Course Catalog 2009-2010 International Basic Pori International Postgraduate Open University |Degrees|     |Study blocks|     |Courses|

Person responsible

Andre Sanches Ribeiro

Implementations

	Lecture times and places	Target group recommended to
Implementation 1	Per 4 : Thursday 14 - 16, TB215

Requirements

Project work (30% of the final grade), take-home exercises (30% of the final grade) and final assignment(40% of the final grade). To pass the course, the student is required to: a) execute all three requirements. b) Attend and complete at least 50% of the exercises lessons.

Learning outcomes

The student will be introduced to a variety of current experimental techniques in molecular biology. The aim is to provide an understanding of the techniques and how to interpret results. The focus of this course will be manipulation and analysis of gene expression in prokaryotic systems, though eukaryotic tools will be briefly described. Students will become familiar with common wet-lab methods used in various fields in biology, and gain an understanding of the objectives, applicability and limitations underlying each of these methods. After the course, the student will be able to: 1) Identify, list and define common techniques used in genetic engineering and gene expression analysis, 2) Interpret data generated from the techniques discussed, classify strengths and weaknesses of the methodologies, summarize results and methods, infer consequences of results, explain procedures. 3) Apply the acquired knowledge to better interpret degrees of confidence in experimental results. 4) Deconstruct results of gene expression measurements. Compare different methodologies for verifying a hypothesis or measuring a variable. 5) Compare and appraise related methods in gene expression studies, and interpret and comment conclusions in such studies, 6) Create and develop an experimental procedure using the methods learned, that can address simple questions regarding gene expression.

Content

Content	Core content	Complementary knowledge	Specialist knowledge
1.	The structure, design and applicability of the bacterial plasmid vector to clone a gene of interest and express protein. Methods used in subcloning, such as PCR, DNA synthesis and sequencing and the process of DNA transfer will be reviewed.
2.	The introduction of genomic insertion by homologous recombination. Methods used to evaluate proper gene insertion, such as Northern and Southern blots, and introduction of mutations by site directed mutagenesis, will be reviewed.
3.	Studies of bacterial gene expression. A number of methods used to detect and quantify changing RNA levels due to external stress will be reviewed. Students will be given a summary of multi-cell techniques, including real-time PCR, serial analysis of gene expression (SAGE), and microarray analysis.
4.	Studies of variability in bacterial gene expression at the single cell level, with an emphasis on cell-to-cell variation. Techniques which are capable of counting individual mRNAs will be evaluated, including fluorescence in situ hybridization (FISH), real-time measurements and single-cell RT-PCR will be reviewed.
5.	Application and analysis of PCR method. This week will involve a wet laboratory experiment. This component will give students hands-on experience in a common molecular biology technique. Over two days (90 min each), students will set up PCR experiments followed with restriction digestion to amplify and verify, respectively, a select region of the luciferase gene.
6.	The theory and practice of fluorescence microscopy, as used to test for protein expression and localization. The advantages and challenges of this technique will be reviewed, by examining the use of fluorescent tags, such as Green Fluorescent Protein (GFP).

Study material

Type	Name	Author	ISBN	URL	Edition, availability, ...	Examination material	Language
Book	Biology of Microorganisms	Madigan, A. T., Martinko, J.M., Dunlap, P.V. and Clark, D.P.			Page 57-65 and all of Chapter 7. This material gives a review of what is expected to be known for this course.		English
Book	Biology of Microorganisms	Madigan, A.T., Martinko, J.M., Dunlap, P.V. and Clark, D.P.			Chapter 12. This chapter onlines several of the methods introduced in this course.		English
Journal	Cloning and mutagenesis, tinkering with the order of things	Smith, C.					English
Journal	Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR, how well do they correlate?	Beesley, A. H., Hoffmann, K., Terry, P. A., Freitas, J. R. and Boag, J. M					English
Journal	Single-molecule approaches to stochastic gene expression	Raj, A and van Oudenaarden, A.,					English
Journal	mRNA quantitation techniques: considerations for experimental design and application	Reue, K					English

Prerequisites

Additional information about prerequisites
Basic knowledge of biology/systems biology/cell biology, e.g. Introduction to Computational Systems Biology (SGN-6056) or equivalent.

Correspondence of content

Additional information

The course is lectured every year. Course webpage:http://www.cs.tut.fi/~sanchesr/SGN-6237/index.htm

More precise information per implementation

	Description	Methods of instruction	Implementation
Implementation 1	The student will be introduced to a variety of current experimental techniques in molecular biology. The aim is to provide an understanding of the techniques and how to interpret results. The focus of this course will be manipulation and analysis of gene expression in prokaryotic systems, though eukaryotic tools will be briefly described. Students will become familiar with common wet-lab methods used in various fields in biology, and gain an understanding of the objectives, applicability and limitations underlying each of these methods.