Učni načrt predmeta

Predmet:
Tehnologije za imobilizacijo in enkapsulacijo celic
Course:
Cell Entrapment and Encapsulation Technologies
Študijski program in stopnja /
Study programme and level		 Študijska smer /
Study field		 Letnik /
Academic year		 Semester /
Semester
Ekotehnologije, 3. stopnja / 1 1
Ecotechnologies, 3rd cycle / 1 1
Vrsta predmeta / Course type
Izbirni / Elective
Univerzitetna koda predmeta / University course code:
EKO3-918
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
15 15 105 5

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:
izr. prof. dr. Aleš Lapanje
Sodelavci / Lecturers:
doc. dr. Tomaž Rijavec
Jeziki / Languages:
Predavanja / Lectures:
slovenščina, angleščina / Slovenian, English
Vaje / Tutorial:
slovenščina, angleščina / Slovenian, English
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Zaključen študij druge stopnje ustrezne (naravoslovne ali tehniške) smeri ali zaključen študij drugih smeri z dokazanim poznavanjem osnov področja predmeta (pisna dokazila, pogovor).

Completed second level studies in natural sciences or engineering or completed second level studies in other fields with proven knowledge of fundamentals in the field of this course (certificates, interview).

Vsebina:
Content (Syllabus outline):

Osnove:
- Opredelitev konceptov enkapsulacije, ujetja in imobilizacije celic,
- Analiza delovanja posamezne celice v primerjavi s populacijo celic,
- Opredelitev mehanskih in fizičnih ovir, ki motijo metabolizem enkapsuliranih celic
- Ekološka interferenca enkapsuliranih celic z naravnimi združbami
- Najsodobnejši material za mikrobno enkapsulacijo ali imobilizacijo

Inženiring/Bioinženiring:
- Strategije enkapsulacije celic, encimov in celičnih komponent
- Elektropredenje, kapljična enkapsulacija
- Glavne strategije za imobilizacijo celic
- Uporaba mikrofluidike pri imobilizaciji in enkapsulaciji
- Nosilci različnih izvorov
- Metode impregnacije nosilca
- Gradnja slojevitih in agregiranih struktur večceličnih nosilcev in umetnih biofilmov
- Strategija enkapsulacije kot pristop izolacije mikrobov

Fiziologija imobiliziranih celic:
- Specifični ukrepi pri uporabi omik v imobiliziranih celicah
- Prostorska analiza z uporabo korelativnih mikroskopskih pristopov
- Meritve na osnovi mikroelektrod

Aplikacije:
- Bioremedijacija različnih medijev, predvsem okoljskih voda, pitne vode in
prsti
- Uporaba v medicini za izdelavo probiotikov in zdravljenje raka
- Uporaba pri predelavi hrane
- Biotehnološke aplikacije
- Protibiokorozivni pristopi
- Pristopi za “upscaling”

Basics:
- Defining the concepts of encapsulation, entrapment and immobilisation,
- Single cell analysis versus population analysis,
- Defining mechanical and physical barriers interfering with the metabolism of encapsulated cells
- Ecological interference of encapsulated cells with natural communities
- State-of-the-art on used material for microbial encapsulation or immobilisation

Engineering/Bioenginering:
- Cell, enzymes and cell components encapsulation strategies
- Electrospinning, droplet encapsulation
- Principal strategies for immobilisation of cells
- Use of microfluidics in immobilisation and encapsulation
- Carriers from different origins
- Carrier impregnation methods
- Construction of layered and aggregated structures of multicellular carriers and artificial biofilms
- Encapsulation strategy as a microbial isolation approach

Physiology of immobilised cells:
- Specific measures in using omics in immobilised cells
- Spatial analysis using correlative microscopy approaches
- Microelectrode based measurements

Applications:
- Bioremediation of different media, mainly environmental waters, drinking
water, soil, etc.
- Use in medicine for probiotic and anticancer therapy
- Use in food processing
- Biotechnological applications
- Anti-biocorrosive approaches
- Plant and agricultural use
- Upscaling approaches

Temeljna literatura in viri / Readings:

Knjiga / Book:
- V. Nedovic, R. Willaert, Application of cell immobilization biotechnology, Springer, 2006
- Mehrotra, T., Dev, S., Banerjee, A., Chatterjee, A., Singh, R. and Aggarwal, S., 2021. Use of immobilized bacteria for environmental bioremediation: A review. Journal of Environmental Chemical Engineering, 9(5), p.105920.
- Manojlović, V., Nedović, V.A., Kailasapathy, K. and Zuidam, N.J., 2010. Encapsulation of probiotics for use in food products. Encapsulation technologies for active food ingredients and food processing, pp.269-302.
- Vemmer, M. and Patel, A.V., 2013. Review of encapsulation methods suitable for microbial biological control agents. Biological control, 67(3), pp.380-389.
- Rybkin, I., Pinyaev, S., Sindeeva, O., German, S., Koblar, M., Pyataev, N., Čeh, M., Gorin, D., Sukhorukov, G. and Lapanje, A., 2022. Modification of bacterial cells for in vivo remotely guided systems. Frontiers in Bioengineering and Biotechnology, 10.
- van Tatenhove-Pel, R.J., Rijavec, T., Lapanje, A., van Swam, I., Zwering, E., Hernandez-Valdes, J.A., Kuipers, O.P., Picioreanu, C., Teusink, B. and Bachmann, H., 2021.
Microbial competition reduces metabolic interaction distances to the low μm-range. The ISME journal, 15(3), pp.688-701.
- Grilc, N.K., Zidar, A., Kocbek, P., Rijavec, T., Colja, T., Lapanje, A., Jeras, M., Gobec, M., Mlinarič-Raščan, I., Gašperlin, M. and Kristl, J., 2023. Nanofibers with genotyped Bacillus strains exhibiting antibacterial and immunomodulatory activity. Journal of Controlled Release, 355, pp.371-384.

Revije / Periodicals:
- Nature Biotechnology
- Frontiers in Bioengineering and Biotechnology
- Biomacromolecules
- Environmental science and technology
- Journal of Controlled Release

Pregledni članki, izbor v tekočem letu/Review articles, yearly selection.

Cilji in kompetence:
Objectives and competences:

Učence seznaniti z osnovami:
- metode za ujetje in enkapsulacijo
- principi celične enkapsulacije
- pristopi določanja nadgradnje postopkov enkapsulacije
- vrste nosilnega materiala

Za seznanitev študentov z naprednimi metodami:
- uporaba imobilizacijskih tehnik v raziskavah
- oblikovanje mikrofluidnih pristopov za agregacijo in enkapsulacijo
- specifične metode združevanja celic
- modeliranje in napovedovanje rezultatov združevanja
- preučevanje medcelične interakcije z imobilizacijo
- koloidne in mikroskopske tehnike za raziskovanje fiziologije ujetih celic
- uporabe različnih pristope za “upscaling”

Kompetence:
- vzpostavitev pristopov za imobilizacijo mikrobnih celic
- uporaba mikrofluidnih pristopov za imobilizacijo celic
- nastavitev operaterskih aplikacij v industriji in okoljskih tehnologijah
- prostorsko in tokovno modeliranje
- tvorjenje umetnih biofilmov
- analitika agregiranih in enkapsuliranih celic

To introduce students to the basics of:
- methods for entrapment and encapsulation
- principles of encapsulation of cells
- approaches of setting the upscaling of encapsulation procedures
- carrier material types

To introduce students to the advanced methods:
- use of immobilisation techniques in research
- designing microfluidic approaches for aggregation and encapsulation
- specific aggregation methods
- modelling and prediction of aggregation outcomes
- studying cell-cell interaction through immobilisation
- colloid and microscopy techniques for interrogating physiology of entrapped cells
- use upscaling approaches

Competencies:
- setting up approaches for immobilisation of microbial cells
- use microfluidic approaches for immobilisation of cells
- setting carrier based applications in industry and environmental technologies
- spatial and flux modelling
- forming artificial biofilms
- analytics of aggregated and encapsulated cells

Predvideni študijski rezultati:
Intendeded learning outcomes:

Študent bo z uspešno zaključenim predmetom pridobil osnovno znanje na naslednjih področjih:
- znanje za izboljšanje izkoristkov v bioprocesnih tehnologijah
- znanje za uporabo celičnih nosilcev v razvoju biotehnoloških procesov
- znanje na postavitev strategij za izvedbo bioremediacije
- znanje za pripravo formulacij za medicinsko uporabo mikrobov (npr. probiotikov)
- vključevanje teh znanj pri reševanju problemov v sklopu disertacije

The student with the successful completion of the course will acquire basic knowledge in the following areas:
- knowledge on different immobilisation strategies and techniques
- knowledge on use of cell carriers in biotechnology processing
- knowledge on setting bioremediation strategies
- knowledge on preparation of formulations for medical use of microbes (e.g. probiotic)
- integration of these skills in problem solving in the context of the dissertation.

Metode poučevanja in učenja:
Learning and teaching methods:

Interaktivno delo s študenti, vezano na njihovo raziskovalno temo.
Webinarji in spletna predavanja v živo vabljenih strokovnjakov s področja omike, mikroskopskih tehnik, bioremediacije, obarjanja kovin in nanodelcev na bio osnovi, patentiranja.
Okrogle mize in diskusijske skupine o reševanju realnih problemov, ki so povezani z raziskovalnim delom študenta.

Interactive work with students related to their research project.
Webinars and web based live lectures of invited experts in omics, microscopy techniques, bioremediation, bio based metal and nanoparticle precipitation, patenting.
Round tables and discussion groups on solving real problems that are related to the research work of the student.

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Seminarska naloga
60 %
Seminar
Ustni izpit
40 %
Oral examination
Reference nosilca / Lecturer's references:
1. RYBKIN, Iaroslav, PINYAEV, Sergey, SINDEEVA, Olga, GERMAN, Sergey, KOBLAR, Maja, PYATAEV, Nikolay, ČEH, Miran, GORIN, Dmitry A., SUKHORUKOV, Gleb B., LAPANJE, Aleš. Modification of bacterial cells for in vivo remotely guided systems. Frontiers in bioengineering and biotechnology. 2023, vol. 10, [article no.] 1070851, str. 1-11, ilustr. ISSN 2296-4185. DOI: 10.3389/fbioe.2022.1070851. [COBISS.SI-ID 139783939]
2. GRILC, Katarina Nina, ZIDAR, Anže, KOCBEK, Petra, RIJAVEC, Tomaž, COLJA, Teja, LAPANJE, Aleš, JERAS, Matjaž, GOBEC, Martina, MLINARIČ-RAŠČAN, Irena, GAŠPERLIN, Mirjana, KRISTL, Julijana, ZUPANČIČ, Špela. Nanofibers with genotyped Bacillus strains exhibiting antibacterial and immunomodulatory activity. Journal of controlled release. [Print ed.]. 2023, vol. 355, str. 371-384, ilustr. ISSN 0168-3659. https://www.sciencedirect.com/science/article/pii/S0168365923000913?via%3Di hub, DOI: 10.1016/j.jconrel.2023.01.082. [COBISS.SI-ID 141431811]
3. DEEV, D., RYBKIN, Iaroslav, RIJAVEC, Tomaž, LAPANJE, Aleš. When beneficial biofilms on materials is needed : electrostatic attachment of living bacterial cells induces biofilm formation. Frontiers in materials. 2021, vol. 8, 1-624631-14-624631, ilustr. ISSN 2296-8016. DOI: 10.3389/fmats.2021.624631. [COBISS.SI-ID 61416963]
4. VERDEL, Nada, RIJAVEC, Tomaž, RYBKIN, Iaroslav, ERZIN, Anja, VELIŠČEK, Žiga, PINTAR, Albin, LAPANJE, Aleš. Isolation, identification, and selection of bacteria with proof-of-concept for bioaugmentation of whitewater from wood-free paper mills. Frontiers in microbiology. Oct. 2021, vol. 12, [article no.] 758702, str. 1-15, ilustr. ISSN 1664-302X. https://www.frontiersin.org/articles/10.3389/fmicb.2021.758702/full, DOI: 10.3389/fmicb.2021.758702. [COBISS.SI-ID 80125955]
5. TATENHOVE-PEL, Rinke van, RIJAVEC, Tomaž, LAPANJE, Aleš, SWAM, Iris van, ZWERING, E., HERNANDEZ-VALDEZ, J. A., KUIPERS, Oscar P., PICIOREANU, Christian, TEUSINK, Bas, BACHMANN, Herwig. Microbial competition reduces metabolic interaction distances to the low [gamma]m-range. The ISME journal. 2020, 21 str. ISSN 1751-7362. DOI: 10.1038/s41396-020-00806-9. [COBISS.SI-ID 39267075]