Last updated: 11/25/09 17:44
Biology W3034/W4034: Biotechnology

2009 Lecture Schedule & Readings: Second half, Chasin lectures.

Always subject to change.  Powerpoints usually not posted until just before class.  

PART II: PROFESSOR LAWRENCE CHASIN               Last updated Wednesday, November 25, 2009 05:44 PM

MAMMALIAN CELL GENETICS cont.:  mutants cont.;

DATE

POWER
POINT

Planned Lecture TOPIC

READINGS in preparation for the class 
Mon.
Nov. 9, 2009   

Class 17

High throughput DNA sequencing

 

Link to addl. reading                          WMA   MP3

Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky
S, Milos P, Causey M. Quantification of the yeast transcriptome by
single-molecule sequencing. Nat Biotechnol. 2009 Jul;27(7):652-8.
  Wed.
Nov. 11, 2009  		Class 18 Class 18 + 19: IN VITRO & mammalian cell culture assays of gene function. Protein from cloned genes; cell hosts; promoters, inducible promoters                                                       MP3

Dale and von Schantz: 224-225, 241-251, 279-305
Strachan and Read: 144-154, 545-558
 
Mon.
Nov. 16, 2009 

Class 19

Some more site-directed mutagenesis; protein-protein interactions, protein-DNA interactions, yeast 2-hybrid systems, DNA microarrays, CHIP-Chip vs. Chip-Seq; Fluorescence activated cell sorter (FACS).

                                        No audio available

 GC Rice, DV Goeddel, G Cachianes, J Woronicz, EY Chen, SR Williams, and DW Leung. Random PCR mutagenesis screening of secreted proteins by direct expression in mammalian cells. PNAS 1992; 89:5467-5471
Wed.
Nov. 18, 2009    		 

Class 20
 

 Catch up                              WMA            MP3

Animal cell culture:  Lodish (online chapter)
Purine and TMP Metabolism:  Biosynthetic pathways

Legend to biosynthetic pathways figure.

For more details about  biosynthetic paths, see chapter from Garret and Grisham's Biochemistry
Mon.
Nov. 23, 2009    		 

Class 21
 

Class 20+21: MAMMALIAN CELL GENETICS:

Cultured mammalian cells as microorganisms; cell mutants     MP3
Wed.
Nov. 25, 2009   

Class 22
 

Drug resistances; selective medium,

cell fusion, cell hybrids, transfection;  gene amplification, co-amplification, high level recombinant protein production in mammalian cells.                     MP3

  
Mon..
Nov. 30, 2009   

Class 23

 

IMMUNOGLOBULIN STRUCTURE AND FUNCTION

Monoclonal antibody synthesis; hybridomas

Antibody-dependent cellular cytotoxicity

Monoclonal antibodies:

Strachan and Read: 613-616

In Janeway et. al., Immunobiology (online): A-12. Monoclonal antibodies.

 
Wed.
Dec. 2, 2009 

Class 24
 

Glycosylation of proteins.

Second generation monoclonal antibodies: Manipulating protein glycosylation

Glycosylation:  Stryer (online): Glycoproteins (Sec.11.3 incl. figs.)

 

Naoko Yamane-Ohnuki, Satoko Kinoshita, Miho Inoue-Urakubo, Machi Kusunoki, Shigeru Iida, Ryosuke Nakano, Masako Wakitani, Rinpei Niwa, Mikiko Sakurada, Kazuhisa Uchida, Kenya Shitara, Mitsuo Satoh.  Establishment of FUT8 knockout Chinese hamster ovary cells: an ideal host cell line for producing completely defucosylated antibodies with enhanced antibody-dependent cellular cytotoxicity.   Biotechnol Bioeng. 2004 Sep 5;87(5):614-22
Mon.
Dec. 7, 2009 

Class 25
 

DIRECTED EVOLUTION and CREATION of NEW PROTEINS:

DNA shuffling, domain shuffling, protein evolution in vitro

 Ribosome display selection:
Hanes, J., Schaffitzel, C., Knappik, A., and Pluckthun, A. 2000. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat Biotechnol 18: 1287-1292.

DNA shuffling:
Maxygen Website: Publications on DNA shuffling. OPTIONAL
Wed.
Dec. 9, 2009    		Class 26
 

RNA-TARGET THERAPY:

Antisense RNA, RNAi, correction of splicing defects

APTAMERS AND RIBOZYMES AS THERAPEUTICS AND BIOSENSORS:

Selection of oligomers that bind a target, aptamers as alternatives to MAbs 

 RNA splicing correction:
Aurélie Goyenvalle, Adeline Vulin, Françoise Fougerousse, France Leturcq, Jean-Claude Kaplan, Luis Garcia, Olivier Danos.  Rescue of Dystrophic Muscle Through U7 snRNA-Mediated Exon Skipping Science 3 December 2004:Vol. 306. no. 5702, pp. 1796 - 1799
Aptamers:
 CP Rusconi, E Scardino, J Layzer, GA Pitoc, TL Ortel, D Monroe, and BA Sullenger. RNA aptamers as reversible antagonists of coagulation factor IXa.  Nature 419: 90-94 (2002).

C Frauendorf, A Jaschke. Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem (2001) 9(10):2521-4.

Mon.
Dec. 14, 2009   

Class 27
 

 ENGINEERING METABOLISM Sunilkumar, G., Campbell, L. M., Puckhaber, L., Stipanovic, R. D., Rathore, K. S. Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. Proc Natl Acad Sci 48: 18054-9 (2006)
Mon.
Dec. 21,
2009
4:10-7:00 		Final Exam

FINAL EXAM

Focused directly on material of the latter half of course, but assuming knowledge of the first half.

 

 

2009 Lecture Schedule & Readings: First half, Kalderon lectures

"OUTLINE" links will let you see lecture notes. "POWERPOINT" links will let you download the PowerPoint slides used in the lecture.
Free PowerPoint viewer: Windows, Mac

**The readings listed for each topic should be done BEFORE arriving to lecture for that topic. **

PART I: PROFESSOR DANIEL KALDERON 

 

DATE

OUTLINE

POWERPOINT

TOPICS

DALE AND SCHANTZ

STRACHAN & READ

OTHER  REFERENCES

1

9/9/09

Topic 1

Topic 1.ppd

BASIC NUCLEIC ACID MANIPULATION
 DNA purification; DNA synthesis; Enzymes;     Electrophoresis; Sequencing; Hybridization

33-49, 299-300, 159-163, 133-134, 117-124

182-185, 156-175

Related Websites 1

2

9/14/09

3

9/16/09

Topic 2

Topic 2.ppd

DNA CLONING
 Vectors; Practical cloning; Libraries;
Basic PCR

25-30, 61-69, 49-57, 69-78, 95-112, 122-128, 78-81, 92-95,135-147, 57-60

 129-136, 140-146, 122-129

 Related Websites 2

4

9/21/09

5

9/23/09

6

9/28/09

Topic 3

Topic 3.ppd

PHYSICAL GENOME MAPPING
Clone contigs; Hierarchical sequencing; Genome shotgun sequencing

113-115, 164-167, 251-261

 213-220, 226-235

Reviews and Articles

3-1, 3-2, 3-3,

7

9/30/09

Topic 4

Topic 4.ppd

GENE CHARACTERIZATION
 Empirical definition of RNA & protein products; Sequence-based prediction of
gene products; Regulation of gene expression

106-112, 201-208, 147-154, 217-219, 167-196, 261-273, 313-326

 186-202, 221-4, 250-252, 291-294, 175-178, 545-553

Reviews and Articles

4-1, 4-2, 4-3, 4-4, 4-5, 4-6, 4-7,4-8

8

10/5/09

9

10/7/09

Topic 5

Topic 5.ppd

CLONING DISEASE GENES & GENETIC TESTING
 Recombination mapping; Candidate gene testing; Testing for inherited mutations

273-275, 287-305

 102-108, 398-413, 416-433, 510-524, (462-483), (616-629)

Reviews and Articles

5-1

10

10/12/09

11

10/14/09

12

10/19/09

 Topic 6 Topic 6.ppd STUDYING PROTEIN FUNCTION
 Making protein;
Protein -protein interactions;
Site directed mutagenesis		 190-196, 81-92, 221-247, 128-130

147-154,562-572, 144-146 

 Reviews and Articles

6-1, 6-2, 6-3, 6-4, 6-5, 6-6

13

10/21/09

Topic 7

Topic 7.ppd

STUDYING GENE EXPRESSION
 Promoter/ Enhancer mapping;
Protein-DNA interactions

209-217

  276-288

Reviews and Articles

14

10/26/09

 Monday

 

MID-TERM EXAM