Abstract: This invention describes genes, metabolic pathways, microbial strains and methods to produce methylbutanol and other compounds of interest from renewable feedstocks.

Abstract: The invention relates to acyl-CoA-independent methods of producing fatty alcohols in recombinant host cells engineered to express an alcohol-forming acyl-ACP reductase. The recombinant host cells may be photosynthetic microorganisms, such as cyanobacteria. Isolated nucleic acid molecules, vectors, and recombinant host cells expressing an alcohol-forming acyl-ACP reductase, and systems for producing fatty alcohols via an acyl-CoA-independent pathway, are also provided. Also provided are microorganisms engineered for the secretion of fatty acids and fatty acid derivatives, including fatty alcohols, and methods of producing fatty acid derivatives using such engineering microorganisms.

Abstract: The present invention provides autonomous replication sequences (ARSs) isolated from Nannochloropsis that support the replication of episomal DNA molecules (EDMs) in eukaryotic cells. The ARSs and EDMs provided herein can be used for expressing genes in organisms including algae and heterokonts.

Abstract: The present invention provides compositions and methods for treating, inhibiting or preventing the developing of a plant pathogenic disease. The compositions comprise volatile organic compounds effective to inhibit the growth of, or kill pathogenic microbes, including Ganoderma boninense. Invention compositions are especially useful in preventing and treating basal stem rot in the oil palm, and can be applied in the vicinity of the plant or used to sterilize the plant growth medium prior to or concurrent with plant growth therein.

Abstract: The present invention relates to methods of joining two or more double-stranded (ds) or single-stranded (ss) DNA molecules of interest in vitro, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule of each pair share a region of sequence identity. The method allows the joining of a large number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest. Kits for performing the method are also disclosed. The methods of joining DNA molecules may be used to generate combinatorial libraries useful to generate, for example, optimal protein expression through codon optimization, gene optimization, and pathway optimization.

Abstract: The present invention provides novel genes encoding Class II acyl-ACP thioesterases and variants thereof that are active on C8, C10, C12, C14, C16, and C18 acyl-ACP substrates. The thioesterases can be introduced into transgenic organisms, including microorganisms and photosynthetic organisms, for producing fatty acids and fatty acid products.

Abstract: The invention provides a mechanism for semi-quantitatively measuring individual isotopomer species of a molecule using gas chromatograph mass spectrometry. The method allows for semi-quantitatively tracking the movement of ions by measuring the individual isotopomer species of a molecule.

Abstract: The present invention discloses methods for assembling a nucleic acid molecule from a set of overlapping oligonucleotides. The method involves contacting a set of overlapping oligonucleotides with a DNA polymerase, a mixture of dNTPs, and a crowding agent to form an assembly mixture. In one embodiment the crowding agent is polyethylene glycol (PEG). The presence of the crowding agent facilitates the nucleic acid assembly process of the invention. The assembly mixture is then subjected to multiple cycles, each cycle comprising an annealing phase, an extension phase, and a denaturation phase, and the desired nucleic acid molecule is thereby assembled. In some embodiments one or more of the phases are time varied.

Abstract: A recombinant cyanobacterium comprising an oxygen-tolerant, hydrogen-evolving hydrogenase, kit, and methods of use.

Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.

Abstract: Mutant photosynthetic microorganisms having reduced chlorophyll and increased photosynthetic efficiency are provided. The mutants have a locked in high light-acclimated phenotype, in which many of the photosynthetic parameters characteristic of high light acclimated wild type cells are found in the LIHLA mutants when acclimated to low light, such as reduced chlorophyll, reduced NPQ, higher qP, higher Ek, higher Pmax per unit chlorophyll with little to no reduction in Pmax per cell, and higher rates of electron transport through photosystem II over a wide range of light intensities. Provided herein are constructs for attenuating or disrupting genes are provided for generating mutants having the LIHLA phenotype. Also provided are methods of culturing LIHLA mutants for the production of biomass or other products.

Abstract: The present invention provides methods for producing a product of one or more enzymatic pathways. The pathways used in the methods of the invention involve one or more conversion steps such as, for example, an enzymatic conversion of guluronic acid into D-glucarate (Step 7); an enzymatic conversion of 5-ketogluconate (5-KGA) into L-Iduronic acid (Step 15); an enzymatic conversion of L-Iduronic acid into Idaric acid Step 7b); and an enzymatic conversion of 5-ketocluconate into 4,6-dihydroxy 2,5-diketo hexanoate (2,5-DDH) (Step 16). In some embodiments the methods of the invention produce 2,5-furandicarboxylic acid (FDCA) as a product. The methods include both enzymatic and chemical conversions as steps. Various pathways are also provided for converting glucose into 5-dehdyro-4-deoxy-glucarate (DDG), and for converting glucose into 2,5-furandicarboxylic acid (FDCA). The methods also involve the use of engineered enzymes that perform reactions with high specificity and efficiency.

Abstract: The present invention relates to the culture and manipulation of microorganisms for biotech applications, and is based on the discovery and characterization of spliced leader sequences identified in transcripts from Nannochloropsis species. In particular, the invention provides nucleic acid compositions comprising a SL sequence operably linked to a protein-encoding gene. Further provided are compositions and methods for enhanced gene expression in recombinant microorganisms as well as methods for identification and/or isolation of nucleic acid molecules tagged with a spliced leader sequence.

Abstract: The presently disclosed invention relates to methods of transferring large nucleic acid molecules or a genome from one cell (the donor) into heterologous host cells in the presence of a crowding agent. The method allows for greater ease and efficiency of transfer of genetic material. Introduction of the donor genetic material into the recipient host cells also allows for manipulation of the donor nucleic acid molecule or genome within the host cells. Methods disclosed herein can be used to alter donor genomes from intractable donor cells in more tractable host cells.

Abstract: Genes and strains of recombinant microorganisms are provided that are engineered to produce fatty alcohols and fatty alcohol derivatives. The organisms can include one, two, three or more transgenes that direct the biosynthesis of one or more fatty alcohols or derivatives. Methods of producing fatty alcohols using transgenic microorganisms are also provided.

Abstract: The present invention provides genes, polypeptides and expression constructs therefor, recombinant photosynthetic microorganisms, and method of use thereof, such as for the production of branched-chain alcohols (including 2-methyl-1-butanol, 3-methyl-1-butanol, and isobutanol) and derivatives thereof for a variety of uses.

Abstract: Methods and materials useful for modulating the sensitivity of cells to an inhibitor of acetohydroxyacid synthase (AHAS) are disclosed. For example, nucleic acid molecules encoding AHAS large subunits are disclosed as well as methods for using such nucleic acid molecules to transform microbial cells and plant cells, and to confer modulated sensitivity to AHAS-inhibiting compounds onto such cells. Further provided are materials and methods useful for modulating growth, development, activity, and characteristics of host cells and organisms.

Abstract: The present invention provides compositions and methods for treating, inhibiting or preventing the developing of a plant pathogenic disease. The compositions comprise volatile organic compounds effective to inhibit the growth of, or kill pathogenic microbes, including Ganoderma boninense. Invention compositions are especially useful in preventing and treating basal stem rot in the oil palm, and can be applied in the vicinity of the plant or used to sterilize the plant growth medium prior to or concurrent with plant growth therein.

Abstract: The present invention relates, e.g., to a method for amplifying a small number of copies (e.g. a single copy) of a single-stranded circular DNA molecule (e.g. having a size of about 5-6 kb) by an isothermal rolling circle mechanism, using random or partially random primers and a F29-type DNA polymerase. The method, which can also be used for amplifying DNAs by non-rolling types of multiple displacement amplification, comprises incubating the reaction components in a small volume, e.g. about 10 ?l or less, such as about 0.6 ?l or less. The degree of amplification can be about 109 fold, or higher. A method for cell-free cloning of DNA, using the rolling circle amplification method of the invention, is described.

Abstract: The present invention describes methods of identifying stimulants for the biogenic production of methane in hydrocarbon-bearing formations. Methods involve the use of microbial nucleic acid sequence information for the determination of gene products that are enzymes in a variety of pathways involved in the conversion of hydrocarbons to methane. Enzymes and stimulants identified by invention methods can be used in processes for enhancing biogenic methane production, for example, by addition to coal seams and coalbed methane wells.