proteins transduce signals from a variety of chemical and physical stimuli including hormones, odorants, neurotransmitters, and light. Up to 50% of all modern prescription drugs target this signaling cascade. However, many aspects of G protein signaling remain unclear. Our goal is to gain insights into non-conventional properties of G protein signaling in mammalian and fungal cells. Particularly, we are interested in precoupling between G proteins and G protein-coupled receptors (GPCRs), dimerization and heteromerization of GPCSs, and development of signaling activity sensors (1-5). In our research we use advanced imaging techniques, including single-molecule imaging, combined with molecular biology, cell biology methods and advanced data processing. We strive to utilize cutting-edge techniques and multidisciplinary approaches to do excellent science.

  

Figure 1.  Outstanding questions in G protein signaling research

  

Figure 2. A snapshot of real time dual channel single-molecule imaging of interactions between G proteins and G protein-coupled receptors in a live cell

  

Publications:

  1. A. Bondar, J. Lazar, Optical sensors of heterotrimeric G protein signaling. FEBS J 288, 2570-2584 (2021).
  2. A. Bondar, O. Rybakova, J. Melcr, J. Dohnalek, P. Khoroshyy, O. Tichacek, S. Timr, P. Miclea, A. Sakhi, V. Markova, J. Lazar  Quantitative Linear Dichroism Imaging of Molecular Processes in Living Cells Made Simple by Open Software Tools Communications Biology 4, 189 (2021).
  3. A. Bondar, W. Jang, E. Sviridova, N. A. Lambert, Components of the Gs signaling cascade exhibit distinct changes in mobility and membrane domain localization upon beta2-adrenergic receptor activation. Traffic 21, 324-332 (2020).
  4. A. Bondar, J. Lazar, The G protein Gi1 exhibits basal coupling but not preassembly with G protein-coupled receptors. J Biol Chem 292, 9690-9698 (2017).
  5. A. Bondar, J. Lazar, Dissociated GalphaGTP and Gbetagamma protein subunits are the major activated form of heterotrimeric Gi/o proteins. J Biol Chem 289, 1271-1281 (2014).
  
   
   
   

Lab Members

  
Researchers:
Tomáš Fessl, Ph.D.
Dr Łukasz Bujak
Radek Litvín, Ph.D.
Prof. František Vácha, Ph.D.

Students:
Eva Sýkorová
Jiří Štangl
Jakub Strejc		  
 

Číst dál …Laboratoř spektroskopie jednotlivých molekul

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Napsáno od František Vácha dne . Zveřejněno v PRF.

Laboratoř aplikované biochemie

Back to Dept. of Chemistry

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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