Immunology

Accreditation valid until: 27. 11. 2029

Chairman of the Subject Area Board:
doc. RNDr. Magdaléna KRULOVÁ, Ph.D.

Department of Cell Biology
Faculty of Science
Charles University
Viničná 7
128 00  Prague 2
phone: +420 221 951 755
e-mail: magdalena.krulova@
natur.cuni.cz

 

Contact person:
RNDr. Nataša Šebková, Ph.D.
Department of Cell Biology
Faculty of Science
Charles University
Viničná 7
128 00  Prague 2
phone: +420 221 951 794
e-mail: natasa.sebkova@natur.cuni.cz

 

Members of the Subject Area Board

Characteristics of the study programme

Immunology is a dynamically evolving discipline integrating the knowledge of molecular and cell biology, physiology, histology and functional morphology (in the context of evolution and ontogenesis) relevant to the immune system, self-defense unit composed of functionally interacting molecules, cells, and tissues involved in immune responses. Immunology outputs show a major impact in a multitude of biomedical fields today. Topics such as transplantation, allergy, immune deficiency, autoimmunity, immunosuppression, immunotherapy, or anti-tumor immunity are typical areas of interest to immunologists. Immunology covers all levels of biological knowledge from molecules (cytokines, immunoglobulins, receptors, signaling molecules), cells (a wide array of immunocompetent cells), whole organisms (having transgenic animal models in use and interaction with immune system is being investigated) and communities (evolution of immune mechanisms, e.g. frequencies of different alleles regulating the immune response within a population). Clinical immunology is an important emancipated immunology specialization, for which human immune system is the object of studies and understanding of the mechanism of its action leads to the development of potential therapeutic applications.

Admission procedure requirement specific to the study programme

The conditions and course of the admission procedure for the part-time of study are the same as the conditions for the full-time form. 

We recommend to contact your potential supervisor in advance and consult the suitable form of preparation for the interview. Each study programme has its own specifics, so the supervisor can help you to prepare for the specialized entrance examination (the interview).

Topics of dissertation thesis

The SAB did not list any topics. The candidate chooses the preliminary topic individually and contacts a potential supervisor. He/she consults with him on the chosen topic and agrees on its more precise specification. In case of any ambiguity, we recommend that you also contact the chairman of the SAB. If necessary, he/she can recommend that he/she consult the topic with another specialist according to the focus of the intended project.

If the candidate does not know which topic/supervisor to choose, he/she will contact the chairman of the SAB, with whom he/she will consult on a suitable topic and a potential supervisor.

This choice is preliminary, the admissions board may, after consultation with the candidate, nominate another supervisor.

Supervisors of the study programme

Each supervisor must be approved by the SAB. The criteria for admitting new supervisors are determined by the SAB. If the proposed supervisor has not yet been approved by the SAB, this must be done no later than the enrollment of the applicant in the study (provided that the applicant is accepted). You can find a list of supervisors approved by the SAB here. After clicking, the supervisor's workplace and contact information will be displayed.

Requirements during the study

Study obligations for full-time and part-time form of study are the same. 

The goal of study is to train students at advanced level in immunology. The students should acquire broad knowledge of the research area, master their research topic, become competent in conducting and planning experiments, get trained in scientific writing, and obtain qualification which would make them competitive candidates for positions in research, teaching, and technologies internationally.

Learning goal 1

Students must take at least three study obligations (courses) and schedule them within the first 3 years of study. When preparing their proposal of the individual study plan (ISP) for approval by the SAB in the SIS, students should include all three courses in the ISP.

All students must take the obligatory “Grant application strategy and preparation of scientific publication” course. After the theoretical background is explained in several lectures, the student will prepare a grant application related to the Ph.D. project in English, using the forms and guidelines of the Grant Agency of the Czech Republic.

Students choose at least two study obligations from the list below. Students should actively seek the opinion of their mentors about the suitability of courses with respect to their project. The prerequisite for the inclusion of courses is that students have not passed them in previous or concurrent study programs.

Learning goal 2

Internships and visits in cooperating laboratories
 
Publication prerequisite
 

Presentations of results

Students are required to attend the conference of doctoral students, which is summoned every year by the SAB. Students actively participate in its organization. During the conference, students present results of their projects and discuss methods and issues of common interest. Both the SAB members and the mentors are invited to the conference. 

Active participation in international conferences according to the focus and possibilities of the mentor’s team is also recommended.

Courses

Theoretical courses

  • Protein dynamics in development and cancer
  • Innate immunity
  • Advances in Immunology 1
  • Immunology
  • Immunology – a practical course
  • Clinical Cases in Immunology
  • Immunology – a systems biology view
  • Animal models in immunology
  • Evolutionary and ecological immunology
  • Molecular mechanisms of immune evolution
  • Regulation mechanisms of immunity (*)
  • Viruses and host immune systém (*)
  • Molecular Biology of Cancer I (*)
  • Molecular Biology of Cancer II
  • Fluorescent microscopy in cell biology
  • Advances in molecular biology and genetics (Institute of Molecular Genetics of the ASCR, v. v. i.) – https://pokroky.img.cas.cz/; according to the information for the current academic year

(*)  enquire about the availability of the course in English

Practical courses

(according to the information for the current academic year)

(according to the information for the current academic year)
 
(according to the information for the current academic year)
 
  • MB140C75E   Fluorescence spectroscopy in biology

Requirements for internships

Students conduct part of their work or training at foreign institution for a total length of at least one month or directly participate in other forms of international cooperation, such as participation in an international creative project with results published or presented abroad. The recommended form is an internship (in total for at least three months) with emphasis on advanced methods or new approaches/ models.

Listed courses

Requirements for the SDE

The state doctoral examination is an important control point of the study, in addition to the annual ISP checks. The examination serves to test student’s understanding of the research project and his/ her orientation in the research field. The committee assesses depth and breadth of knowledge of developmental and cell biology with emphasis on areas related to the project. The recommended timing of the examination is the second semester of the second year of study or the first semester of the third year, so that the examination can serve as a useful feedback for the student. Postponing the examination after the 3rd year without reason may affect student’s grading during the subsequent annual evaluation.

Examination topics for the SDE

A. Immunology

I. Basic components and principles of the immune system

  1. Functions of T lymphocytes, non-classical T cells, ILC, functional methods of studying T lymphocytes
  2. Function of B lymphocytes, functional methods of studying B lymphocytes
  3. Development and functions of monocytes/macrophages
  4. Development and functions of granulocytes and mast cells
  5. Ontogenesis of immunity, immunological development of the child
  6. Immunological memory
  7. Mucosal immune system, proteins and peptides with antimicrobial activity
  8. Mechanisms of elimination of autoreactive lymphocytes
  9. Regulation of the immune response – general principles
  10. Regulatory cells of the immune system, MDSCs
  11. Regulation of immune responses by the nervous and endocrine systems, and microbiome
  12. Phylogeny of immunity
  13. Mechanisms of immunological tolerance
  14. Relationship and cooperation of innate and adaptive immunity
  15. Cellular components of innate immunity and their functions, recognition of microorganisms by innate immunity cells and molecules
  16. Antigen-specific lymphocyte receptors: structure and function, structure and expression of genes encoding antigen-specific receptors
  17. Development of T and B lymphocytes and selection of the repertoire of their specific receptors, molecular mechanisms
  18. Antigen-presenting cells, molecular mechanisms of their function
  19. Mechanisms of signal transduction by lymphocyte surface receptors; “positive” and “negative” signals; “activation” of T and B lymphocytes
  20. Structure and function of secreted immunoglobulins, affinity and avidity
  21. Structure and function of MHC glycoproteins, the biological significance of MHC glycoprotein polymorphism
  22. Leukocyte adhesive molecules, role in lymphocyte activation and effector function, migration of T lymphocytes to lymphoid vs. non-lymphoid tissues
  23. Costimulatory molecules; signaling, role in activation, expansion and effector functions of T and B lymphocytes
  24. Effector mechanisms of cellular immunity
  25. Effector mechanisms of humoral immunity
  26. Structure and function of complement receptors, complement cascade, regulation of the complement system
  27. Cytokines, chemokines and other soluble immunoregulatory molecules
  28. Use of living organisms in immunological research, mutant, transgenic and knock-out model organisms

II. Physiological and pathophysiological aspects of immunity

  1. Mechanisms of inflammation; inflammatory mediators
  2. Immunological importance of breastfeeding, the relationship between the immune system of the mother and the fetus
  3. Immunodeficiency - causes, types, principles of therapy
  4. Primary immunodeficiencies
  5. Acquired (secondary) immunodeficiencies
  6. Immunopathological reactions accompanying physiological immune responses
  7. Autoimmune diseases – causes, types, therapy
  8. GIT immune disorders
  9. Immune disorders of the respiratory system and skin
  10. Immune disorders of the nervous system,
  11. Immune disorders of endocrine system
  12. Systemic immune-mediated diseases
  13. Immunopathological reactions (hypersensitivity)-general principles, types, mechanisms, treatment options
  14. Lymphoproliferative diseases
  15. Mechanisms of anti-infective immunity (specifics for different types of pathogens)
  16. Mechanisms of the evasion of immune responses by microorganisms
  17. Mechanisms of tissue damage by pathogens and immunopathological reactions
  18. Mechanisms of the antitumor immunity, tumor antigens
  19. Mechanisms of the evasion of immune responses by tumor cell
  20. Immunotherapy – basic principles and approaches (stimulation, suppression)
  21. Antigen-specific immunotherapy (vaccines, passive immunization, specific immunosuppression), adjuvants and their mechanisms of action
  22. Experimental models of immunopathological conditions
  23. Transplant immunology, principles, xenotransplantation, graft-versus-host disease
  24. Classical and non-classical HLA antigens, HLA typing methods, therapeutic approaches of transplant immunology
  25. Immunologically privileged sites

B. Molecular and cell biology

Proteins

  1. Protein structure (primary, secondary, tertiary, quaternary)
  2. Metabolic turnover of proteins (proteosynthesis vs. degradation, proteasomes)
  3. Posttranslational protein modifications (glycosylation, phosphorylation, acylation, prosthetic groups)
  4. Membrane proteins (origin, types of association with the membrane, examples)

Cell structure and function

  1. Membrane structure (bilayer, amphipathic properties, lateral diffusion, phospholipids, steroids, proteins), membrane function (semi-permeability, compartmentalization, asymmetry, transporters, receptors, nuclear-cytosol transport, nuclear pore, dynamics during mitosis, lamins)
  2. Cell energy metabolism, mitochondria (DNA, electron transport chain, uncoupling proteins, proton gradient)
  3. Endoplasmic reticulum (rough vs. smooth ER, posttranslational protein modifications, lipid synthesis)
  4. Protein signal sequences (address labeling, SRP, membrane transport mechanism)
  5. Golgi system (localization, function, glycosylation, sorting of molecules to different destinations)
  6. Lysosomes (endocytosis, clathrin, acidic pH, hydrolases, mannose 6-phosphate receptor)
  7. Endocytosis and exocytosis (principle, endosomes - early, clathrin, recycling, late endosomes, regulation of exocytosis)
  8. MHC I and ER (mechanism of MHC I peptide loading, peptide transporters, transport to plasmid membrane)
  9. MHC II and endosomes (mechanism of MHC II peptide loading, invariant chain, late endosomes)
  10. Comparison of the types of the cytoskeleton (logic of structure, similarities and differences in structure and function)

Extracellular signaling

  1. Types of extracellular signaling (autocrine, paracrine, endocrine, cell contact-dependent, synaptic)
  2. Types of receptors (surface vs. intracellular, kinases, cyclases, ion channels, associated molecules)
  3. Types of signaling molecules (nitric oxide, carbon monoxide, steroids, peptides, proteins, prostaglandins…)
  4. Types of second messengers (cyclic GMP and AMP, Ca2 +, diacylglycerol, inositol phosphates)
  5. Types of signaling pathways (receptors associated with G-proteins, ion channels, kinase activity)
  6. G-protein-coupled receptors (trimeric G-protein, receptor structure, cAMP, cGMP, PKA, diacylglycerol, phospholipase C-β, IP3, Ca2 +, PKC, calmodulin)
  7. Receptors utilizing enzymatic activity (receptor tyrosine kinases, tyrosine kinase associated receptors, receptor tyrosine phosphatases, receptor serine/threonine kinases, receptor guanylyl cyclases)
  8. Signal transduction by protein tyrosine kinases (receptor PTK, autophosphorylation, dimerization, SH2 domains, adapter proteins, Src family kinases, PLC-γ, Ras proteins, MAP kinase pathway, PI 3-kinase)

Cell cycle and programmed cell death

  1. Cell cycle definition (G1, G2, M, S phase, interphase, modification, duration)
  2. Cell cycle regulation (checkpoints, examples of sensors – Rb protein and p53, Cdk, cyclins)
  3. Malignant transformation (mechanisms of tumor cell formation, key factors and molecules)
  4. Apoptosis (definition, apoptosis vs. necrosis, caspases, role of mitochondria, Fas, Bcl-2, phosphatidylserine), apoptosis in the immune system
  5. Autophagy

Methods

  1. Reverse genetics (transgenes, knock-out, knock-in, Crispr-Cas9, RNA interference, ES cells).
  2. Flow cytometry: principles, applications
  3. Hybridoma technology (immunization, myeloma cell, selection)
  4. Mass spectrometry (use, advantages, limitations)
  5. DNA and RNA detection (fluorescent and radioactive probes, in situ hybridization, sequencing)
  6. DNA cloning (restriction endonucleases, vectors, amplification)
  7. PCR (principle, thermostable DNA polymerases, primers, PCR variants – real-time, nested etc., primer modifications)
  8. Methods for determining the structure of proteins (X-ray crystallography, cryo-EM)
  9. Methods based on antigen-antibody interaction (ELISA, Western blot, nephelometry)
  10. Light microscopy (resolution, fluorescence microscopy, confocal microscopy, electron microscopy (resolution, scanning vs. transmission)
  11. Use of fluorescent proteins (logic, in vivo studies, fusion proteins, FRAP, FRET)

Publication activity requirements

The applicant must be an author/ co-author of at least two papers accepted in peer-reviewed journals indexed in the Web of Science (preferably with IF above the research field median) and should be a first author on at least one publication (shared first authorship should be communicated ex ante with the SAB). In exceptional and warranted cases, the SAB may decide otherwise; an example of such situation may be one excellent first author publication

Defence requirements

The thesis should be written as concise, fair and comprehensive information about the applicant's scientific achievements. It should enable the reviewers and the defense committee to assess whether the candidate has acquired both theoretical knowledge and methodical experience as prerequisite for independent scientific work in the field. The candidate should address the scientific problems and open questions of the project and formulate his/ her independent opinions.

The text contains:

a)  Abstract – It should summarize the project’s aims and results for the public; it should not exceed 500 words.

b) Introduction – It should be outlined as brief review of current knowledge related to the project. Recommended length is ca 20 pages of standard manuscript formatting.

c) Methods, Results – These sections should describe in detail the methods and the results of experiments carried out by the applicant, which have not become part of the published papers/ submitted manuscripts. The published papers/ submitted manuscripts should be included as supplements.

d) Discussion – This section gives the author the opportunity to present her/ his independent opinions on the results and their significance. It should reflect the level of knowledge at the date of thesis submission and it should mention relevant literature containing supportive or contradictory results. Minimum length is 10 pages.

e) Summary – Summary of the main results. Recommended length is one page.

f) Accompanying sections – list of abbreviations, list of references, information on data repositories or websites where appropriate, statement describing the contribution of the applicant to the published work, including a detailed statement about his/ her role in the preparation of the publications.

g) Publications and submitted manuscripts which contain the results obtained by the student. 

The text in parts a) to e) should be written by the student and must not be contained elsewhere. The text cannot be copied, even in part, from the publications in section g) or other texts. The text can be written in English, Czech or Slovak. Formatting of the text, figures, tables and accompanying data should comply with the rules for manuscript submission of a journal of choice, such as the journal where one of the author’s papers was published.

The SAB of the programme does not require a separate Summary of the Dissertation Thesis.

Profile of a graduate of the study programme

Our graduate has an excellent knowledge of modern immunology, ranging from theoretical molecular and cellular bases, through practical methodological aspects of experimental immunology, to the basics of clinical immunology. In addition to specialized knowledge of immunology in the strict sense, they also acquire good theoretical knowledge and basic practical experimental skills in related fields of molecular and cell biology, biochemistry and microbiology. After defending the doctoral thesis, students are familiar with specialized experimental methods, tools for critical evaluation of literature and with general principles of ethics and scientific work soft skills. Graduates are able to solve both theoretical and practical problems they encounter in their research activities. 

Information about graduate employment

Graduates are mainly employed in scientific and teaching positions at domestic and foreign universities and scientific institutes engaged in basic and applied microbiological research or related fields, as well as in similarly focused research and technology centres. In the non-academic sphere, it is applied in applied research at development workplaces and corporate laboratories, for example in the following areas: biotechnological and pharmaceutical production, clinical microbiology – molecular and biochemical diagnostics of infectious diseases, food microbiology, bioremediation, water management.

Created: 19. 5. 2021 / Modified: 16. 3. 2022 / Responsible person: ThDr. Jitka Sýkorová, Ph.D.