Genomic flux

Dover underlined that there is no rigid one-to-one relationship between evolutionary mechanisms and environmental processes, but noticed nonetheless that a certain correspondence does exist. He concluded therefore that adaptation is the normal result of natural selection just as exaptation is characteristic of neutral drift, and adoptation is typical of molecular drive. To our purposes, what matters is that we can indeed speak of three mechanisms of evolution the first two are natural selection and neutral drift, while the third mechanism can be called either genomic flux or molecular drive. 

C. H. Schilling, J. S. Edwards, and B. 0. Palsson, Towards metabolic phenomics Analysis of genomic data using flux balances. Biotechnol. Pmg. 15, 288 295 (1999). 

M. K. Hellerstein, In vivo measurement of fluxes through metabolic pathways The missing link in functional genomics and pharmaceutical research. Annu. Rev. Nutr. 23, 379 402 (2003). 

A. R. Fernie, P. Geigenberger, and M. Stitt. Flux an important, but neglected, component of functional genomics. Curr. Opin. Plant Biol. 8, 174 182 (2005). 

Furthermore, in rodents a member of a third class of NMDA receptor subunits (NR3A) has been cloned (Sucher et al., 1995). Expression of this NR3A subunit together with NR1 and NR2 subunits has been shown to cause in vitro an attenuation of the NMDA-induced ion fluxes and consequently NR3A knock-out mice show in vivo enhanced NMDA receptor activity (Das et al., 1998). Meanwhile a second member (NR3B) of this third class of subunit with comparable features has been cloned from mouse genome (Nishi et al., 2001). 

At each of these general steps, there are many molecular mechanisms that can be involved in drug handling that have a significant bearing on chemical genomics. For example, absorption should not be thought of as a passive process but as a dynamic flux, forwards and backwards, across a set of molecular barriers... 

Skulachev VP (1988) Membrane bioenergetics. Springer, Berlin Heidelberg New York Snel B, Bork P, Huynen MA (2002) Genomes in flux the evolution archaeal and proteobacter-ial gene content. Genome Res 12 17-25... 

In another example, comparative genome comparison was combined with constraints-based flux analysis to develop metabolic engineering strategies for the enhanced production of succinic acid by E. coli [1, 39, 40]. Comparative genome analysis of E. coli and M. succiniciproducens predicted five candidate genes to be manipulated for overproducing succinic acid in E. coli. Then, constraints-based flux... 

Wang Q, Chen X, Yang Y et al (2006) Genome-scale in silica aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production. Appl Microbiol Biotechnol 73 887-894... 

Hiiser AT, Chassagnole C, Lindley ND et al (2005) Rational design of a Corynebacterium glutamicum pantothenate production strain and its characterization by metabolic flux analysis and genome-wide transcriptional profiling. Appl Environ Microbiol 71 3255-3268... 

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