A mathematical approach to molecular organization and proteolytic disintegration of bacterial inclusion bodies

Mathematical Medicine and Biology

Volumn 22, Issue 3, 2005, Pages 209-226

  Cubarsi, R ^a   Carrio M M ^b   Villaverde, A ^b  

^a UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Finite mixtures; Ill conditioned problem; Least squares estimates; Ordinary differential equations; Sparse systems

Indexed keywords

APPROXIMATION ALGORITHMS; ESTIMATION; ITERATIVE METHODS; LEAST SQUARES APPROXIMATIONS; MIXTURES; NUMERICAL METHODS; ORDINARY DIFFERENTIAL EQUATIONS;

FINITE MIXTURES; ILL CONDITIONED PROBLEMS; IN-VIVO; INCLUSION BODIES; KINETIC ANALYSIS; LEAST SQUARES ESTIMATE; MATHEMATICAL APPROACH; MOLECULAR ORGANIZATION; PROTEOLYTIC DIGESTION; SPARSE SYSTEMS;

RECOMBINANT PROTEINS;

ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; CELL INCLUSION; ESCHERICHIA COLI; FRAGMENTATION REACTION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NONHUMAN; POISSON DISTRIBUTION; PREDICTION; PROTEIN DEGRADATION; REGRESSION ANALYSIS;

EID: 24044507957     PISSN: 14778599     EISSN: None     Source Type: Journal    
DOI: 10.1093/imammb/dqi007     Document Type: Article

References (17)

1. Björck, Å. (1996) Numerical Methods for Least Squares Problems Philadelphia, PA: SIAM.
2. Carrió, M. M., Cubarsi, R. & Villaverde, A. (2000) Fine architecture of bacterial bodies. FEBS Lett., 471, 7-11.
3. Carrió, M. M. & Villaverde, A. (2001) Protein aggregation as bacterial inclusion bodies is reversible. FEBS Lett., 489, 29-33.
4. Corchero, J. L., Cubarsi, R., Enfors, S.-O. & Villaverde, A. (1997) Limited in vivo proteolysis of aggregated proteins. Biochem. Biophys. Res. Commun., 237, 325-330.
5. Corchero, J. L., Viaplana, E., Benito, A. & Villaverde, A. (1996) The position of the heterologous domain can influence the solubility and proteolysis of β-galactosidase fusion proteins. J. Biotechnol., 48, 191-200.
6. Cubarsi, R., Carrió,M. M. & Villaverde, A. (2001) In situ proteolytic digestion of inclusion body polypeptides occurs as a cascade process. Biochem. Biophys. Res. Commun., 282, 436-441.
7. Cubarsi, R., Corchero, J. L., Vila, P. & Villaverde, A. (1998) Numerical techniques and mathematical modelling for CI857-controlled gene expression and cell growth in recombinant E. coli. IMA J. Math. Appl. Biol. Med., 15, 257-278.
8. D'Haeseleer, P., Liang, S. & Somogyi, R. (2000) Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
9. Friedman, N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
10. Kim, H., Golub, G. H. & Park, H. (2005) Missing value estimation for DNA microarray gene expression data: Local least squares imputation. Bioinformatics, 21, 187-198.
11. Kincaid, D. & Cheney, W. (1991) Numerical Analysis. Belmont, CA: Brooks-Cole Publishing.
12. Oba, S., Sato, M., Takemasa, I., Monden, M., Matsubara, K. & Ishii, S. (2003) A Bayesian missing value estimation method. Bioinformatics, 19, 2088-2096.
13. Papoulis, A. (1989) Probability, Random Variables, and Stochastic Processes. Singapore: MacGraw-Hill.
14. Stuart, A. & Ord, J. K. (1987) Kendall's Advanced Theory of Statistics, Vol. 2, Classical Inference and Relationship. London: Ch. Griffin.
15. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D. & Altman, R. B. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520-525.
16. Villaverde, A. & Carrió, M. M. (2003) Protein aggregation in recombinant bacteria: Biological role of inclusion bodies. Biotechnol. Lett., 25, 1385-1395.
17. Yeang, C.-H. & Jaakkola, T. (2003) Time series analysis of gene expression and location data. Proceedings of the Third IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003), IEEE Computer Society Press, Los Alamos, CA, pp. 305-312.