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BB1190 Schedule

BB1190 VT15 P4: Genteknik och molekylärbiologi

Updated: 18 MAR 2015

Instructor

Bitr. Lektor Paul Hudson huds@kth.se / Office: Gamma 5 Science for Life Laboratory

Doodle to sign up for laboratory week: http://doodle.com/5xs9yu58zne4ku3a

Course Schedule

No.	Date	Time	Room	Lecture Title	Key Concepts	Preparatory Reading (before lecture)
1	M 23/03	08-10	FD5	Biology and biotechnology	-Early molecular biotech -Fundamentals	-Ch. 2 C&P DNA, RNA, Protein (p 33-58) -Zimmer: E.coli and the elephant (excerpt)
2	W 25/03	08-10	FD5	Gene structure and genome organization	-What is a gene? -Chromosomes and complexity	-Ch. 9 Strachan: Human genome (all) -Optional: Gregory 2014: Junk DNA
3	F 27/03	10-12	FD5	DNA synthesis and sequencing.	-PCR theory and application -DNA sequencing	-Ch. 4 C&P DNA Synthesis (all) -Opt: Ch 9 Brown: PCR -Opt: Ch 10 Brown: DNA Seq
4	M 30/03	13-15	FD5	DNA cloning: building genes and genomes	-Cloning eukaryotic DNA -Cloning methods
5	T 31/03	08-10	FD5	In class problem 1: Genome assembly	-Individual work (1 hr) -Peer review of answers (1 hr)	-Church 2009: Genome engineering
6	W 01/04	13-15	FD5	Genetic engineering of E.coli	-Plasmids -Homologous recombination -Laboratory strains	-Ch. 3 C&P Recombinant DNA (p 79-88) -Ch. 13 Brown: Proteins from cloned genes
7	T 14/04	13-15	FD5	Designing a cell factory	-Bioinformatics tools -Metabolic modeling	-Keasling 2009: Manufacturing molecules -Palsson 2010: Flux balance analysis
8	H 16/04	10-12	FR4	In class problem 2: Cell factory	-Group work (1 hr) -Peer-grading (1 hr)	-Ch. 13 C&P Pathway Eng. (p 371-385)
9	T 21/04	13-15	FD5	Molecular dioagnostics Lektor Peter Savolainen	-SNP analysis -Forensic analysis	-Ch. 3 C&P Recombinant DNA (p. 63-73) -Ch. 24 C&P Forensics (all)
10	H 23/04	10-12	FD5	Antibody engineering	-Antibody diversity in the genome -Natural antibody libraries	-Ch 6 C&P: Antibodies (p 173-191) -Opt: Ch 10 Glick, Antibodies (p 399-422)
11	M 27/04	15-17	FD5	In class problem 3: Antibody development	-Individual work (1 hr) -Peer review (1 hr)
12	W 29/04	10-12	FD5	Protein engineering Prof Per Åke Nygren	-Rational protein engineering -Directed evolution of proteins	-Ch 11 C&P: Protein Engineering (all) -Opt: Baker 2011 Prot eng overview
13	M 04/05	10-12	FD5	Vaccine creation	-Case study: Influenza vaccines -Case study: HIV vaccines	-Ch 6 C&P: Vaccines (p 191-201) -Opt: Ch 12 Glick, Vaccines (p. 460-472)
14	H 07/05	10-12	FD5	Cancelled
15	M 11/05	10-12	FD5	Gene therapy	-Case: Glybera -Case: Zinc-finger nucleases	-Ch 17 C&P: Gene Therapy (all) -Ch 5 C&P: Ribozymes (p 152-168)
16	T 12/05	8-10	FD5	Synthetic biology	-Simple gene regulation -Genetic logic	-Alon 2007: Network motifs (p 450-455) -Opt: Collins 2014, Synbio history
17	W 13/05	13-15	FD5	Applied genomics Lektor Anders Andersson	-Genome reconstruction -Case: Metagenomics Baltic Sea	-Ch. 12 C&P: Environ. Biotech (all)
R1	M 18/05	10-12	FD5	In class problem 4: Synthetic biology	-Group work (1 hr) -Peer-grading (1 hr)
R2	M 25/05	08-12	Q2	Review session	-Peer grading assigned problems	Do the assigned problems
Ex	W 03/06	14-19	FB 52-54	Exam

Laboratory

You will be provided with a laboratory manual (Uploaded)

Helpful texts (optional) for lab are from Brown: Ch 3 “Purification of DNA from cells,” and Ch 5 “Introduction of DNA into cells.” (Uploaded)

Course reading materials

C&P text I assume you have. Selections from others will be uploaded. Optional are not required but typically give more detail in an area.

-C&P: Clark and Pazdernik Biotechnology (2^nd ed, both 2009 and 2012 versions OK).

-Strachan and Read: Human molecular genetics (4^th ed 2010)

-Brown TA: Gene cloning and DNA analysis (6^th ed 2010)

-Glick, Pasternak, and Patten: Molecular Biotechnology (4^th ed 2010)

Grading

Final grade is the exam grade. Exam will be based on what we cover in class and the assigned reading, unless explicitly written as Optional.

Grading rubric: <50 F, 50-60 E, 60-70 D, 70-80 C, 80-90 B, 90-100 A