Abstract: Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received, each such request specifying a genetic change to L. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion of ARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.

Abstract: Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received, each such request specifying a genetic change to L. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion ofARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.

Abstract: The present invention provides genetically modified host cells and use of same for producing isoprenoid compounds.

Abstract: Provided herein are, among other things, jet fuel compositions and methods of making and using the same. In some embodiments, the fuel compositions comprise at least a fuel component readily and efficiently produced, at least in part, from a microorganism. In certain embodiments, the fuel compositions provided herein comprise a high concentration of at least a bioengineered fuel component. In further embodiments, the fuel compositions provided herein comprise a C10 bicyclic isoprenoid such as carane, pinane, sabinane or a combination thereof.

Abstract: Provided herein are, among other things, jet fuel compositions and methods of making and using the same. In some embodiments, the fuel compositions comprise at least a fuel component readily and efficiently produced, at least in part, from a microorganism. In certain embodiments, the fuel compositions provided herein comprise a high concentration of at least a bioengineered fuel component. In further embodiments, the fuel compositions provided herein comprise limonane.

Abstract: Provided herein are composition comprising a farnesene interpolymer. The farnesene interpolymer can be derived from a farnesene and at least one vinyl monomer. In some embodiments, the mole percent ratio of the farnesene to the at least one vinyl monomer is from about 1:4 to about 100:1. In certain embodiments, the farnesene is ?-farnesene, ?-farnesene or a combination thereof. In some embodiments, the at least one vinyl monomer is ethylene, an ?-olefin such as styrene, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: Provided herein are farnesene interpolymers derived from a farnesene and at least one vinyl monomer. In certain embodiments, the farnesene is ?-farnesene, ?-farnesene or a combination thereof. In some embodiments, the at least one vinyl monomer is ethylene, an ?-olefin such as styrene, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: Provided herein are composition comprising a farnesene interpolymer. The farnesene interpolymer can be derived from a farnesene and at least one vinyl monomer. In some embodiments, the mole percent ratio of the farnesene to the at least one vinyl monomer is from about 1:4 to about 100:1. In certain embodiments, the farnesene is ?-farnesene, ?-farnesene or a combination thereof. In some embodiments, the at least one vinyl monomer is ethylene, an ?-olefin such as styrene, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: Provided herein are farnesene interpolymers derived from a farnesene and at least one vinyl monomer. In certain embodiments, the farnesene is ?-farnesene, ?-farnesene or a combination thereof. In some embodiments, the at least one vinyl monomer is ethylene, an ?-olefin such as styrene, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: A fuel composition comprises at least a C5 isoprenoid compound or its derivative and a conventional fuel additive. The C5 isoprenoid compound or its derivative can be used as a fuel component or as a fuel additive in the fuel composition. The fuel composition may further comprise a conventional fuel component selected from a diesel fuel, jet fuel, kerosene or gasoline. Methods of making and using the fuel composition are also disclosed.

Abstract: A fuel composition comprises farnesane and/or farnesane derivatives and a conventional fuel component selected from diesel fuel, jet fuel, kerosene or gasoline. The farnesane or farnesane derivative can be used as a fuel component or as a fuel additive in the fuel composition. The fuel composition may further comprise a conventional fuel additive. Methods of making and using the fuel composition are also disclosed.

Abstract: The invention provides methods and systems for selecting and blending conventional fuel components into fuel compositions using an input system and for supplying a selected fuel composition into a storage container. The methods and systems incorporate a mixer to mix at least one conventional petroleum-derived fuel component received from the conventional fuel component supply system with at least one second non-petroleum fuel component received from the second fuel component supply to form fuel compositions. The present invention provides for systems and methods of supplying selected blends of conventional petroleum fuel with a non-petroleum derived fuel to provide greater consumer accessibility for petroleum blended with alternative fuels.

Abstract: A method for producing isoprene comprising an aqueous medium including genetically modified host cells capable of producing isoprene, where the resulting isoprene composition is processed through at least one separation and/or purification process to provide an isoprene enriched composition and a system for doing the same.

Abstract: A fuel composition comprises at least a tetramethylcyclohexane and a fuel component. The tetramethylcyclohexane can be used as a fuel component or as a fuel additive in the fuel composition. The fuel composition may further comprise a conventional fuel component selected from a petroleum-based fuel component such as diesel fuel, jet fuel, kerosene or gasoline; or a coal-based fuel component. Methods of making and using the fuel composition are also disclosed.

Abstract: Provided herein are compositions comprising a polyfarnesene. The polyfarnesene can be a farnesene homopolymer derived from a farnesene (e.g., ?-farnesene or ?-farnesene) or a farnesene interpolymer derived from a farnesene and at least a vinyl monomer. In some embodiments, the at least one vinyl monomer is ethylene, an ?-olefin such as styrene, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: Compositions comprising a farnesane dimer and/or a farnesene dimer and a compound selected from squalene, squalene and dehydrosqualene are described. The compositions provided comprise conventional additives. Methods of making and using the compounds and composition are also disclosed.

Abstract: Farnesene interpolymer comprises units derived from a farnesene (e.g., ?-farnesene or ?-farnesene) and units derived from at least one vinyl monomer. The farnesene interpolymer can be prepared by copolymerizing the farnesene and at least one vinyl monomer in the presence of a catalyst. In some embodiments, the farnesene is prepared from a sugar by using a microorganism. In other embodiments, the at least one vinyl monomer is ethylene, an ?-olefin, or a substituted or unsubstituted vinyl halide, vinyl ether, acrylonitrile, acrylic ester, methacrylic ester, acrylamide or methacrylamide, or a combination thereof.

Abstract: Provided herein are polyfarnesenes such as farnesene homopolymers derived from a farnesene and farnesene interpolymers derived from a farnesene and at least a vinyl monomer; and the processes of making and using the polyfarnesenes. The farnesene homopolymer can be prepared by polymerizing the farnesene in the presence of a catalyst. In some embodiments, the farnesene is prepared from a sugar by using a microorganism.

Abstract: Provided herein are, among other things, jet fuel compositions and methods of making and using the same. In some embodiments, the fuel compositions comprise at least a fuel component readily and efficiently produced, at least in part, from a microorganism. In certain embodiments, the fuel compositions provided herein comprise a high concentration of at least a bioengineered fuel component. In further embodiments, the fuel compositions provided herein comprise amorphane.

Abstract: The present invention provides methods for a robust production of isoprenoids via one or more biosynthetic pathways. The invention also provides nucleic acids, enzymes, expression vectors, and genetically modified host cells for carrying out the subject methods. The invention also provides fermentation methods for high productivity of isoprenoids from genetically modified host cells.