Didactic Offer - Wydział Biotechnologii i Hodowli Zwierząt ZUT

Course title

Protéomique

Teaching method

Cours théoriques et exercices en laboratoire

Person responsible for the course

Prof. Assist. Małgorzata Ożgo

E-mail address to the person responsible for the course

Malgorzata.ozgo@zut.edu.pl

Course code

(if applicable)

ECTS points

Type of course

Optionnel

Level of course

S1/S2/S3

Semester

Eté

Language of instruction

Francais

Hours per week

2

Hours per semester

30

Objectives of the course

·         Connaissances théoriques et pratiques des techniques de séparation des protéines basées sur gel et chromatographiques

·         Capacité des participants à utiliser des outils bioinformatiques avancés pour analyser les données protéomiques (gels 1D et 2D, spectres de masse)

·         Utilisation pratique du MS MALDI-TOF (spectromètre de masse matrix-assisted laser desorption/ionisation time of flight) pour l'identification de protéines

Entry requirements

Bases en biologie cellulaire et en biochimie des protéines.

Course contents

Introduction à la protéomique. Importance biologique des modifications post-transcriptionnelles et post-translationnelles des protéines. Organisation du protéome. Les principes généraux de l'analyse protéomique. Techniques de séparation des protéines basées sur gel. Les composants de la matrice du gel de séparation. Electrophorèse en gel de polyacrylamide contenant du dodécylsulfate de sodium (SDS-PAGE), le principe et les applications de l'électrophorèse sur gel natif PAGE. Electrophorèse bidimensionnelle (2-DE) – principe de la méthode, préparation des échantillons pour la 2-DE, bandes d'IPG (IPG strips), focalisation isoélectrique. Méthodes de détection des protéines: coloration au Bleu de Coomassie, coloration à l'argent, coloration inverse avec des ions (cuivre, zinc), autoradiographie, fluorographie, coloration fluorescente. Analyse différentielle sur un gel unique (two-dimensional difference in gel electrophoresis 2D-DIGE) – principe et applications de la méthode. Acquisition d'image et analyse de gels 1D et 2D. Logiciels d'analyse des gels 1D et 2D. Applications de la spectrométrie de masse (MS) pour l'identification des protéines. Méthodes d'ionisation en spectrométrie de masse. Types d'analyseurs de masse. Cartographie peptidique massique (peptide mass fingerprinting PMF). Méthodes chromatographiques pour la séparation des protéines. Chromatographie en phase liquide (LC). Chromatographie liquide bidimensionnelle (2D LC). Les stratégies protéomiques basées sur la chromatographie liquide : LC-MS, LC-MS/MS, LC-MS/MS multidimensionnelle. Chromatographie d'affinité. Types de protéomique : structurelle, fonctionnelle et clinique.

Assessment methods

·         Evaluation continue du travail en laboratoire

·         Examen écrit à la fin du cours

Recommended readings

1.        Sheehan D., Tyther R. (Ed.). Two-dimensional electrophoresis protocols. Humana Press, New York, 2009.

2.        Garfin D., Ahuja S. (Ed.). Handbook of isoelectric focusing and proteomics. Elsevier Academic Press, Amsterdam, 2005.

3.        Heftmann E. (Ed.). Chromatography, sixth edition. Elsevier Academic Press, Amsterdam, 2004.

4.        Walker J.M. (Ed.), second edition. The proteomics protocols handbook. Humana Press, New Jersey, 2002.

5.        Rabilloud T. (Ed.). Proteome research: two-dimensional gel electrophoresis and identification methods. Springer, Berlin, 2000.

6.        Hames B.D. (Ed.), third edition. Gel electrophoresis of proteins: a practical approach. Oxford University Press, England, 1998.

Course title

Proteomics

Teaching method

Lectures and laboratory exercises

Person responsible for the course

Ph.D. Agnieszka Herosimczyk/

Ph.D Adam Lepczyński

E-mail address to the person responsible for the course

agnieszka.herosimczyk@zut.edu.pl

adam.lepczynski@zut.edu.pl

Course code

(if applicable)

ECTS points

Type of course

Optional

Level of course

S1/S2/S3

Semester

Summer

Language of instruction

English

Hours per week

2

Hours per semester

30

Objectives of the course

·         Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.

·         The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).

·         Practical use of MALDI-TOF MS (matrix-assisted laser desorption/ionisation time of flight mass spectrometer) for protein identification.

Entry requirements

Basic of the cell biology and the protein biochemistry.

Course contents

Introduction to proteomics. Biological significance of  post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic analysis. Gel-based protein separation techniques. The components of resolving gel matrix. Sodium-dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), the principle and application of native PAGE electrophoresis. Two dimensional electrophoresis (2-DE) – the principle of the method, sample preparation for 2-DE, IPG strips, isoelectric focusing. Protein detection methods: coomassie stain, silver stain, negative ion staining (copper, zinc), autoradiography, fluorography, fluorescent staining. Two-dimensional difference in gel electrophoresis (2D-DIGE) – the principle and application of the method. Image acquisition and analysis of 1-D and 2-D gels. 1-D and 2-D gels analysis softwares. Application of mass spectrometry (MS) for protein identification. Ionization methods in mass spectrometry. Types of mass analyzers. Peptide mass fingerprinting (PMF). Chromatographic methods for protein separation. Liquid chromatography (LC). Two-dimensional liquid chromatography (2-D LC). The proteomic strategies based on liquid chromatography: LC-MS, LC-MS/MS, multidimensional LC-MS/MS. Affinity chromatography (AC). Types of proteomics: structural, functional and clinical.

Assessment methods

·         Continuous assessment of the laboratory work 

·         Written test at the end of the course

Recommended readings

1.        Sheehan D., Tyther R. (Ed.). Two-dimensional electrophoresis protocols. Humana Press, New York, 2009.

2.        Garfin D., Ahuja S. (Ed.). Handbook of isoelectric focusing and proteomics. Elsevier Academic Press, Amsterdam, 2005.

3.        Heftmann E. (Ed.). Chromatography, sixth edition. Elsevier Academic Press, Amsterdam, 2004.

4.        Walker J.M. (Ed.), second edition. The proteomics protocols handbook. Humana Press, New Jersey, 2002.

5.        Rabilloud T. (Ed.). Proteome research: two-dimensional gel electrophoresis and identification methods. Springer, Berlin, 2000.

6.        Hames B.D. (Ed.), third edition. Gel electrophoresis of proteins: a practical approach. Oxford University Press, England, 1998.

Course title

Animal Physiology

Teaching method

Lecture / Laboratory Exercises

Person responsible for the course

Ph.D. Katarzyna Michałek

E-mail address to the person responsible for the course

katarzyna.michalek@zut.edu.pl

Course code

(if applicable)

ECTS points

Type of course

Obligatory

Level of course

S1/S2/S3

Semester

Summer

Language of instruction

English

Hours per week

2

Hours per semester

30

Objectives of the course

·         To develop the general understanding of  the fundamental processes of the animal body system

·         To learn about how animals adapt physiologically to environmental challenges.

·         To develop the ability to think critically about issues in animal physiology..

Entry requirements

Basics of the biology and the physiology

Course contents

Introduction to Animal Physiology. Definition of comparative animal physiology. General features of a central nervous system. Neurons and synapses. Propagation of the nervous impulse in vertebrates. The autonomic nervous system (the sympathetic and parasympathetic system). The receptors. Cutaneous receptors. Proprioceptors. The excitation of receptors. Sense organs. The general composition of the blood. The red blood corpuscles. Structure and role of haemoglobin. The white blood corpuscles (granulocytes, monocytes and lymphocytes). The blood platelets. Composition and role of the blood plasma. Oxygen transport in blood. Carbon dioxide transport in blood. The coagulation of the blood. Blood groups. Circulatory system. General features of the circulation. Pulmonary circulation. Systemic circulation. Physiology of the mammalian heart. Cardiac muscle. The properties of cardiac muscle. The sequence of events in the cardiac cycle. The nervous regulation of the heart. Respiration. Mammalian lungs. The mechanics of the respiratory movements. Lung volume. Exchange of gases in the lungs. Exchange gases in the tissues. The control of the respiratory movements. The respiratory centers. The temperature and heat balance of the body. Endothermy and heterothermy. Regulation of body temperature. The regulation of heat production and loss. Behavioral temperature regulation. Hibernation and estivation. Hyperthermia, hyperthermia and fever. The physiology of digestion. Digestion in the oral cavity. The secretion of saliva. Digestion in the stomach. Gastric juice. The actions of gastric juice. The secretion of gastric juice. Intestinal digestion. The pancreatic juice. Properties of pancreatic juice. The liver and bile. Bile storage and expulsion. Functions of the small and the large intestine. The absorption of the foodstuffs. Ruminates. Renal excretion. The composition and characters of the urine. Structure and functions of the kidneys (the secretion of urine and hormones, regulation of the extracellular homeostasis). Functions of the glomerulus and the renal tubules. The regulation of the renal functions.

Assessment methods

·         Continuous assessment of the laboratory work

·          Written test at the end of the course

Recommended readings

1.        C. Etchberger, M. Nordie, J. Fowles, P. Munn. Principles of human physiology. Addison-Wesley Longman. 2004.

2.        C. Ladd Prosser (Ed.). Comparative animal physiology. New York: Wiley-Liss. 1991.

3.        C.L. Stanfielsd, W.J.German. Principles of human physiology. Pearson Education. 2008.

4.        K. Schmidt-Nielsen. Animal physiology: adaptation and environment. Cambridge University Press. New York. 1997.

5.        P. Carew Withers. Comparative animal physiology. Saundersa College Pub. 1992.

6.        R. W. Hill, G.A. Wyse, M. Anderson. animal Physiology. Sinauer Associates, Incorporated. 2008.