Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution

Gene regulation is one important mechanism in producing observed phenotypes and heterogeneity. Consequently, the study of gene regulatory network (GRN) architecture, function and evolution now forms a major part of modern biology. However, it is impossible to experimentally observe the evolution of GRNs on the timescales on which living species evolve. In silico evolution provides an approach to studying the long-term evolution of GRNs, but many models have either considered network architecture from non-adaptive evolution, or evolution to non-biological objectives. Here, we address a number of important modelling and biological questions about the evolution of GRNs to the realistic goal of biomass production. Can different commonly used simulation paradigms, in particular deterministic and stochastic Boolean networks, with and without basal gene expression, be used to compare adaptive with non-adaptive evolution of GRNs? Are these paradigms together with this goal sufficient to generate a range of solutions? Will the interaction between a biological goal and evolutionary dynamics produce trade-offs between growth and mutational robustness? We show that stochastic basal gene expression forces shrinkage of genomes due to energetic constraints and is a prerequisite for some solutions. In systems that are able to evolve rates of basal expression, two optima, one with and one without basal expression, are observed. Simulation paradigms without basal expression generate bloated networks with non-functional elements. Further, a range of functional solutions was observed under identical conditions only in stochastic networks. Moreover, there are trade-offs between efficiency and yield, indicating an inherent intertwining of fitness and evolutionary dynamics

Optimization of cultivation of carotenogenic yeasts on mixed waste substrates

V rámci diplomové práce je řešena problematika kultivací vybraných druhů karotenogenních kvasinek na odpadních produktech potravinářského průmyslu za pomoci laboratorního bioreaktoru. Buňky karotenogenních kvasinek produkují v průběhu kultivace velmi hodnotné metabolity nacházející se převážně v lipidické části buněk. Konkrétně jde o karotenoidy, ergosterol, koenzym Q a mastné kyseliny. Práce je rozdělena na dvě hlavní části, teoretickou část, a praktickou část. V teoretické části jsou popsány jednotlivé druhy kvasinek, typy odpadních substrátů, zkoumané metabolity a metody jejich analýzy. V experimentální části je řešeno zpracování odpadních produktů potravinářského průmyslu, konkrétně živočišného tuku, syrovátky a kávové sedliny do podoby využitelných substrátů pro kultivaci kvasinek. Dále je řešena problematika kultivace se zaměřením na zisk sledovaných metabolitů a jejich analýza pomocí HPLC/PDA a GC/FID. Při práci byly využity kvasinkové rody Rhodotorula mucilaginosa (CCY 19-4-6), Rhodotorula kratochvilae (CCY 20-2-26), Rhodosporidium toruloides (CCY 062-002-001), Sporidiobolus pararoseus (CCY 19-9-6) a Cystofilobasidium macerans (CCY 10-1-2). Jako jeden z nejlepších kmenů byl vyhodnocen Sporidiobolus pararoseus (CCY 19-9-6), který dosahoval velmi vysokých produkcí karotenoidů, koenzymu Q a ergosterolu.The master thesis addresses the issue of cultivation of selected strains of carotenogenic yeasts on waste materials of the food industry using a laboratory bioreactor. Carotenogenic yeasts are able to produce highly valuable metabolites during cultivation, which are located predominantly in the lipid part of the cells. Particularly, they are carotenoids, ergosterol, coenzyme Q and fatty acids. The thesis is divided into two main parts, the theoretical part and the practical part. The theoretical part describes individual yeast strains, types of waste materials, produced metabolites and methods of their analysis. The experimental part deals with the processing of waste materials of the food industry, specifically animal fat, whey and spent coffee grounds into the form of substrates usable as nutrition sources for yeast cultivation. Furthermore, cultivations focused on the recovery of the monitored metabolites and their analysis by using HPLC/PDA and GC/FID assemblies were studied as well. The yeast strains Rhodotorula mucilaginosa (CCY 19-4-6), Rhodotorula kratochvilae (CCY 20-2-26), Rhodosporidium toruloides (CCY 062-002-001), Sporidiobolus pararoseus (CCY 19-9-6) a Cystofilobasidium macerans (CCY 10-1-2) were used in this work. As one of the best producing strains Sporidiobolus pararoseus (CCY 19-9-6) was found, which achieved very high productions of carotenoids, coenzyme Q and ergosterol.