Excellentie Traject: Molecular Systems Biology

Excellence Traject: Molecular Systems Biology

Studiewijzer 2015/2016

Globale inhoud

(Medical) Molecular Systems Biology reflects the study of the molecular basis of the chemistry of life. In this advanced course for the bachelor Biomedical Sciences we will introduce you to a thorough understanding of how networks of molecules (molecular systems) take care of all the important chemical and cellular processes that occur during health and disease. The recurrent theme is integration: genetic, signal transduction and metabolic reactions form an integrated complex network of reactions that is at constant steady state (homeostasis) with its environment. Alterations like environmental stress / life style induced perturbations of homeostasis, mutations and polymorphisms in single molecules not only affect single chemical processes but also cellular behavior and can have a severe impact on the proper functioning of the biological system under study. 

The research tools used span a wide range of techniques from genome-sequencing and genome-wide transcript analyses to metabolic profiling, mass spectrometry for proteome analyses as well as advanced microscopy. Mostly these studies are no longer performed in the test tube but in complete cells, tissues or organisms. The course is meant to provide you with a basic framework of the cellular functioning and signaling in sufficient depth to allow you to work independently on a research essay. What we hope to accomplish is not for you to memorize detailed knowledge or books by heart, but use integrated insight of the molecular basis of metabolism and disease processes relevant to biomedical research. Note that the newest 2015 edition of Molecular Biology of the Cell (Alberts) is recommended especially in view of chapter 8 on technologies and analysis of signaling networks using mathematical tools.

The course consists of initially four 2 hour meetings from 17:00-maximally 19:00 for which presence is obligatory. During the meetings research topics are introduced by top researchers spanning systems biology challenges in bacteria, yeasts, other model organisms and man. You can also ask questions on basic cell biology that was taught in Molecular Biology of the Cell (Alberts) during previous courses. The most relavnt chapters are indicated 

Next you are challenged to choose a topic of your prime interest on which you will work in the second part of the course preferentially individually. You will also individually receive supervision of a researcher. The meetings all take place at Science Park in small scale lecture theaters or if less than 10 participants take part in the course in room C3265.  

The examination will be on a day in the final week at a suitable time not interfering with other courses, preferably the Friday.

Studiemateriaal

Literatuur

• Molecular Biology of the Cell, Alberts et al., Taylor & Francis Inc (6th edition)

• Hand-outs & papers posted on Blackboard.

Leerdoelen

(Medical) Molecular Systems Biology reflects the study of the molecular basis of the chemistry of life. In this advanced course for the bachelor Biomedical Sciences we will introduce you to a thorough understanding of how networks of molecules (molecular systems) take care of all the important chemical and cellular processes that occur during health and disease.

After the course the students;

-understand the basics of signalling network integration at the genetic, signal transduction and metabolic level.

-understand the basics of how this integrated complex network of reactions that is at constant steady state (homeostasis) with its environment operates.

-can analyse how alterations like environmental stress / life style induced perturbations of homeostasis, mutations and polymorphisms in single molecules affect single chemical processes and network behavior.

-can analyse the impact of network perturbation by external compounds or genetic mutation on the proper functioning of a biological system under study. 

-can use research tools that span a wide range of techniques from genome-wide micro-arrays to metabolic profiling, mass spectrometry of peptides, proteins and other bio-molecules as well as advanced microscopy.

-understand how mostly the chemistry of cellular behaviour is no longer studied in the test tube but in complete cells, tissues or organisms.

After the course the students will have,

-a basic framework of the cellular functioning and signaling in sufficient depth to allow them to work independently on a research essay.

-the capability of writing an English essay on a research area of choice in which they use integrated insight of the molecular basis of metabolism and disease processes relevant to biomedical research.

Onderwijsvormen

• Hoorcollege
• Presentatie/symposium
• Zelfstudie
• Begeleiding/feedbackmoment

Lectures, assignments. The assignment involves a research proposal, an oral presentation and the assessment and discussion of another proposal. The oral presentation and discussion of a proposal of others is obligatory but purely meant to practice. The own assignment is marked. It is foreseen that combined with Self-Study an equivalent of 6EC is spent on the course. Specifically assigned hours amount to: 
Lectures: 14 hours 
Tutorials with teachers: 20 hours 
Assignment: 120 hours (as unsupervised individual work) 
Question ‘hours’: 3 hours 
Exam: 3 hours

Verdeling leeractiviteiten

Aanwezigheid

Aanwezigheidseisen opleiding (OER-B):

• Deelname aan alle practica, computerpractica en werkcolleges in het curriculum is verplicht.
  

Aanvullende eisen voor dit vak:

Aanvullende eisen voor dit vak:

All meetings are obligatory. Please contact the coordinator of the course, prof. dr. Stanley Brul, if you are unable to attend a meeting.

Toetsing

Opdrachten

Essay

• Write an essay on the subject chosen according to the methods that you have learned in the first year (especially when writing your literature review for the course Academic Skills). The paper(s) associated with the topic are meant as a guide for the topic assigned. Do not literally reproduce the (experimental) info present in the paper(s) provided! You are supposed to write a brief review essay. Do NOT sum up experimental details! The essay should be at least 1500 words and maximally 3500 (excluding the figures and references).  The essays will be supervised by the respective researchers and commented by them, the Academic Skills lecturers and your fellow students. The mark is given by the researcher of the individual essay topic, the coordinator (both mainly focusing on content) and a Academic Skills Lecturer (focusing on form and structure).

Oral Presentation

• The topics will be presented orally in a powerpoint presentation of 15 minutes maximum, including a discussion. The oral presentation in English is not part of the final mark for the essay. It is obligatory though and meant to learn!

Discussion on the Essay

• The discussion session - held after the oral presentation - is where you will get most out for later! So be open and discuss! The questions and feedback you receive from the researchers and other students can be used to improve your essay.

Onderstaande opdrachten komen aan bod in deze cursus:

•    Naam opdracht 1 : beschrijving 2
•    Naam opdracht 2 : beschrijving 1
•    ....

Fraude en plagiaat

Dit vak hanteert de algemene 'Fraude- en plagiaatregeling' van de UvA. Hier wordt nauwkeurig op gecontroleerd. Bij verdenking van fraude of plagiaat wordt de examencommissie van de opleiding ingeschakeld. Zie de Fraude- en plagiaatregeling van de UvA: www.uva.nl/plagiaat

Weekplanning

Rooster

Contactinformatie

Coördinator

• prof. dr. S. Brul