Tampere university of technology - Course Catalog 2013-2014

Course Catalog 2013-2014 Postgraduate
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Course Catalog 2013-2014

SGN-53806 Techniques in Molecular Biology and Applications to Gene Expression, 3 cr

Additional information

The course is lectured every year. Course webpage:http://www.cs.tut.fi/~sanchesr/SGN-53806/index.htm
Suitable for postgraduate studies

Person responsible

Andre Sanches Ribeiro

Lessons

Study type P1 P2 P3 P4 Summer Implementations Lecture times and places

Lectures

2 h/week

SGN-53806 2013-01 Tuesday 14 - 16, TB214

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

Journal Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR how well do they correlate?, Dallas, P. B., et al Yes    English

Journal Single-molecule approaches to stochastic gene expression Raj, A et al Yes    English

Journal Techniques: recombinogenic engineering new options for cloning and manipulating DNA Muyrers, J. P. P., et al Yes    English

Journal mRNA quantitation techniques: considerations for experimental design and application Reue, K Yes    English

Prerequisite relations (Requires logging in to POP)

Correspondence of content

Course Corresponds course Description

SGN-53806 Techniques in Molecular Biology and Applications to Gene Expression, 3 cr SGN-6266 Techniques in Molecular Biology and Applications to Gene Expression, 3 cr

More precise information per implementation

Implementation Description Methods of instruction Implementation

SGN-53806 2013-01 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.

Last modified 05.12.2012

Study type	P1	P2	P3	P4	Summer	Implementations	Lecture times and places
Lectures				2 h/week		SGN-53806 2013-01	Tuesday 14 - 16, TB214

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).

Type	Name	Author	ISBN	URL	Edition, availability, ...	Examination material	Language
Journal	Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR how well do they correlate?,	Dallas, P. B., et al				Yes	English
Journal	Single-molecule approaches to stochastic gene expression	Raj, A et al				Yes	English
Journal	Techniques: recombinogenic engineering new options for cloning and manipulating DNA	Muyrers, J. P. P., et al				Yes	English
Journal	mRNA quantitation techniques: considerations for experimental design and application	Reue, K				Yes	English

Course	Corresponds course	Description
SGN-53806 Techniques in Molecular Biology and Applications to Gene Expression, 3 cr	SGN-6266 Techniques in Molecular Biology and Applications to Gene Expression, 3 cr

Implementation	Description	Methods of instruction	Implementation
SGN-53806 2013-01	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.

Course Catalog 2013-2014 Postgraduate

Course Catalog 2013-2014