Department of Biotechnology

Granting Departments:	Institute of Microbiology of the CAS, v.v.i. Department of Biotechnology
Study Programme/Specialization:	Biotechnology of Pharmaceuticals ( in English language )
Supervisor:	prof. Ing. Jan Masák, CSc.

Annotation

Actinomycetes, known for their production of bioactive metabolites such as antibiotics, anticancer agents, and immunosuppressants, were thought to be an exhausted resource due to the frequent rediscovery of known compounds. That this is not the case has been revealed through advanced sequencing techniques that have identified the potential of actinomycetes for new compounds at the genome level. The challenge is that many compound-producing biosynthetic pathways in actinomycetes are inactive under standard lab conditions. In this project, we will focus on our unique collection of actinomycetes from different parts of the world. Through genome sequencing of these strains, we have identified gene clusters encoding biosynthesis of metabolites with unusual structural motifs. Our goal is to employ modern methods to activate these pathways and characterize the produced compounds structurally and functionally. Optionally, we will focus on how the compounds are formed by studying key enzymes involved their biosynthesis. To accomplish this, we will employ a multidisciplinary approach that includes culturing bacteria, DNA editing, heterologous expression, bioinformatics, LC-MS with state-of-the-art instrumentation, and bioactivity testing against a panel of clinically relevant pathogens.

Institute of Microbiology of the CAS, v.v.i.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Microbiology ( in English language )
Supervisor:	RNDr. Jana Kamanová, Ph.D.

Annotation

The classical Bordetella species infect the respiratory tract of mammals. B. bronchiseptica induces chronic respiratory infections in various mammals, while the human-adapted species B. pertussis and B. parapertussis HU lead to an acute respiratory disease known as whooping cough or pertussis. These bacteria establish biofilms on both abiotic surfaces and within the respiratory tract, functioning as an immune evasion mechanism and a focal point for the development of novel antimicrobial agents. The objective of this PhD thesis is to unravel the signaling pathways underlying Bordetella colonization of respiratory epithelia and biofilm formation. The PhD candidate will employ an air-liquid interface model of human nasal epithelia and a microengineered biomimetic system, an organ-on-a-chip, combined with metabolomics, dual RNA-Seq and genetic engineering.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	doc. RNDr. Pavla Bojarová, Ph.D.

Annotation

The project for this dissertation focuses on developing a three-step enzymatic synthesis of bioactive chitooligomers (COS) useful in organic crop protection. Chitooligomers are ?-1-4-linked oligosaccharides composed of N-acetylglucosamine and glucosamine units whose biological activity depends mainly on their degree of polymerization (DP) and degree of acetylation (DA). COS are known for their ability to induce an immune response in plants and can thus be used as natural crop protection agents against microbial pests. The project will prepare mutant variants of a novel fungal chitinase with enhanced hydrolytic activity to increase the efficiency of chitin cleavage, by which COS fractions with lower DP will be prepared. In the next step, mutant variants of chitinases and ?-N-acetylhexosaminidases with transglycosidase activity suitable for preparing COS with degrees of polymerization of 5-10 on a preparative scale will be used. These chitooligomers will be partially deacetylated with novel chitin deacetylases, yielding COS fractions with different degrees of polymerization and acetylation that are not yet available. The biological activity of the prepared well-defined COS will be tested in collaboration with the Institute of Experimental Botany of the CAS.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	doc. RNDr. Pavla Bojarová, Ph.D.

Annotation

Galectins are animal lectins with affinity to beta-D-galactosides, which in vivo participate in, e.g., cancerogenesis, cardiopathologies, they are connected with the modulation of immune response and the course of allergic reaction. The concentration of extracellular galectins in vivo may be used as diagnostic markers in pathologies, such as colorectal carcinoma. A targeted inhibition of extracellular galectins is a prospective therapeutic approach to the treatment of pathologies associated with galectin overproduction. A range of recent structure-function studies is devoted to defining structural requirements for high-affinity and selective carbohydrate ligands of individual galectins. The avidity of specific carbohydrate inhibitors to selected galectins may also be increased by multivalent presentation. The aim of this work is to synthesize new carbohydrate ligands (glycomimetics) with a high afinity and possibly also selectivity for target galectins. Besides usually studied galectins Gal-1 and Gal-3, attention will be devoted to the group of tandem-repeat galectins (Gal-4, Gal-8, and Gal-9). The inhibitory and binding potential of these glycomimetics to galectins will be assayed by in vitro methods of ELISA and other biophysical methods. Structure-affinity relations will be discussed in relation to molecular modeling. Prepared ligands with a high affinity may be used in subsequent experiments with cell cultures, which are available at the supervisor workplace.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	doc. RNDr. Pavla Bojarová, Ph.D.

Annotation

Human milk oligosaccharides (HMOs) are the third most important component of breast milk after lactose and fat. HMOs pass through the digestive tract without major changes and are partially absorbed into the bloodstream through the intestinal wall. They serve as prebiotics for the gut microbiome of infants, which is important for allergy susceptibility. HMOs prevent adhesion of pathogens to the intestinal epithelium and directly regulate the immune system, e.g. by altering cytokine production. HMOs have been found to prevent or alleviate allergy symptoms. Bacterial cell factories have been used for the high-yield enzymatic synthesis of HMOs without the need for purification of recombinant enzymes. Genetically modified strains of Escherichia coli are suitable for the production of breast milk oligosaccharides. To date, applications have mostly been limited to a basic selection of HMOs, while a broader spectrum of these structures is not available. The subject of this thesis is the development of the synthesis of selected complex HMOs, in particular fucosylated and/or sialylated, on the E. coli platform. These compounds will be further tested in biological experiments concerning their effect on processes related to the initiation and development of allergies, such as passage through the intestinal membrane, expression of relevant biomarkers in epithelial cells, etc.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Microbiology ( in English language )
Supervisor:	Dr. Ing. RNDr. Petr Baldrian, Ph.D.

Annotation

Forest harvesting is economically important but due to the ecological importance of forests, it also represents a dramatic event in the ecosystem development. While clearcutting is a common practice in the temperate and boreal forests, variable retention harvesting is an alternative silvicultural practice in which some portion of the pre-harvest stand is retained after harvest. The broad objective is to maintain structural and functional elements from the pre-harvest condition to promote rapid recovery of biodiversity and ecological functions in the regenerating stands compared to clearcut stands. Harvesting of trees has profound effects on ecosystem processes that are associated with changes in the quality and decreases in the quantity of plant C inputs into the surrounding soil, as well as effects on soil nutrient availability and microclimatic conditions. Harvested stands also offer the opportunity to study the effect of reduced primary production on soil processes. Forest harvesting is known to have major effects on the main symbiotic fungi living on the roots of temperate trees, ectomycorrhizae, however, little is known about harvesting effects on symbiotic arbuscular mycorhizal fungi and bacteria. This project proposes to analyse the short-term effects of forest harvesting on the activity and composition of soil microbial communities in forests with dominant ectomycorrhizal and arbuscular mycorrhizal symbiosis and those with mixed ECM/AM. Changes in ecosystem properties and functioning, such as decomposition and N cycling will be linked to the community composition of soil microbes and their transcriptional activity. The project should give a view of the temporary changes of forest stand manipulations as well as answer the response of individual groups of microbes. This is important both for the consideration of future forest management strategies and the predictions of forest management effects on the C balance of forest soils.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	Mgr. Leoš Valášek, Ph.D.

Annotation

Imagine a gene is a sentence starting with a capital letter and ending with a period, and a genome as a book telling an entire story. In some protozoans, extra periods have infiltrated the sentences, replacing specific letters of arbitrary words (E and W). As a r.sult, readers are confus.d as to .here thes. sentences really .nd and th. story becom.s disjointed. In this issu. of Nature (https://www.nature.com/articles/s41586-022-05584-2), we describ. a molecular mechanism that thes. organisms must hav. developed to allo. the reader to navigat. the s.ntences as if there .ere no .xtra periods. Th. sentences are so specifically .ncrypted that read.rs of no other organisms but thos. very fe. can decipher the story in a prop.r .ay. The trick lies in the l.ngth of the tRNA molecul., and in the uniqu. modification of a prot.in that normally ensur.s dot recognition in c.lls - the precis. end of prot.in synthesis. By the intEraction of thesE tWo modified moleculEs, the ribosomE of this protozoan knoWs when to correctly terminatE, notWithstanding the many dots, and whEn to replace thE dots with the two original lettErs, which returns mEaning to the genetic information. LEt’s Explore hoW it is possible on thE molecular levEl and WhEther it could bE used for the benEfit of human hEalth! *This PhD thesis topic and the supervisor are subject to approval by the Faculty's Scientific Council.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	doc. RNDr. Pavla Bojarová, Ph.D.

Annotation

Chitin is the second most abundant polymer in nature. Partial deacetylation of chitin produces chitosan, a linear polymer composed mainly of glucosamine units (GlcN) and to a lesser extent of N-acetylglucosamine units (GlcNAc) linked ?(1?4) by glycosidic bonds. Chitosan is biocompatible and can therefore be advantageously used in a variety of biological and biomedical applications. For many biological applications, it is advantageous to work with shorter chains of chitosan, the so-called chitooligosaccharides (COS). COS have been intensively researched for decades in the fields of medicine, pharmaceuticals, textile industry, food industry and agriculture. Despite their tremendous potential use, poorly characterized heterogeneous mixtures are used in most studies due to the unavailability of well-defined COS. The thesis will focus on the preparation of authentic, pure and fully structurally characterized chitooligosaccharides and their analysis. Exoskeletons of crustaceans, insects (grasshoppers, bees, tarantulas) and fungi will be used as a source of chitin/chitosan. Subsequently, the defined COS chains will be used as carriers for multivalent presentation of bioactive carbohydrates, especially rutinose and galactosyl-carrying glycomimetics, for biological tests with lectins.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Biochemistry and Bioorganic Chemistry ( in English language )
Supervisor:	doc. Ing. Kateřina Valentová, Ph.D.

Annotation

Flavonoids, natural compounds found in various plants and foods, continue to attract great interest due to their known positive biological effects. However, these effects are compromised by their low bioavailability after oral administration. In the frame of this work new derivatives of flavonoids will be synthesized and the effect of various modifications on the bioavailability and biological activity of flavonoids will be evaluated. We will focus on the ability of the prepared derivatives to modulate drug resistance of bacteria, the chelatory activity and platelet aggregation inhibitory activity of flavonoids.

Granting Departments:	Department of Biochemistry and Microbiology Institute of Microbiology of the CAS, v.v.i.
Study Programme/Specialization:	Microbiology ( in English language )
Supervisor:	Dr. Ing. RNDr. Petr Baldrian, Ph.D.

Annotation

Peatlands of Northern Europe are an important source of greenhouse gases (GHG) with a strong influence on global climate - methane, nitrous oxide and carbon dioxide. One of the approaches to limit GHG production is the drainage of peatlands and their afforestation. Although this land use change can somehow reduce GHG production, it still partly continues to depend on the management of forests. The fluxes of GHG are, however, also regulated by other factors, such as the seasonal activity of vegetation and microorganisms. Since microorganisms are responsible for GHG production in the soils of forested peatlands, they represent the key to the understanding of GHG production rates and factors that affect them. In this work, we will use field experiments in southern Finland, where GHG production is monitored and where the analysis of microbiome composition and function at different depths of peat can be thus linked to the observed ecosystem-level gas fluxes. This project will offer a combination of fieldwork, labwork and analysis of bioinformatic data. When successful, the results of the thesis should help to indicate what management of peatland forests has the highest potential to mitigate GHG emissions and increase the storage of carbon in forest soils.