SumSci Summer Internships in laboratories of Faculty of Science

Přírodovědecká fakulta
jaro 2018
0/0/40. 20 kr. Doporučované ukončení: zk. Jiná možná ukončení: z.
Mgr. Iva Buriánková, Ph.D. (cvičící)
doc. RNDr. Vít Gloser, Ph.D. (cvičící)
doc. RNDr. Petr Kubíček, CSc. (cvičící)
Mgr. Michaela Kuchynka, Ph.D. (cvičící)
doc. Mgr. Jan Lochman, Ph.D. (cvičící)
prof. RNDr. Luděk Bláha, Ph.D.
Přírodovědecká fakulta
Kontaktní osoba: Mgr. Petr Bureš
Dodavatelské pracoviště: Přírodovědecká fakulta
Omezení zápisu do předmětu
Předmět je otevřen studentům libovolného oboru.
  • Mgr. Iva Buriánková, Ph.D. - Department of Experimental Biology
    Topic: Methanogen hunters wanted! Breathless microbes - how to study methanogenic Archaea
    Students: Evelyn Miranda Bastidas, Wai Kwan Cheng (Noel Cheng)

    Methanogens are microorganisms that produce methane as a metabolic by product in anoxic conditions. They uniquely belong to the domain of Archaea. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. Laboratory of anaerobic microorganism is focusing on fermentation process in biogas reactors, where methanogens play a key role in methan production. We offer the opportunity to try the methods of work with methanogens as cultivation and molecular methods especially (eg. fluorescent dyeing, FISH, PCR, DGGE etc., cloning) for students.

    1. Biogas plant - methanogenic Archaea composition and collaps?
    This project is focused at determining the potential change in the composition of the methanogenic community of the active biogas plant and the collapsed biogas plant.

    2. Diversity of methanogenic Archaea – where are they from?
    This project is aimed at determining the diversity of methanogens in environmental samples obtained from different types of environments as rivers and lakes.

    3. Methanogens on Antarctida?
    Analysis of Antarctic permafrost and searching for presence of methanogenic Archaea.

    doc. RNDr. Vít Gloser, Ph.D. - Department of Experimental Biology
    Topic: Early response of plants to drought: differences in dynamics among species
    Student: Daniel Hernandez Mota
    Drought is one of the most limiting factors of food production worldwide. Knowledge of processes behind plant response to decline of water availability and consequent regulation of plant water use is critically needed but still poor. Student will perform a cultivation experiment focused on relationships between water availability in soil and response of plants in selected traits. Response of 2-3 species with different water use strategies will be compared. Student will learn how to conduct and evaluate experiments with plants in regulated conditions. Work experience will also include use of instruments for monitoring of plant and soil water status, destructive sampling of plant material and simple chemical analyses. The results of project will serve for improvement of irrigation scheduling and also for identification of possible mechanism behind sensing of soil water availability by plants.

    Requirements: - basic knowledge of plant cultivation
    - basic knowledge of data handling (e.g. calculations in spreadsheet, creation of simple graphs)
    - some technical experience/skills may be advantage

    Mgr. Michaela Tvrdoňová - Department of Chemistry
    Topic: Imaging of elements in biological tissues
    Students: Aiya Yesbolatova, Jason Searl
    Laser ablation connected with inductively coupled plasma and mass spectrometry (LA-ICP-MS) offers the ability of imaging of elements in the different types of biological tissues with very good spatial resolution from units to hundreds µm. This method is used in biomedical research, such as study of elements distribution of various types cancer diseases. A wide range of applications also provides information about distribution of essential elements in organs (liver, kidneys). Aim of this study will be to determine the distribution of elements of interests in tumour tissues (e.g. prostatic tumour) and organ (kidney and liver) tissues. The participant will have the opportunity to learn and understand this analytical technique with very good spatial resolution and detection limit as well as sample preparation and data evaluation.

    Requirements: some experience work in chemical laboratory, interest in research work

    doc. Mgr. Jan Lochman, Ph.D. - Department of Biochemistry
    Topic: Characterization of regions needed for elicitins recognition by ELR protein (Molecular plant microbes interactions)
    Student: Hieu Pham
    Short Summary: The laboratory on molecular pathology at Department of Biochemistry of Faculty of Science, Masaryk university is offering one position for Student Fellowship to investigate fundamental molecular questions relevant to recognition of pathogens and activation of immune response in plants. Our group undertakes systemic approaches to defense reactions in plants, putting a strong emphasis on the role of beta-aminobutyric acid in the process of defense priming and on perception of elicitins secreted by oomycete genus Phytophthora causing devastating disease of tomato and potato. Project: Characterization of regions needed for elicitins recognition by ELR protein
    This project aims to characterize regions of ELR protein needed for interaction with elicitins represented by proteins infestin and cryptogein secreted by pathogenic oomycetes Phytophthora infestans and cryptogea, respectively. The projects will benefit from a substantial reservoir of unpublished data and vectors for transient gene expression in Nicotiana benthamiana plants mediated by Agrobacterium tumefaciens system. as well as a variety of novel reagents and access to cutting-edge technologies. Our group has established a number of well-defined genetic systems and disease models and we have access to leading core facilities for systems-level approaches (e.g. chemical biological drug screens, metabolomics, next-generation sequencing, proteomics). The students will acquire basic knowledge in the methods of transient expression of genes in plants (gateway cloning), immunoprecipitation of receptor complexes, western blot analysis or confocal microscopy for localization of fluorescently tagged proteins in plants.

    Desire skills and experiences:
    We are looking for highly motivated student from background in biochemistry and molecular biology who is enthusiastic to join our quest of addressing fundamental biological questions with relevance to global problems of plants diseases. You should be a student with a creative mind to think the unthinkable and a team player.
    Our Recent publications:
    Uhlíková H, Solanský M, Hrdinová V, Šedo O, Kašparovský T, Hejátko J, Lochman J. MAMP (microbe-associated molecular pattern)-induced changes in plasma membrane-associated proteins. J Plant Physiol. 2017 Mar; 210:51-57. doi: 10.1016/j.jplph.2016.12.005.
    Satková, P., Starý, T., Plešková, V., Zapletalová, M., Kašparovský, T., Činčalová-Kubienová, L., Luhová, L., Mieslerová, B., Mikulík, J., Lochman, J. and Petřivalský M. Diverse responses of wild and cultivated tomato to BABA, oligandrin and Oidium neolycopersici infection (2016) Annals of Botany, doi:10.1093/aob/mcw188
    Sandor, R., Der, C., Grosjean, K., Anca, I., Noirot, E., Leborgne-Castel, N., Lochman, J., Simon-Plas, F. and Gerbeau-Pissot, P. Plasma membrane order and fluidity are diversely triggered by elicitors of plant defence (2016) Journal of Experimental Botany, doi:10.1093/jxb/erw284
    Dadakova, K., Havelkova, M., Kurkova, B., Tlolkova, I., Kasparovsky, T., Zdrahal, Z., Lochman, J. Proteome and transcript analysis of Vitis vinifera cell cultures subjected to Botrytis cinerea infection (2015) Journal of Proteomics, 119, pp. 143-153

    doc. RNDr. Petr Kubíček, Ph.D. - Department of Geography
    Topic: Drone supported mapping
    Student: Julia Moore
    An unmanned Aerial Vehicle (UAV) system has the ability to quickly and inexpensively collect highly detailed data of smaller areas. UAV systems and laser scanners are currently used for mapping both natural and man-made phenomena. The main objective of the project is the use of remotely piloted aircraft systems for the acquisition of accurate spatial data to model landscape features, visualize them and employ in specific applications. The results will increase the competitiveness of a commercial partner and extend the portfolio of application services offered to the public administration (PLA - protected landscape area, microregions), the private sector, and the general public. Practical outputs will lead to the development of awareness of selected localities and the potential growth of tourism.
    We are looking for a strongly motivated person interested to learn the whole spatial data cycle starting from the field work planning, UAV data acquisition, processing, and presentation (visualization). Successful candidate will start with the planning and preparation of UAV flights, field work (acquisition of primary data), and data processing in special software, and he/she also will help with the final presentation of results including the discussion and comparison with other existing solutions (background research).

    - Background in GIS (ideally ArcGIS, other open source GIS is an advantage)
    - Basic knowledge of UAV data processing software (Agisoft, Meshlab, CloudCompare)
    - Enthusiastic approach and willingness to work in the field
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Předmět je dovoleno ukončit i mimo zkouškové období.
Předmět je vyučován jednorázově.
Poznámka k periodicitě výuky: 28.5. - 20. 7. 2018.
Výuka probíhá blokově.
Poznámka k četnosti výuky: 28.5. - 20. 7. 2018.
Předmět je zařazen také v obdobích jaro 2019.