ImmunoBiology 2013:

ImmunoBiology

Immunobiology course starts on monday 22 April 2013. The course book is Parham's The Immune System (3rd edition).

Practical Information

Purpose

The immune system comprises innate and acquired defense mechanisms against (pathogenic) microorganisms. Immunology has traditionally been a qualitative science describing the cellular and molecular components of the immune system and their functions. In the last twenty years this traditional approach is being replaced by a systems biology approach, where theoretical studies helps to interpret experimental data, to resolve controversies, and --most importantly-- to suggest novel experiments allowing for more conclusive and more quantitative interpretations. This course is planned to give an overview of wet and theoretical immunological research. We aim to:

provide insight into the function of the immune system in health and disease

give an introduction to the use of mathematical models and bioinformatics in immunological research.

Schedule

Monday April 22nd (9:00-11:00)
Hoorcollege (DDW 1.30): Introduction to the course, Chapters 1-2 (Kesmir).
Self Study: Chapter 3
Wednesday April 24th (9:00-11:00)
Hoorcollege (BBL 001): Chapter 5 (Bontrop)
Friday April 26th (9:00-11:00)
Hoorcollege (BBL 001): Chapters 4 and 6 (de Haard).
Self Study : Read Kiepelia et al and Kosmrlj et al (only the first page)
Monday April 29th (9:00-13:00)
Hoorcollege (DDW-1.22): Neural networks and predicting MHC class I binding (Kesmir). Additional reading material on MHC class I binding predictions.
Computer Exercise (MIN 023 and 025): Predicting HIV-1 Gag responses
Wednesday May 1st (9:00-11:00)
Hoorcollege (DDW 1.22): Chapter 7 & 8 (Bontrop)
Self Study: Read the Anderson et al. 2001 paper on tolerance.
Friday May 3th (11:00-13:00):
Hoorcollege (DDW 1.30): NK cell biology and modelling the diversity of NK cell receptors (Carrillo-Bustamante)
Monday May 6th (9:00-13:00)
Hoorcollege (BBL 001): Computational Immunology Lecture 1, discussion of Anderson et al. 2001 (De Boer)
Computer exercise (MIN 018 & 022): You will receive handouts published here.
Monday May 13th (9:00-13:00)
Hoorcollege (BBL 061) Chapter 9. Preparation for the practicum (De Haard, Klarenbeek).
Article discussions (BBL 061) (De Haard)
Wednesday May 15th (9:00-17:00)
Practica: (Kruyt Z428) Group A (Klarenbeek) Protocol .
Article discussions (10:30-12:00, Kruyt O307) : Group B (Kesmir & Carrillo-Bustamante)
Friday May 17th
Practica (9:00-17:00): (Kruyt Z428) Group B (Klarenbeek) Protocol .
Article discussions (10:30-12:00, Kruyt O307) : Group A (Kesmir & Carrillo-Bustamante)
Wednesday May 22nd
Practica (9:00-17:00): (Kruyt Z428) Group A (Klarenbeek) Protocol .
Self study: Chapter 11
Friday May 24th
Practica (9:00-17:00): (Kruyt Z428) Group B (Klarenbeek) Protocol .
Self study: Chapter 11

Self study:

Hoogenboom et al

Monday May 27th (9:00-13:00)
Hoorcollege (BBL 001): Viral and CD4+ T-cell dynamics in HIV infection(Borghans).
Computer exercise (DDW 0.42): See handouts.
Wednesday May 29th (9:00-15:00)
Discussion of the practica results (BBL 001, 9:00-9:45): (De Haard & Klarenbeek)
Predicting V-D-J recombinations (BBL 001, 10:00-11:00) (Kesmir).
Computer Exercise (MIN 018 & 022, 11:00-15:00) : Analysis of nanoantibody sequences.
Self Study: Chapter 10 from Parham's book.
Friday May 31th (9:00-13:00)
Hoorcollege (BBL 001): Acute immune responses to viruses and Chapter 10 (DeBoer)
Computer exercise (MIN 023 & 025): See the handouts from the last practical.
Monday June 3rd (9:00-13:00)
Hoorcollege (BBL 001): Quantification of T-cell dynamics: from telomeres to DNA labelling (Borghans).
Computer exercise (MIN 0.23-025): handouts for computer exercises.
Wednesday June 5th (9:00-13:00)
Hoorcollege (BBL 001): Evolution of the immune system. (Bontrop) and article discussions (Kesmir & Carrillo-Bustamante) Self study: AIRE Evolution
Friday June 7th (11:00-15:00)
Hoorcollege (DDW 1.22): Sequence analysis will be reviewed in the context of AIRE Evolution(Kesmir)
Additional reading material is in your Bioinformatics reader from 1st year course (also available online).
Computer Exercise (MIN 018 and 022): Evolution and origin of NK cells (scan through before hand Gascoyne et al).
Monday June 10th (9:00-13:00)
Hoorcollege (BBL 061): Analysis and modeling of immune cell migration (Textor)
Computer exercise (Min 018 & 022): You will receive handouts published here.
Wednesday June 12th (9:00-17:00)
Visit to Biomedical Primate Research Center (Rijswijk).
Research discussions: (Kesmir & Bontrop)
Deadline for the reports on nanobodies (experimental and theoretical part). Please deliver on paper, if it is not possible send it (ONLY PDF!!) via email to c.kesmir(at)uu(dot)nl
Friday June 14th (9:00-13:00)
Hoorcollege (BBL 001): Chapter 14 Vaccines, Computational approaches for vaccine design and analysis of vaccine efficiency and article discussions (Kesmir, de Boer, Carrillo-Bustamante)
Self study: Chapter 13
Monday June 17th (9:00-13:00)
Computer practical (Min 018 & 022): Catch-up practicals from previous days (Kesmir, DeBoer, Carrillo-Bustamante).
Wednesday June 19th (9:00-12:30)
Hoorcollege (BBL 001): Presentations on ongoing research in theoretical immunology (Perie & Textor).
Friday June 21nd (9:00-11:00)
Article discussions (BBL 001): (Kesmir & Carrillo-Bustamante)
Monday June 24th (9:00-11:00)
Hoorcollege (BBL 001): Chapter 15 Transplantation of organs and tissues (Spierings)
Friday June 28th: Exam (9:00-11:00 BBL 001 and 061). The exam lasts 2 hours.Sample exam questions and Answers
Exam questions from 2011. Reading material for the exam: Chps 1-15, excluding 12 from the book, and all the concepts, BUT NOT THE DETAILS, that we discussed during the article presentations, computer exercises, and the experimental part.

Assessment

Active participation in the computer assignments required. The assessment takes place through the exam (40%), and two written assignments on practicals and computer exercises (20% and 25%, respectively) and participation in article discussions (15%). Assignment I is about the experimental part, and the analysis of the nanobody sequences obtained (20%). This can be written in the form of a short report with an introduction, materials and methods, presentation of the results and a discussion and conclusion. Assignment II will be about an exercise of your choice concerning the mathematical modeling or bioinformatics (25%). We expect this report to be more in the form of a short article. You can find a more elaborate guide on assignment writing here.