B) Coloid biology, biopolimers

1. Biological succession of electrostatically attached cells

In the laboratory, we have developed methods that allow the formation of biofilms on the surface of different composition. Because bacteria divide and grow, however, the physical and biological properties of such artificial biofilms change over time. In doing so, we want to find out how this changes during biological succession from the transition from artificially imposed biofilm to natural one. For these purposes, the student will master the procedures of using QCM by dissipation, fluorescence microscopic techniques and molecular biological methods.

Mentor: dr. Aleš Lapanje (ales.lapanje@ijs.si)

2. Interaction of artificial biofilms with natural microbiota

Using the methods of molecular biology and microbiology, the student will determine the interaction between the artificially attached bacteria with the processes of attachment of natural communities as well as succession of the biofilms. Student will measure structure and activities of attached natural microbial communities, changes in the species composition and production of substances. The data obtained will subsequently be used to gain knowledge about the processes that affect the metabolism of mercury methylators bacteria, present in the environment.

Mentor: dr. Aleš Lapanje (ales.lapanje@ijs.si)

3. Gene expression of lignin degrading bacterial enzymes under different culture growth conditions

Lignin is an abundant biopolymer found in plants and in important waste product of paper industry. Chemical processes of lignin removal from plant biomass produce black liquor, that imposes an important environmental and economic issue. Fortunately, bacteria were found to successfully degrade lignin by producing lignin degrading enzymes. Production of lignin degrading enzymes is very much dependent on environmental factors, such as substrate (i.e. lignin) availability, concentrations of carbon and nitrogen, presence of lignin degrading products and even enzyme cofactors – copper ions Cu²⁺. All these can act as inducers of gene expression and trigger transcription, which ultimately leads to production of enzymes by the cell. To achieve lignin degradation, optimal enzyme production is needed and since it is very much dependant on the factors listed above, research needs to be conducted to better understand enzyme expression processes. Methods used would include mRNA extraction from bacteria growing under different environmental conditions in order to evaluate all the possible factors impacting enzyme production.

Mentor: dr. Aleš Lapanje (ales.lapanje@ijs.si)

4. Inheritance or Bet Hedging in bacterial resistance against positively charged polyelectrolytes

The surface of bacterial cells can be artificially modified by encapsulating cells into polyelectrolyte capsules to control essential cellular characteristics such as surface charge, surface composition, growth and etc. However, interaction of bacterial cell surface and positively charged polyelectrolytes remain toxic. Here it is needed to investigate how bacterial cells sustain encapsulation into polymers or they can transfer this property to next generations to became resistant.

Mentor: dr. Aleš Lapanje (ales.lapanje@ijs.si)

5. Preparation of multispecies aggregates for building specific metabolic pathways

Artificial assembling made by adding one cell to another can significantly improve organization of bacterial community for establishing new diverse metabolic pathways with controlled properties of further development. The research work is proposed to be in the direction of preparation such aggregates, methods for their construction and scale up to gain high amount of such biocatalytic units.

Mentor: dr. Aleš Lapanje (ales.lapanje@ijs.si)