Teaching

Molecular Systems Bioengineering Laboratory

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Integrative Molecular and Cellular Bioengineering

16:125:584, Spring 2007

Meets Tues./Fri., 8:40-10:00 a.m. in BME-128

Contact information

Instructor	Professor Charles M. Roth
Office	BME 205
Email	cmroth@rci.rutgers.edu
Office hours	By appointment

Course outline (as of 3/23/07)

Textbooks :

There is no textbook to adequately cover the course material. A set of readings will be posted on the course website. In addition, it is recommended that students have one of the following texts as a reference:

Bruce Alberts et al., Molecular Biology of the Cell, 4th. ed. Garland Pub., 2002 (ISBN: 0815332181).
Or Harvey Lodish et al., Molecular Cell Biology. W.H. Freeman and Company, 1995 (ISBN: 071673706X)

Date	Topic	Reading
I. Molecular Building Blocks: Genomics, Proteomics and Bioinformatics
Jan 16	Organization of the genome (guest lecture: Prof. Li Cai)	Wasserman and Sandelin, Nat. Rev. Genet., 5:276 (2004).
Jan 19	Course introduction
Jan 23	Large-scale sequencing methodologies and genetic diagnostics	Science Sequencing Collection
Jan 26	Gene expression measurements – DNA microarrays	Baker et al., Chem. Res. Toxicol., 14:1218 (2001).
Jan. 30	Gene expression measurements – DNA microarrays (cont'd)
Feb 2	Gene expression measurements – real-time PCR	Ding and Cantor , J. Biochem. Mol. Biol., 37:1 (2004).
Feb 6	Genetic engineering	Coco et al., Nature Biotechnol., 20 :1246 (2002).
Feb 9	Gene transfer and gene silencing	Chiu et al., Chem. Biol., 11:1165 (2004).
Feb 13	Gene transfer and gene silencing (cont'd)
Feb 16	Structure and function of proteins	Squires, Science, 295:1002 (2002).
Feb 20	Protein molecular recognition	Boder et al., PNAS, 97:10701 (2000).
Feb 23-27	Proteins at surfaces – adsorption and biocompatibility	Yoon et al., Biotechnol. Bioeng., 78:1 (2002).
Mar 2-20	Protein detection and quantitation	Iwadate et al., Cancer Res., 64:2496 (2004).
Mar 6	First Exam
Mar 9	BME Showcase
Mar 10-18	Spring Break
II. Molecular Networks and Systems in a Cellular Context
Mar 20-23	Ligand-receptor trafficking	Andrews and Arkin, Curr. Biol., 16:R523 (2006).
Mar 30	Metabolic engineering	Gombert and Nielsen, Curr. Opin. Biotechnol., 11:180 (2000).
Mar 27	Biomolecular networks and pathways (guest lecture : Prof. Ioannis Androulakis)	Barabasi and Oltvai, Nat. Rev. Genetics, 5:101 (2004)
April 10	Synthetic biology	Elowitz and Liebler , Nature, 403:305 (2000).
III. Understanding and Engineering Cell Phenotypes
April 3	Cell cycle and proliferation
April 6	Stem cell bioengineering (guest lecture -- Natesh Parashurama, MD)	Metallo et al., Biotech. Prog., 23:18 (2007) Pritsker et al., PNAS, 103:6946 (2006)
April 13	Cell-cell communication	Khetani et al., Hepatology, 40:545 (2004).
April 17	Classes canceled -- flooding
April 20	Drug delivery – controlled release Drug delivery – targeted delivery	Shea et al., Nature Biotechnol., 17:551 (1999)
April 24	Lab demo: Flow cytometry (Lavanya Peddada; report to ENG C-261)
April 27	Final project presentations

Assessment and Evaluation

Your grade in the course will be based on assessments in the following areas:

Grades will be based on the following formula:
            Homework and Lab Reports; Class Participation            40%
            Integrative Project                                                     40%
            Exams (1)                                                                 20%

Assignments

Assignment	Due Date	Solution
HW1	January 30 (Tues.)	solution hw1 position weight matrix matlab code
HW2 Baker data	February 13 (Tues.)	solution hw2 fibronectin hits immediate early genes
HW3	March 2 (Fri.)	solution hw3
HW4	April 20 (Fri.)
Lab report (extra credit) Lab demo data	May 4 (Fri.)

Exams

Exam 1, Spring 2006

Term Project

Please read the Term Project Instructions and pay heed to the due dates.