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 (2nd ed, both 2009 and 2012 versions OK).¶ -Strachan and Read: Human molecular genetics (4th ed 2010)¶ -Brown TA: Gene cloning and DNA analysis (6th ed 2010)¶ -Glick, Pasternak, and Patten: Molecular Biotechnology (4th 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 ABB1190 Course schedule and reading