Biofilmi

Opis predmeta

Sestava biofilmov (biološka, kemijska).
Struktura, dinamika in razvoj biofilmov.
Vpliv okoljskih dejavnikov na razvoj biofilmov.
Transport in medcelične komunikacije v biofilmih.
Koristni in škodljivi biofilmi ter njihova perzistentnost v agroživilstvu.
Mehanska, kemijska in fizikalna kontrola rasti v biofilmih.
Napredne tehnike za določanje sestave, strukture in dinamike biofilmov (npr. konfokalna laserska vrstična mikroskopija, optična pinceta, interfazna reologija, mikrofluidika).

Cilji in kompetence

Cilj predmeta je, da študent uporablja različne eksperimentalne pristope za gojenje in karakterizacijo rasti biofilmov. Uporablja različne mehanske in fizikalno-kemijske pristope za kontrolo rasti mikroorganizmov v biofilmih, spozna in razume vpliv biotskih/abiotskih dejavnikov okolja na razvoj biofilmov. Nauči se uporabe naprednih tehnik za določanje sestave, strukture in dinamike biofilmov.

Metode poučevanja in učenja

Študent v dogovoru z nosilcem in izvajalci določi raziskovalni projekt in opravi praktično delo v laboratoriju, ki je vezano na rast in karakterizacijo biofilmov. V okviru predmeta je možna uporaba raziskovalnih orodij, ki smo jih razvili v laboratorijih, za potrebe raziskovalnega dela doktorskega študenta. V seminarskem delu študent pripravi poročilo o svojem raziskovalnem projektu.

Predvideni študijski rezultati

Študent skozi individualno raziskovalno delo v laboratoriju spozna glavne biološke in kemijske komponente biofilmov. Razume njihovo strukturno in dinamično obnašanje. Razume dinamiko nastanka in propada biofilma. Pozna spremembe v celični fiziologiji, ki omogočajo nastanek biofilma. Razume transportne pojave v biofilmu, vpliv signaliziranja in pozna glavne tehnike za proučevanje biofilmov. Pozna škodljive in koristne vplive biofilmov ter načine za preprečitev oziroma uporabo biofilmov.

Reference nosilca

Prof. Dr. David Stopar

1. HORVAT, Maruša, PANNURI, Archana, ROMEO, Tony, DOGŠA, Iztok, STOPAR, David. Viscoelastic response of Escherichia coli biofilms to genetically altered expression of extracellular matrix components. Soft matter. 2019, vol. 15, str. 5042-5051, ilustr. ISSN 1744-683X. DOI: 10.1039/c9sm00297a. [COBISS.SI-ID 5060728]

2. BAŠ, Sara, KRAMER, Mateja, STOPAR, David. Biofilm surface density determines biocide effectiveness. Frontiers in microbiology. 2017, vol. 8, str. 1-9. ISSN 1664-302X. DOI: 10.3389/fmicb.2017.02443. [COBISS.SI-ID 1388638]

3. SRETENOVIĆ, Simon, STOJKOVIĆ, Biljana, DOGŠA, Iztok, KOSTANJŠEK, Rok, POBERAJ, Igor, STOPAR, David. An early mechanical coupling of planktonic bacteria in dilute suspensions. Nature communications. Aug. 2017, vol. 8, str. 1-10, ilustr. ISSN 2041-1723. https://www.nature.com/articles/s41467-017-00295-z, DOI: 10.1038/s41467-017-00295-z. [COBISS.SI-ID 33363673]

4. BENIGAR, Elizabeta, DOGŠA, Iztok, STOPAR, David, JAMNIK, Andrej, KRALJ CIGIĆ, Irena, TOMŠIČ, Matija. Structure and dynamics of a polysaccharide matrix : aqueous solutions of bacterial levan. Langmuir. 2014, vol. 30, issue 14, str. 4172-4182. ISSN 0743-7463. DOI: 10.1021/la500830j. [COBISS.SI-ID 4381304]

5. BENIGAR, Elizabeta, ZUPANČIČ-VALANT, Andreja, DOGŠA, Iztok, SRETENOVIĆ, Simon, STOPAR, David, JAMNIK, Andrej, TOMŠIČ, Matija. Structure and dynamics of a model polymer mixture mimicking a levan-based bacterial biofilm of Bacillus subtilis. Langmuir. 2016, vol. 32, iss. 32, str. 8182-8194, ilustr. ISSN 0743-7463. http://pubs.acs.org/doi/full/10.1021/acs.langmuir.6b02041, DOI: 10.1021/acs.langmuir.6b02041. [COBISS.SI-ID 1537177283]

6. LORENZETTI, Martina, DOGŠA, Iztok, STOŠICKI, Tjaša, STOPAR, David, KALIN, Mitjan, KOBE, Spomenka, NOVAK, Saša. The influence of surface modification on bacterial adhesion to titanium-based substrates. ACS applied materials & interfaces. [Print ed.]. 2015, vol. 7, str. 1644-1651, ilustr. ISSN 1944-8244. DOI: 10.1021/am507148n. [COBISS.SI-ID 4496504]

7. STOJKOVIĆ, Biljana, SRETENOVIĆ, Simon, DOGŠA, Iztok, POBERAJ, Igor, STOPAR, David. Viscoelastic properties of levan-DNA mixtures Important in microbial biofilm formation as determined by micro- and macrorheology. Biophysical journal. 2015, vol. 108, iss. 3, str. 758-765. ISSN 0006-3495. DOI: 10.1016/j.bpj.2014.10.072. [COBISS.SI-ID 4506744]

8. BORIĆ VEZJAK, Maja, DANEVČIČ, Tjaša, STOPAR, David. Viscosity dictates metabolic activity of Vibrio ruber. Frontiers in microbiology. July 2012, vol. 3, no. article 255, str. 1-12. ISSN 1664-302X. http://www.frontiersin.org/Microbial_Physiology_and_Metabolism/10.3389/fmicb.2012.00255/full, DOI: 10.3389/fmicb.2012.00255. [COBISS.SI-ID 4146552]

9. ŠARC, Andrej, KOSEL, Janez, STOPAR, David, ODER, Martina, DULAR, Matevž. Removal of bacteria Legionella pneumophila, Escherichia coli, and Bacillus subtilis by (super)cavitation. Ultrasonics Sonochemistry. Apr. 2018, vol. 42, str. 228-236, ilustr. ISSN 1350-4177. https://ac.els-cdn.com/S1350417717305072/1-s2.0-S1350417717305072-main.pdf?_tid=8731f192-db3f-11e7-96e6-00000aacb35d&acdnat=1512645336_7ae6f9b0762e2f47704d5873693ed3c0, DOI: 10.1016/j.ultsonch.2017.11.004. [COBISS.SI-ID 15787803]

10. SIMUNIČ, Urh, PIPP, Peter, DULAR, Matevž, STOPAR, David. The limitations of hydrodynamic removal of biofilms from the dead-ends in a model drinking water distribution system. Water research. [Print ed.]. 2020, vol. 178, str. 1-13, ilustr. ISSN 0043-1354. https://www.sciencedirect.com/science/article/pii/S0043135420303754?via%3Dihub, DOI: 10.1016/j.watres.2020.115838. [COBISS.SI-ID 12956163]

Prof. dr. Ines Mandić Mulec

XU, Zhihui, MANDIĆ-MULEC, Ines, ZHANG, Huihui, LIU, Yan, SUN, Xinli, FENG, Haichao, XUN, Weibing, ZHANG, Nan, SHEN, Qirong, ZHANG, Ruifu. Antibiotic bacillomycin D affects iron acquisition and biofilm formation in Bacillus velezensis through a Btr-mediated FeuABC-dependent pathway. Cell reports, ISSN 2211-1247, Oct. 2019, vol. 29, iss. 5, str. 1192-1202, e1-e5, ilustr., doi: 10.1016/j.celrep.2019.09.061. [COBISS.SI-ID 5118072]
ŠPACAPAN, Mihael, DANEVČIČ, Tjaša, MANDIĆ-MULEC, Ines. ComX-induced exoproteases degrade ComX in Bacillus subtilis PS-216. Frontiers in microbiology, ISSN 1664-302X, Feb. 2018, vol. 9, article 105, str. 1-11, ilustr., doi: 10.3389/fmicb.2018.00105. [COBISS.SI-ID 4876664]
GUBRY-RANGIN, Cecile, NOVOTNIK, Breda, MANDIĆ-MULEC, Ines, NICOL, Graeme, PROSSER, James Ivor. Temperature responses of soil ammonia-oxidising archaea depend on pH. Soil biology & biochemistry, ISSN 0038-0717. [Print ed.], 2017, vol. 106, str. 61-68, ilustr., doi: 10.1016/j.soilbio.2016.12.007. [COBISS.SI-ID 4743288]
DRAGOŠ, Anna, ŠTEFANIČ, Polonca, VATOVEC, Sabina, BEIGOT GLASER, Sara, RUPNIK, Maja, MANDIĆ-MULEC, Ines. Exploring ComQXPA quorum-sensing diversity and biocontrol potential of Bacillus spp. isolates from tomato rhizoplane. Microbial biotechnology, ISSN 1751-7915. [Online ed.], 2015, vol. 8, issue 3, str. 527-540, doi: 10.1111/1751-7915.12258. [COBISS.SI-ID 4494968]
AUSEC, Luka, ČRNIGOJ, Miha, ŠNAJDER, Marko, POKLAR ULRIH, Nataša, MANDIĆ-MULEC, Ines. Characterization of a novel high-pH tolerant laccase-like multicopper oxidase and its sequence diversity in Thioalkalivibrio sp. Applied microbiology and biotechnology, ISSN 0175-7598, 2015, vol. 99, str. 9987-9999, doi: 10.1007/s00253-015-6843-3. [COBISS.SI-ID 4548472]
DOGŠA, Iztok, DRAGOŠ, Anna, ŠTEFANIČ, Polonca, MANDIĆ-MULEC, Ines. Social interactions and biofilm formation in Bacillus subtilis. Food technology and biotechnology : journal of the Faculty of Food Technology and Biotechnology University of Zagreb, ISSN 1330-9862, 2014, vol. 52, no. 2, str. 149-157. [COBISS.SI-ID 4381816]

Temeljni viri in literatura

Microbial Biofilms, Second Edition; (ur.). Mahmoud Ghannoum, Matthew Parsek, Marvin Whiteley, Pranab K. Mukherjee, American Society for Microbiology, 2015
Hans-Curt Flemming, Jost Wingender, Ulrich Szewzyk, Peter Steinberg, Scott A. Rice & Staffan Kjelleberg, Nature Reviews Microbiology, 2016, 14, 563–575.
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