Modern Trends in Molecular Biology 1400-MTiMB-en
1. Part I - Eukaryotes
1.1. Chromatin structure and transcription regulation: Epigenetic mechanisms controlling expression and gene silencing: DNA modifications, histone modifications, chromatin remodeling complexes, Polycomb repressive complexes, noncoding RNA. The function of epigenetic factors in development and human diseases (oncohistones). Selected methods for studying chromatin i.a. ChIP-seq, CUT&RUN, ATAC-seq. Epigenetic cancer therapeutics. (M. Koblowska)
1.2 The transcription cycle: Histone code versus RNAPII-CTD code. Properties and composition of transcriptional condensates: RNA polymerase II (RNAPII), Mediator, Transcription Factors, enhancers. Single molecule tracking (SMT) for measurements of the location and motions of nuclear factors. Transcription regulation: promoter-proximal pausing, RNAP backtracking, R-loops, gene loops, G4 RNA structures. (M. Koblowska).
1.3 Types of ncRNAs. Methods for studying noncoding RNA-chromatin association i.e. chromatin-associated RNA sequencing (ChAR-seq). Gene silencing by ncRNA. siRNA signal amplification - RNA-dependent RNA polymerases. RNA-directed DNA methylation in plants. RNA variants in transgenerational inheritance. (M. Koblowska)
1.4 Coordination and feedback between transcription, RNA processing, translation and decay. The role of subcellular condensates and aggregates as hubs of RNA-related activities. Contribution of alternative and fail-safe processes to RNA homeostasis and diversity. (J. Kufel)
1.5 Non-canonical processes: alternative RNA capping, cytoplasmic mRNA adenylation, uridylation and recapping. mRNA modifications: mechanisms, machinery (writers, readers, erasers) and their specific functions. (J.Kufel)
1.6 Non-canonical processes: transcription and translation: upstream ORFs, internal ORFs, non-AUG initiation, stop-codon readthrough, programmed ribosomal frameshifting, small peptides (sPEPs) encoded in “non-coding RNAs”. (J. Kufel)
1.7 Quality Control (QC) mechanisms and regulation of gene expression: Specialized RNA surveillance pathways. Ribosome Quality Control. Specialized ribosomes and localized translation (J. Kufel)
1.8 Standard and non-standard amino acids, selenocysteine, pyrrolysine, recoding. Orthogonal translation. Post-translational modifications of proteins. Protein stability, protein quality control and degradation pathways; proteasomes and lysosomes. (M. Gapińska)
1.9. Protein structure. Methods to study protein-protein and protein-nucleic acid interactions: in silico, in vivo, in vitro. MALS, DLS, DSF, MST, mass photometry, affinity chromatography, CoIP, BiFC, BioID, TurboID, split-luciferase system, yeast two-hybrid system, AlphaFold. Modern proteomics approaches. (M. Gapińska)
2. Part II – Bacteria and viruses
2.1 Compartmentalization in bacteria. Transcription-translation coupled or uncoupled? RNA polyadenylation and polyadenylation-assisted mRNA decay. Bacterial translation quality control. Regulation of transcription and translation by non-coding RNAs and alarmones. (J. Kufel)
2.2. Adaptive bacterial immunity. DNA restriction and modification systems. CRISPR-Cas and anti-CRISPR systems. Non-coding RNAs. DNA interference and prokaryotic AGO proteins. Application of bacterial defense systems in biotechnology. (T. Ishikawa)
2.3. Transcription and translation of respiratory viruses (e.g. SARS-CoV2, IAV, hRSV). Gene expression regulation. Cross-talk between virus and host. Viral strategies to antagonize the host antiviral immunity. (A. Kwiatek)
Part III Applications.
3.1 Molecular methods in evolutionary studies. Evolutionary genomics. Phylogenomics. Genomics and population studies – archaeogenetics and archaeogenomics. Ancient DNA. (P. Golik)
3.2 RNA-based therapeutics. The mechanisms of action, challenges, solutions, and clinical application of RNA-based molecules. mRNA manufacturing process - in vitro transcription, transcript purification and formulation. (P. Sikorski)
Main fields of studies for MISMaP
biology
Type of course
elective courses
Mode
Prerequisites (description)
Course coordinators
Learning outcomes
KNOWLEDGE
P8S_WG: After completing the course, the student knows and understands the main scientific trends and research methodology in the field of molecular biology to a degree that allows to formulate and solve research problems.
SKILLS
P8S_UW: After completing the course, the student is able to critically analyze and evaluate the results of scientific research and their contribution to the development of science. The student is able to independently define the purpose and subject of scientific research, formulate research hypotheses and design an experiment leading to the solution of a research problem. The student is able to use English at a level B2 to a degree that allows participation in scientific discussions in an international environment.
SOCIAL ABILITIES
P8S_KK: After completing the course, the student is ready to critically evaluate the achievements in molecular biology. The student is ready to recognize the importance of knowledge in solving cognitive problems.
P8S_KR: After completing the course, the student is ready to independently conduct research activities.
Assessment criteria
Course credit is based on a graded writen exam in a form of a test with single choice answers.
To pass the written exam, students must achieve a minimum grade of 55%
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