The aim of studying and bibliography

The main aim of study: Introduction of basic techniques for controlled manipulation of prokaryotic and eukaryotic genomes for development of desired product

The general information about the module: Module is carried out in sixth semester, and comprise of 30 h of lectures, 15 h of experiments and 15 h of computational training. Module finishes with test

Teaching materials: Instrukcja do ćwiczeń i laboratoriów

Bibliography required to complete the module

Bibliography used during lectures

1	Węgleński P	Genetyka molekularna	PWN, Warszawa.	1998
2	Winter PC., Hickey GI., Fletcher HLK.	Krótkie wykłady; Genetyka	PWN.	2002
3	Turner PC., Mc Lennan AG., Bates AD., White MRH,	Krótkie wykłady. Biologia molekularna	PZWN, Warszawa .	2007
4	Baxevanis AD, Ouellette BFF	Bioinformatyka. Podręcznik do analizy genów i białek	PWN, Warszawa.	2005

Basic requirements in category knowledge/skills/social competences

Formal requirements: registration at respective semester

Basic requirements in category knowledge: Knowledge of basic mechanisms of cell function on biochemical level

Basic requirements in category skills: Basic techniques of work with DNA and microorganisms

Basic requirements in category social competences: Knowledge of safety rules in biological laboratory individually and in team. Responsibility required when working with biological material.

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	Knows genetic engineering techniques for conrtolled manipulation of genetic material	lecture	written exam	K_W06+++	P6S_WG
02	Basic knowledge on construction of vectors for overexpression in transgenic organisms, controlled expression of genes and production and modification of recombinant proteins produced in prokaryotic and eukaryotic expression systems	lecture	written exam	K_W09+++	P6S_WG
03	Is familiar with trends and directions in genetic engineering and the modern techniques used for manipulation of genetic material.	lecture	written exam	K_W12+++	P6S_WG
04	Knows techniques of manipulation of genetic material for production of recombinant proteins	lecture	written exam	K_W14+++	P6S_WG
05	Knows methods of purification and analysis of recombinant proteins and peptides	lecture	written exam	K_W14+++	P6S_WG
06	Is able for self-education	lecture	written exam	K_U06+++	P6S_UU
07	Knows how to design and properly conduct and annotate experiment from the field of genetic engineering targeting bacterial transformation, selection and isolation of recombinant protein	laboratory	written test	K_U09+++	P6S_UO P6S_UW
08	Have the knowledge to analyze and evaluate usefulness of currently used genetic engineering techniques	lectures	written exam	K_U15+++	P6S_UW
09	Is able to design process to obtain recombinant protein at prokaryotic system with the use of suitable techniques of genetic engineering	lecture,laboratory	written exam, written test	K_U19+++	P6S_UO P6S_UW
10	Understand the need for updating of knowledge and upgrading professional qualifications that results from the rapid development of techniques and knowledge used in genetic engineering	lecture	exam written	K_K01+++	P6S_KK P6S_KR
11	Isable to work individually and in team, able to make decisions and follow the supervisor's orders	laboratory	observation of performance	K_K03+++	P6S_KR
12	Understand the need for dissemination of information about advantages and drawbacks of genetic manipulations and transgenic organisms. Is able to transfer these information in plain manner	lecture		K_K07+++	P6S_KO

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
6	TK01	Methods for obtaining DNA fragments: cutting the genomic DNA with restriction enzymes, chemical synthesis, reverse transcription, polymerase chain reaction (PCR). The use of these fragments for various purposes in molecular genetics. Molecular cloning of genes in prokaryotic and eukaryotic cells. Plasmid vectors, cosmids, phage vectors, shuttle vectors, YAC (yeast artificial chromosome). Construction of vectors: restriction enzymes, ligation. Mechanisms for obtaining transgenic organisms: transformation, transduction, transfection. Techniques for analysis and identification of transformants. Expression systems in bacteria and eukaryotic cells. Manipulation of gene expression. Controlled in-vitro mutagenesis. Techniques for transgenic plants and animals. Purification and identification of the recombinant proteins obtained by different methods of analysis: affinity chromatography, electrophoresis and immunoblotting, mass spectrometry.	-	MEK01 MEK02 MEK03 MEK04 MEK05 MEK06
6	TK02	Evolution of NCBI model. Understanding the diversity of DNA sequences deposited in the databases. Finding and selective use of information in planning experiments. Designing PCR primers for the selected sequence and in any orientation, with attached restriction sites occurring at the start and stop codons for protein domains. The construction of restriction map, characterization of restriction enzymes. Cloning without the use of restriction enzymes. Codon optimization. Designing SNP detection methods (PCR-RFLP, minisequencing)	-	MEK02 MEK03 MEK06 MEK07 MEK08 MEK09 MEK10
6	TK03	Application of the techniques of genetic transformation for cloning, sequencing and overexpression. Transformation of transgenic E. coli with pET expression vector or pGlo coding GFP protein. Cultivation of bacteria on the discriminating medium. The chemical transformation and electrotransformation. Isolation of colonies containing cloned gene. Preparation of competent bacteria and plasmids for transformation.	-	MEK07 MEK11 MEK12

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 6)	The preparation for a test: 10.00 hours/sem.	contact hours: 18.00 hours/sem.
Laboratory (sem. 6)	The preparation for a Laboratory: 3.00 hours/sem.	contact hours: 18.00 hours/sem.	Finishing/Making the report: 2.00 hours/sem.
Advice (sem. 6)
Exam (sem. 6)	The preparation for an Exam: 25.00 hours/sem.	The written exam: 1.00 hours/sem.

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture	50%; A positive mark for the test (W). Credit rating of the course depends on the number of points scored 3.0 (50.0% -60.0%); 3.5 (60.1% -70.0%); 4.0 (70.1% -80.0%); 4.5 (80.1% -90.0%); 5.0 (90.1% -100%).
Laboratory	25%. Pass note is granted to the students who obtained positive mark for written report for laboratory, computational exercises and written test. Final score is composed of written test (60%) and report (40%).
The final grade	OK = ZW * 0.5 * in * 0.25 + L * a + C * 0.25 * in; where: C, L, ZW represents an positive assessment of the exercises, laboratory and lectures, respectively in - factor including term credit or examination, w = 1.0 the first term, w = 0.9 the second term, w = 0.8 a third term.

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	B. Bakera; M. Rakoczy-Trojanowska; M. Szeliga; M. Święcicka; M. Tyrka	Identification of candidate genes responsible for chasmogamy in wheat	2023
2	M. Dżugan; A. Łyskowski; M. Miłek	Assessing the Antimicrobial Properties of Honey Protein Components through In Silico Comparative Peptide Composition and Distribution Analysis	2023
3	P. Bednarek; A. Dorczyk; T. Drzazga; D. Jasińska; P. Krajewski; B. Ługowska; R. Martofel; P. Matysik; M. Niewińska; D. Ratajczak; K. Rączka; T. Sikora; D. Tyrka; M. Tyrka; E. Witkowski; U. Woźna-Pawlak	Genome-wide association mapping in elite winter wheat breeding for yield improvement	2023
4	Ł. Byczyński; P. Król; M. Sochacka-Piętal	Hydrophilic polyurethane films containing gastrodin as potential temporary biomaterials	2023
5	A. Czmil; S. Czmil; M. Ćmil; J. Gawor; M. Piętal; D. Plewczynski; M. Sochacka-Piętal; D. Strzałka; T. Wołkowicz; M. Wroński	NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology	2022
6	M. Dyda; G. Gołębiowska; M. Rapacz; M. Szechyńska-Hebda; M. Tyrka; I. Wąsek; M. Wędzony	Quantitative trait loci and candidate genes associated with freezing tolerance of winter triticale (× Triticosecale Wittmack)	2022
7	M. Dyda; G. Gołębiowska; M. Rapacz; M. Tyrka; M. Wędzony	Genetic mapping of adult-plant resistance genes to powdery mildew in triticale	2022
8	M. Dyda; G. Gołębiowska; M. Rapacz; M. Tyrka; M. Wędzony	Mapping of QTL and candidate genes associated with powdery mildew resistance in triticale (× Triticosecale Wittm.)	2022
9	P. Krajewski; R. Marcinkowski; R. Martofel; P. Matysik; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Rokicki; S. Stojałowski; M. Tyrka; U. Woźna-Pawlak; B. Żmijewska	Genome-Wide Association Analysis for Hybrid Breeding in Wheat	2022
10	V. Csitkovits; K. Gruber; C. Kratky; B. Kräutler; A. Łyskowski	Structure-Based Demystification of Radical Catalysis by a Coenzyme B12 dependent Enzyme – Crystallographic Study of Glutamate Mutase with Cofactor Homologues	2022
11	A. Pietrusińska; M. Tyrka	Linkage of Lr55 wheat leaf rust resistance gene with microsatellite and DArT-based markers	2021
12	B. Bakera; P. Krajewski; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Szeliga; M. Święcicka; M. Tyrka	Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses	2021
13	B. Bakera; P. Krajewski; P. Matysik; M. Mokrzycka; M. Rakoczy-Trojanowska; M. Rokicki; S. Stojałowski; M. Szeliga; D. Tyrka; M. Tyrka	Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach	2021
14	J. Buczkowicz; T. Drzazga; B. Ługowska; P. Matysik; K. Rubrycki; M. Semik; D. Tyrka; M. Tyrka; E. Witkowski	Identyfikacja efektywnych genów odporności na wybrane choroby wirusowe i grzybowe pszenicy zwyczajnej	2021
15	J. Buczkowicz; T. Drzazga; G. Fic; M. Jaromin; P. Krajewski; P. Matysik; R. Mazur; P. Milczarski; T. Sikora; M. Szeliga; D. Tyrka; M. Tyrka; E. Witkowski	Selekcja genomowa pszenicy ozimej	2021
16	K. Chen; Ł. Jaremko; M. Jaremko; A. Łyskowski	Genetic and Molecular Factors Determining Grain Weight in Rice	2021
17	B. Król; P. Król; K. Pielichowska; M. Sochacka-Piętal; Ł. Uram; M. Walczak	Synthesis and property of polyurethane elastomer for biomedical applications based on nonaromatic isocyanates, polyesters, and ethylene glycol	2020
18	E. Ciszkowicz; E. Kaznowska; P. Porzycki; M. Semik; M. Tyrka	MiR-93/miR-375: Diagnostic Potential, Aggressiveness Correlation and Common Target Genes in Prostate Cancer	2020
19	G. Czajowski; M. Karbarz; M. Pojmaj; A. Strzembicka; D. Tyrka; M. Tyrka; A. Wardyńska; M. Wędzony	Quantitative trait loci mapping of adult-plant resistance to powdery mildew in triticale	2020
20	J. Ciura; M. Szeliga; M. Tyrka	Representational Difference Analysis of Transcripts Involved in Jervine Biosynthesis	2020
21	D. Antos; M. Kołodziej; A. Łyskowski; W. Piątkowski; I. Poplewska; P. Szałański	Determination of protein crystallization kinetics by a through-flow small-angle X-ray scattering method	2019
22	J. Ciura; M. Grzesik; M. Szeliga; M. Tyrka	Identification of candidate genes involved in steroidal alkaloids biosynthesis in organ-specific transcriptomes of Veratrum nigrum L.	2019
23	M. Dyda; M. Szechyńska-Hebda; M. Tyrka; I. Wąsek; M. Wędzony	Local and systemic regulation of PSII efficiency in triticale infected by the hemibiotrophic pathogen Microdochium nivale	2019
24	M. Dziurka; K. Hura; T. Hura; A. Ostrowska; M. Tyrka	Participation of Wheat and Rye Genome in Drought Induced Senescence in Winter Triticale (X Triticosecale Wittm.)	2019
25	Z. Banaszak; A. Fiust; Z. Nita; W. Orłowska-Job; M. Pojmaj; M. Rapacz; M. Tyrka; M. Wójcik-Jagła	Sposób selekcji mrozoodpornych genotypów jęczmienia ozimego	2019