Abstract: The present invention provides for the manipulation of cofactor usage in a recombinant host cell to increase the formation of desirable products. In some embodiments, the invention provides for a recombinant microorganism comprising a mutation in one or more native enzymes such that their cofactor specificity is altered in such a way that overall cofactor usage in the cell is balanced for a specified pathway and there is an increase in a specific product formation within the cell. In some embodiments, endogenous enzymes are replaced by enzymes with an alternate cofactor specificity from a different species.

Abstract: The present invention provides for the manipulation of carbon flux in a recombinant host cell to increase the formation of desirable products. The invention relates to cellulose-digesting organisms that have been genetically modified to allow the production of ethanol at a high yield by redirecting carbon flux at key steps of central metabolism.

Abstract: The present invention provides for the manipulation of carbon flux in a recombinant host cell to increase the formation of desirable products. The invention relates to cellulose-digesting organisms that have been genetically modified to allow the production of ethanol at a high yield by redirecting carbon flux at key steps of central metabolism.

Abstract: The present invention provides for the manipulation of cofactor usage in a recombinant host cell to increase the formation of desirable products. In some embodiments, the invention provides for a recombinant microorganism comprising a mutation in one or more native enzymes such that their cofactor specificity is altered in such a way that overall cofactor usage in the cell is balanced for a specified pathway and there is an increase in a specific product formation within the cell. In some embodiments, endogenous enzymes are replaced by enzymes with an alternate cofactor specificity from a different species.

Abstract: The present invention is directed to a process for biologically converting carbohydrates from lignocellulosic biomass comprising the steps of: suspending lignocellulosic biomass in a flow-through reactor, passing a reaction solution into the reactor, wherein the solution is absorbed into the biomass substrate and at least a portion of the solution migrates through said biomass substrate to a liquid reservoir, recirculating the reaction solution in the liquid reservoir at least once to be absorbed into and migrate through the biomass substrate again. The biological converting of the may involve hydrolyzing cellulose, hemicellulose, or a combination thereof to form oligosaccharides, monomelic sugars, or a combination thereof; fermenting oligosaccharides, monomelic sugars, or a combination thereof to produce ethanol, or a combination thereof. The process can further comprise removing the reaction solution and processing the solution to separate the ethanol produced from non-fermented solids.

Abstract: The present invention is directed to a process for biologically converting carbohydrates from lignocellulosic biomass comprising the steps of: suspending lignocellulosic biomass in a flow-through reactor, passing a reaction solution into the reactor, wherein the solution is absorbed into the biomass substrate and at least a portion of the solution migrates through said biomass substrate to a liquid reservoir, recirculating the reaction solution in the liquid reservoir at least once to be absorbed into and migrate through the biomass substrate again. The biological converting of the may involve hydrolyzing cellulose, hemicellulose, or a combination thereof to form oligosaccharides, monomelic sugars, or a combination thereof; fermenting oligosaccharides, monomelic sugars, or a combination thereof to produce ethanol, or a combination thereof. The process can further comprise removing the reaction solution and processing the solution to separate the ethanol produced from non-fermented solids.

Abstract: The present invention provides a bacterium having a genome that is genetically engineered to be at least 2 to 14% smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.

Abstract: The present invention provides a method for discovering the basis of changes in the observable properties of organisms by subjecting an organism to selection. Individual organisms with observable differences will thus become more prevalent in a population during selection. The basis for the differences are then determined by identifying genetic differences among the individual organisms and the original organism, followed by evaluation of the effects of each genetic difference either alone or in combination by using site-directed mutagenesis followed by observation of the effects.

Abstract: The present invention discloses that a bacterium having a genome that is genetically engineered to be at least 10% smaller than the genome of its native parent strain has better transformation competence. Specific E. coli strains, having significantly reduced genome sizes, are disclosed which are highly transformation competent. A medium and methodology is taught which enables transformation efficiencies to be increased further.

Abstract: The present invention provides a bacterium having a genome that is genetically engineered to be at least 2 to 14% smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.

Abstract: The present invention provides a bacterium having a genome that is genetically engineered to be at least 2 to 14% smaller than the genome of its native parent strain. A bacterium with a smaller genome can produce a commercial product more efficiently. The present invention also provides methods for deleting genes and other DNA sequences from a bacterial genome. The methods provide precise deletions and seldom introduces mutations to the genomic DNA sequences around the deletion sites. Thus, the methods can be used to generate a series of deletions in a bacterium without increasing the possibility of undesired homologous recombination within the genome. In addition, some of the methods provided by the present invention can also be used for replacing a region of a bacterial genome with a desired DNA sequence.