Last updated: 12/18/11 16:01
Biology w3034/W4034: Biotechnology

2011 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

PART I: PROFESSOR DANIEL KALDERON **The readings listed for each topic should be done BEFORE arriving to lecture for that topic. **

 

DATE

OUTLINE

POWERPOINT

TOPICS

DALE AND SCHANTZ

STRACHAN & READ

OTHER  REFERENCES

1

9/7/11

Topic 1

Topic 1.ppt

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

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

217-219, 192-207

Reviews, articles and Web sites

2

9/12/11

3

9/14/011

Topic 2

Topic 2.ppt

DNA CLONING
 Ligase-free cloning, Site-directed mutagenesis

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

 164-177, 214-217, 182-189

Reviews, articles and Web sites

4

9/19/11

5

9/21/11

6

9/26/11

7

9/28/11

Topic 3

Topic 3.ppt

DNA MAPPING, GENOME SEQUENCING, 2ND GENERATION SEQUENCING
Clone contigs; Hierarchical sequencing; Genome shotgun sequencing; 2nd generation sequencing

113-115, 164-167, 251-261

 220-235

Reviews, articles and Web sites

8

 10/3/11

9

__

10

10/5/11

 __________

10/10/11

Topic 4

Topic 4.ppt

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

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

 235-245, 372-375, 274-288, 362-264, 207-211, 245-253

Reviews, articles and Web sites

Topic 5

Topic 5.ppt

CLONING DISEASE GENES & GENETIC TESTING
Recombination mapping; Candidate gene testing; Testing for inherited mutations; Genome-wide association studies

273-275, 287-305

 62-70, 442-464, 479-494, 498-515, 519-535, 570-591

Reviews, articles and Web sites

11

10/12/11

12

10/17/11

13

10/19/11

  

Topic 6

 

 Topic 6.ppt STUDYING PROTEIN FUNCTION
Producing protein from DNA; Protein-protein interactions		 275-6, 279-299

178-182, 396-400

 

 

Reviews, articles and Web sites

14

10/24/11

 Monday

 

MID-TERM EXAM

 

 
 

2011 Lecture Schedule & Readings: Second half, Chasin lectures.

The list below is initially based on the material from 2010 in brown). The 2011 material and schedule will be similar and will appear as we go along, appearing in black. Powerpoints are usually not posted until the morning before class. Profcast files present the PowerPoints synchronized to the audio of the lecture. They are best viewed by downloading and viewing with QuickTime rather than playing within the browser. In FireFox, you can download by right-clicking and choosing "Save link as."  Windows Media Player v.11 or later may work.

PART II: PROFESSOR LAWRENCE CHASIN               Last updated Sunday, December 18, 2011 04:01 PM

DATE

POWER
POINT

(brown links work)

Planned Lecture TOPIC
 (brown links do not work)

READINGS in preparation for the class 
 (brown links do not work)
Wed.
Oct.26, 2011   

Class 15

Third generation DNA deep sequencing. Applications of deep sequencing. Profcast

High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Luca Mannoccia et al. PNAS 105:17670–17675, 2008. Example of a novel sequencing application for drug discovery. Chemical details not important here.

Mon.
Oct.31, 2011		 Class 16 Some DNA sequencing applications. Some more site-directed mutagenesis. Gene expression systems. Useful promoters.
mp3  wma Profcast

Dale and von Schantz: 224-225, 241-251, 279-305
Strachan and Read: 144-154, 545-558
 
Wed.
Nov.2, 2011 

Class 17

Gene expression systems: yeast,  mammalian cells. Promoters. Transcription. DNA binding proteins. RNA analysis. mp3  wma Profcast

 Animal cell culture:  Lodish (online chapter) 
For next time: Clonal selection and in vivo quantitation of protein interactions
with protein-fragment complementation assays, I. Remy and S.W. Michnick
PNAS 96, 394–5399, 1999
Mon.
Nov.7, 2011  		  Academic holiday  
Wed.
Nov.9, 2011    		 

Class 18
 

 RNA analysis. Protein-protein interaction measurement.  Yeast 2-hybrid system.
mp3   wma  Profcast (audio lost after 30%)

 

 

Dale and von Schantz: 10.2 to 10.3.3; 11.3.3.
Read after this class: Imaging individual mRNA molecules using multiple singly labeled probes. A.Raj, P. van den Bogaard, S. A. Rifkin, A.van Oudenaarden & S. Tyagi. Nat. Meth. 5: 877-879, 2008
Mon. .
Nov.14, 2011		   Class 19 Fragment complementation assay. Fluorescence activated cell sorter (FACS).2nd generation recombinant therapeutic proteins. (Rice et al.) Profcast  mp3 wma

READ FOR Monday Nov. 14:

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.16, 2011   

Class 20
 

Mammalian cell genetics. Drug resistances; selective medium, cell fusion, cell hybrids, transfection.    Profcast.  mp3 wma

Paper on targeted mutagenesis in vitro:

Santiago et al., (2008) Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. PNAS 105: 5809–5814.

Purine and TMP Metabolism:  the biosynthetic pathways

Legend to biosynthetic pathways figure.

 For more details about  biosynthetic paths, see chapter from Garret and Grisham's Biochemistry 
Mon..
Nov.21, 2011   

Class 21

 

Transfection. Gene amplification, co-amplification, high level recombinant protein production in mammalian cells.  
  No Profcast    mp3   wma		  
Wed.
Nov. 23, 2011 

Class 22
 

Immunoglobulin structure and function.  Antibody-dependent cellular cytotoxicity. Monoclonal antibody synthesis;  hybridomas.  mp3  wma  Profcast

Monoclonal antibodies:

Strachan and Read: 683-685, In Janeway et. al., Immunobiology (online): A-12. Monoclonal antibodies. Antibodies and the immune system overview: Strachan and Read: 119-131
Mon.
Nov. 28, 2011 

Class 23
 

Single chain antibodies. Phage display. Glycosylation of proteins. Manipulating protein glycosylation.. mp3  wma  Profcast

Glycosylation:  Stryer (online): Glycoproteins (Sec.11.3 incl. figs.)
 Naoko Yamane-Ohnuki, et al.  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
Wed.
Nov.30, 2011    		Class 24
 

Creation of new antibodies: ribosome display. Synthetic antibody libraries.  DNA shuffling. 
Profcast  No mp3, wma :(

 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.
Mon.
Dec.5, 2011   

Class 25

More  DNA shuffling. Receptor domain shuffling.

Pre-mRNA splicing as a therapeutic target.

mp3 wma Profcast
Dendrion.MP3   Dendrion.WMA

 OPTIONAL: RNA splicing correction: Aurélie Goyenvalle et al., Rescue of Dystrophic Muscle Through U7 snRNA-Mediated Exon Skipping Science  2004:Vol. 306. no. 5702, pp. 1796 - 1799 =OPTIONAL
Wed.
Dec.7, 2011		 Class 26 Pre-mRNA splicing as a therapeutic target. RNAi.
mp3    wma    Profcast (Twist only)		 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).
OPTIONAL:  DNAzymes;  C Frauendorf, A Jaschke. Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem (2001) 9-10:2521-4.
Mon.
Dec.12, 2011 		Class 27 RNAi cont. RNA and DNA aptamers. Ribozymes. DNAzymes  
Metabolic engineering not covered
mp3   wma      Profcast

OPTIONAL: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).
Wed.
Dec.21, 2011 1:10PM to 4:00 PM		 Final Exam
517 Hamilton

FINAL EXAM

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

          (Dr. Kalderon's lectures after the midterm will not be explicitly covered)Questions on papers will not require detailed recollections but will seek evidence that the  paper has been read and understood beyond the Abstract. Papers marked OPTIONAL will not be included. There will be no question on purine metabolism and selection. There will be a question on aptamers/DNAzymes/ribozymes. Otherwise all topics are fair game but not all will be covered. Lat year's exam and most answers can be found on the Homework and Exams page.