Syllabus
1) Critical reading of literature, wise writing/structuring and “selling” your own work: - what to focus on when reading a paper - introduction into a proper structuring and writing your own paper - publishing/editorial process - identifying a knowledge gap / writing a grant - grant evaluation process
2) Translational control i. - history and what it teaches us - a genius of the past that has not yet been surpassed!
3) Translational control ii. - presence and future - have we really learnt anything? - new advances in translational control research: “The dogma is dead, long live the dogma!” - introduction into (pros and cons of) translational complex sequencing, single molecule/cells assays, other cutting-edge technology
4) CRISPr: - history - differences in CRISPR types (pros and cons of) - knock-down, -out, -ins - activation and inhibition of gene expression with CRISPR - CRISPR and modifying of the genome - visualization of the genome with CRISPR - targeting into cell compartments using CRISPR
5) The power of tRNAs and their fragments - canonical versus non-canonical roles of tRNAs and their fragments and their prospective exploitation in medicine
6) RNAs as a tool for therapy - history - advantages of RNA therapy - types of RNA therapy - types of RNA delivery methods - future of RNA therapy
7) circRNAs and their metabolism (or other ncRNA) - biogenesis (how they are formed) - detection - function - diseases
8) modifications of RNAs - types of modifications - function - detection (m6A-seq, capture-seq, mass-spec, Nanopore DNA sequencing) - readers, erasers - challenges
9) degradation of RNAs - mechanisms - how to study the RNA turnover (in vivo metabolic labelling, Akron-seq, PARE-seq, degradome-seq, TAIL-seq, SLAM-seq) - degron systems, siRNA
10) visualization of RNAs in a cell - FISH, molecular beacon, FIT - visualization techniques - pros and cons - for living cells (aptamers - protein based, fluorophore-aptamer pair, dye and quencher)
11) RNA structures and RNPs - function - methods for RNA structure determination (SHAPE-seq, DMS-seq, LIGR-seq) - the computational methods for RNA secondary structure modeling (RNAfold, iFOLD, Ufold,…) - advances in experimental RNA structure determination - RNP (domains, helicases)
12) Guided “journal club” - presentation of the most recent exciting paper or two - preparation for the exam - Part A
13) Guided “paper creating process” - presentation of all you should know to build your own story/paper - preparation for the exam - Part B
Annotation
While the central dogma of molecular biology still somehow stands, many other dogmas in the field of gene expression are falling like ripe pears from a pear tree. Indeed, much of what appeared to be indisputable truth when we were students like you, has fallen into oblivion over time. But, is it really the case that much of the old knowledge is simply no longer valid? Or is it also partly a matter of the
"publish or perish" competition and the pursuit of sensationalism in science at any cost? Let’s look at the new discoveries in the field of gene expression regulation, the underlying cutting-edge methodology, the old dogmas falling and new ones emerging. However, let’s be critical, let’s be interactive, let’s learn together.
- this is an advanced course for MSc. and PhD students including Erasmus (in English)
- signing up for the course is HIGHLY recommended only after the completion of the bachelor program
- limit is 15 students per class contacts: Leos Valasek (724731661; valasekl@biomed.cas.cz)
Adriana Roithova (739679009; adriana.roithova@biomed.cas.cz)