SubjectsSubjects(version: 901)
Course, academic year 2022/2023
Advances in molecular genetics of bacteria - MB140P45
Title: Pokroky v molekulární genetice bakterií
Czech title: Pokroky v molekulární genetice bakterií
Guaranteed by: Department of Genetics and Microbiology (31-140)
Faculty: Faculty of Science
Actual: from 2022
Semester: winter
E-Credits: 3
Examination process: winter s.:written
Hours per week, examination: winter s.:2/0 Ex [hours/week]
Capacity: unlimited
Min. number of students: 5
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Level: specialized
Explanation: kód přednášky v MS Teams je: 7qojk62
Additional information:
Note: enabled for web enrollment
Guarantor: RNDr. Irena Lichá, CSc.
Teacher(s): RNDr. Jan Bobek, Ph.D.
RNDr. Pavel Branny, CSc.
RNDr. Linda Doubravová, Ph.D.
RNDr. Irena Lichá, CSc.
RNDr. Jaroslav Nunvář, Ph.D.
Ing. Miroslav Pátek, CSc.
Mgr. Kateřina Petříčková, Ph.D.
RNDr. Branislav Večerek, Ph.D.
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: RNDr. Irena Lichá, CSc. (27.10.2019)
The lecture series “Advances in Molecular Genetics of Bacteria” aims to acquaint students in Phd studies but also advanced master students with new trends in research related to molecular biology and genetics of bacteria. Individual lectures are divided into thematic areas: evolution, regulation of gene expression, adaptation to stress, cell division and differentiation of cell populations. The lectures will be mainly led by external experts who specialize in the field. Topics can be modified according to students' interest and developments in the field.
Literature -
Last update: RNDr. Irena Lichá, CSc. (27.10.2019)

Original scientific articles related to individual topics that will be provided to students if they are not freely available.

Requirements to the exam -
Last update: RNDr. Irena Lichá, CSc. (08.08.2019)

Students will be evaluated on the basis of a written test. It consists of 10 questions covering the topics of the lectures. The time for elaboration is 60 min. Students can achieve a maximum of 50 points, with the achievement of at least 20 points is a prerequisite for passing the exam with a good assessment.

Syllabus -
Last update: RNDr. Irena Lichá, CSc. (27.10.2019)

Evolution of bacterial genomes - current view of old phenomena (RNDr. Jaroslav Nunvář, Phd, Faculty of Science, Charles University,).

• general properties of the bacterial genome (GC skew, coding density)
• Genomic adaptation (reductive evolution of symbionts and pathogens) and its mechanisms
• pangenomas, core genomes and their importance

From Genome to Bioactive Substances - Research on new antibiotics. (RNDr. Kateřina Petříčková, Phd., First Faculty of Medicine)

• history of research on antibiotics and biologically active substances
• sources of biologically active substances
• methodical procedures:
“-Omic” techniques - metagenomics, genomics, transcriptomics, proteomics, metabolomics
• single-cell fermentation
• genome-mining
• co-cultivation

Regulation of gene expression at transcriptional level, regulatory networks (Ing. Miroslav Pátek, CSc., MBU)

Latest methods of global analysis of bacterial RNoma (RNA-seq, DE RNA-seq, differential RNA-seq, GRIL-seq, RIL-seq, GRAD-seq, dual RNA-seq). (RNDr. Branislav Vecerek, Phd, MBU). 

 • The aim of the lecture is to acquaint students with the possibilities of gene expression analysis, which were brought by the latest applications of the RNA-seq method. 

 • We will mainly focus on dRNA methods (global determination of transcriptional origins and promoters), DE-RNA-seq (global comparison of gene expression), GRIL-seq / RIL-seq (global identification of sRNA-regulated target mRNAs) and other apps.

Regulation of gene expression at the level of antisense RNA (RNDr. Jan Bobek, Phd, First Faculty of Medicine)

• Basic categorization of bacterial asRNA.
• Regulatory role or manifestation of ubiquitous transcription?
• Specific mechanisms of asRNA: common degradation or stabilization of duplexes of asRNA-mRNA, termination of transcription, inhibition of translation and processing of transcripts.
• The importance of asRNA in genome flexibility and evolution.

Regulation of gene expression at post-transcriptional level, role of small RNA and RNA chaperones. (RNDr. Branislav Vecerek, Phd, MBU)

• The aim of the lecture is to acquaint students with post-transcriptional mechanisms that enable bacteria to react quickly and effectively to stressful stimuli in particular.
• We will deal mainly with the role of non-coding regulatory RNAs (cis / trans-encoded sRNA, riboswitch structures, antisense RNA) and RNA chaperones (Hfq, ProQ) in regulation of gene expression.

Regulation of protein function at posttranslation level, signal transduction, signaling pathways, unusual bacterial protein kinases. (RNDr. Pavel Branny, CSc., MBU)

• The lecture deals with the importance of one of the most widespread posttranslational modifications of proteins, phosphorylation, and its importance for bacterial cell physiology.
• In detail, it introduces the mechanisms of phosphate group transfer using the "classical" two-component signaling system and its various modifications.
• It also deals with unusual bacterial phosphorylation pathways and their role in the regulation of various cellular processes.

Regulation of cell division in bacteria. (RNDr. Linda Doubravova, Phd., MBU)

• Selection of dividing site: dependence on the shape of the bacteria and polarization; molecular mechanisms that positively and negatively affect the positioning of the septum; synchronization of DNA splitting and partitioning structures;
• Partition barrier formation: bacterial cytoskeleton; assembling a divisome in time and space; peptidoglycan synthesis and degradation; cell division proteins universally spread and / or specific for certain microorganisms;
• Coordination of growth and division depending on cell shape and specific equipment;
• Cell division regulators in different bacterial species.

Adaptation to stress - study at the level of one cell. (RNDr. Irena Lichá, CSc, Faculty of Science, Charles University, )

• The aim of the lecture is to introduce students to the problems of bistability, epigenetics and bet-hedging strategies in bacteria.
• The case study of general stress response in Bacillus subtilis will show the stochasticity of inducing general stress versus specific stress adaptation.
• Methods of study - mathematical modeling versus single-cell tracking methods will be described.

Persistence phenomenon. (RND. Irena Licha, CSc, Faculty of Science, Charles University)

• The lecture will introduce the phenomenon of persistence, well-known mechanisms of persistent cells induced by stochastic or stress.
• In particular, the known regulatory pathways for entering persistence in E. coli and other bacterial species will be discussed. (TA systems, stress responses, bet-hedging strategies).
• Some research methods will be presented.

Intercellular communication and multicellularity in bacteria (RNDr. Kateřina Petříčková, Phd., First Faculty of Medicine)

• cell differentiation and multicellularity in prokaryotes - definitions and examples:
•  biofilm
• specialization of cell subpopulations in streptomycetes and bacilli about sporulation
• Social behavior of myxobacteria - movement, sporulation and hunting



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