Research Honours: Molecular Systems Biology

Studiewijzer 2023/2024

Globale inhoud

The course is coordinated by prof Stanley Brul and Dr. Nina Scheres (honours coordinator BMW) and consists of initially five 2 hour meetings for which presence is obligatory. During the meetings research topics are introduced by researchers spanning systems biology challenges in bacteria, yeasts, other model organisms and man. This part of the course will also be followed by students taking the 3 EC version of the course. You can also ask questions on basic cell biology that was taught in Molecular Biology of the Cell (Alberts) during previous courses. The most relevant chapters are all chapters until 15 with aspects of cell cycle in chapter 17 being discussed in the parallel Cellular Oncology course. 

Next you are challenged to choose a research topic of your prime interest on which you will work in the second part of the course  individually. You will also individually receive supervision by the Principal Investigator who is responsible for the area of research that you chose. 

In week 3 and 4 you work with your PI on the topic of interest and can consult the course coordinator on progress. One element of the work is that you will prepare a poster that is to be presented in the 4th week during a poster presentation session. The other element is that you are preparing your own essay on the field of choice that will be handed maximally one week after the end (of the 4th week) of the course.

Studiemateriaal

Literatuur

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

• Hand-outs of the lecturers

Software

• Depending on the needs of individual PI's

Overig

• Papers posted on Canvas

Leerdoelen

• 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.
• 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
• Werkcollege
• Presentatie/symposium
• Zelfstandig werken aan bijv. project/scriptie
• Begeleiding/feedbackmoment
• Zelfstudie

Lectures, assignments. The assignment involves a poster presentation and the generation of an essay regarding a chosen field of research. The 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 (individually with teachers): 20 hours 
Assignment: 120 hours (as unsupervised individual work) 
Writing the final thesis text and setting up the poster presentation 6 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:

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) counts for 75% of the final grade and is associated with the topic of choice. 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 lecturer can give advise and your fellow students will give feedback during the poster session. The mark is given by the researcher of the individual essay topic, and the  course coordinator.

   

  Source of information

  For each topic up to three papers are available. You have to find at least 2 other scientific papers on the subject and use those for your essay as well.

  Source of papers: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

   

  Outline of the essay

  Title

  Abstract

  Introduction

  Discussion of the subject, split up in separate paragraphs

  Conclusions

  References

   

Oral Presentation

• The topics will be presented orally in a poster presentation during a 5 minutes pitch, including a discussion. The poster is marked and counts for 25%.

Discussion on the Essay

• The discussion session - held at the poster 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.

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: http://student.uva.nl

Weekplanning

Honoursinformatie

NOTE that for the Research Honours students there may be parallel honours courses running. Contact MSB course coordinators in case of any scheduling conflict. 

Aanvullende informatie

Students must have successfully completed BSc1 Bio-medical Sciences and the BSc2 courses ‘Moleculaire Biologie en  Celbiologie’ or equivalent in other bachelor courses. Science faculty honours regulations apply for admission with this premise that biomedical science excellence track students have preference. The maximum number of participants is 16.

Maximum number of students is 16.

Contactinformatie

Coördinator

• prof. dr. Stanley Brul

Docenten

• dr. Renée van Amerongen
• prof. dr. L.W. Hamoen
• Hilde Herrema
• dr. R.H.L. Houtkooper
• dr. H.J. Krugers
• dr. Nina Scheres
• Age Smilde
• dr. P.J. Verschure
• dr. Meike Wortel
• dr. rer. nat. J. Zhang