Abstract: This invention relates to recombinant microorganisms capable of producing isoprene and isoprene production with the use of such recombinant microorganism with good efficiency. In this invention, functional activity of the ispA gene is altered to reduce the production of isoprenoid molecules in recombinant cells engineered to produce isoprene or in cells otherwise susceptible to isoprenoid accumulation during fermentation. This decreased ispA gene functional activity enables enhanced synthesis of isoprene in a host microorganism.

Abstract: Carbon-containing materials, such as biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) or coal are processed to produce useful products, such as fuels, carboxylic acids and equivalents thereof (e.g., esters and salts). For example, systems are described that can use feedstock materials, such as cellulosic and/or lignocellulosic materials and/or starchy materials, to produce ethanol, butanol or organic acids (e.g., acetic or lactic acid), salts of organic acids or mixtures thereof. If desired, organic acids can be converted into alcohols, such as by first converting the acid, salt or mixtures of the acid and its salt to an ester, and then hydrogenating the formed ester. Acetogens or homoacetogens which are capable of utilizing a syngas from a thermochemical conversion of coal or biomass can be utilized to produce the desired product.

Abstract: The present invention provides a method of producing a polymer, which comprises the step of performing a polymerization reaction using, as a starting material, an organic acid obtained by allowing a microorganism or a treated cell thereof to act on an organic raw material, wherein said microorganism has an ability to produce an organic acid and has been modified so as to produce less aromatic carboxylic acid as compared to an unmodified strain.

Abstract: The present invention relates to an engineered bacteria for producing short chain fatty acid with the overexpression of a long chain (>C12) acyl-ACP thioesterases (long-TE) and a short chain (?C12) acyl-ACP thioesterases (short-TE).

Abstract: Methods and compositions for the production of dielectric fluids from lipids produced by microorganisms are provided, including oil-bearing microorganisms and methods of low cost cultivation of such microorganisms. Microalgal cells containing exogenous genes encoding, for example, a sucrose transporter, a sucrose invertase, a fructokinase, a polysaccharide-degrading enzyme, a lipid pathway modification enzyme, a fatty acyl-ACP thioesterase, a desaturase, a fatty acyl-CoA/aldehyde reductase, and/or an acyl carrier protein are useful in manufacturing dielectric fluids.

Abstract: The present invention relates to nucleic acids derived from Limonomyces roseipellis. The invention also relates to the individual coding sequences and to proteins encoded by these sequences as well to a process for converting oleic acid to linoleic acid to linoleic acid and the production of arachidonic acid, eicosapentaenoic acid and/or docosahexaenoic acid in a plant.

Abstract: The present invention relates to the recombinant manufacture of polyunsaturated fatty acids. Specifically, it relates to acyltransferase polypeptides, polynucleotides encoding said acyltransferases as well as vectors, host cells, non-human transgenic organisms containing said polynucletides. Moreover, the present invention contemplates methods for the manufacture of polyunsaturated fatty acids as well as oils obtained by such methods.

Abstract: The disclosure relates to engineered enone reductase polypeptides having improved properties, polynucleotides encoding the engineered polypeptides, related vectors, host cells, and methods for making the engineered enone reductase polypeptides. The disclosure also provides methods of using the engineered enone reductase polypeptides for chemical transformations.

Abstract: The invention relates to novel enzymes that provide acetylated sphingoid bases.

Abstract: The present invention provides an enzymatic process for the preparation of (S)-5-(4-Fluoro-phenyl)-5-hydroxy-1morpholin-4-yl-pentan-1-one by the reduction of 1-(4-Fluoro-phenyl)-5-morpholin-4-yl-pentane-1,5-dione by using a suitable enzyme or by the resolution of (R,S)-5-(4-Fluoro-phenyl)-5-hydroxy-1morpholin-4-yl-pentan-1-one by using an enzyme. The present invention also provides process for the preparation of Ezetimibe comprising the steps of a) protecting the compound (S)-5-(4-Fluoro-phenyl)-5-hydroxy-1morpholin-4-yl-pentan-1-one with hydroxy protecting group b) hydrolyzing the obtained compound c) condensing with a chiral auxiliary d) reacting with an protected imine compound e) converting to alkyl ester f) cyclizing and g) deprotecting to obtain Ezetimibe.

Abstract: The present invention relates to genetically modified microorganisms capable of producing beta-glucans, characterized in that the genetically modified microorganism overexpresses (i) a polynucleotide encoding a polypeptide having 1,3-?-D-glucan synthase-activity, and/or (ii) a polypeptide having 1,3-?-D-glucan synthase-activity, compared to a corresponding non-modified control microorganism of the same strain. The present invention also relates to the use of a polynucleotide encoding a polypeptide having 1,3-?-D-glucan synthase-activity or the use of such a polypeptide for producing ?-glucans. Furthermore, the present invention relates to methods for producing ?-glucans comprising the introduction of a promoter upstream of a polynucleotide encoding a polypeptide having 1,3-?-D-glucan synthase-activity thereby increasing the expression of the polynucleotide, or a polynucleotide encoding a polypeptide having 1,3-?-D-glucan synthase-activity into a microorganism being able to synthesize ?-glucans.

Abstract: Biomass (e.g., plant biomass, animal biomass, and municipal waste biomass) or other materials are processed to produce useful intermediates and products, such as energy, fuels, foods or materials. For example, systems and methods are described that can be used to treat feedstock materials, such as cellulosic and/or lignocellulosic materials, in a vault in which the walls and optionally the ceiling include discrete units. Such vaults are re-configurable.

Abstract: The present disclosure relates to an enzyme derived from Candida bombicola that is capable of lactonizing or polymerizing carbohydrate-containing compounds, lipids, fatty acids, hydroxylated fatty acids, alcohols, dicarboxylic acids or mixtures thereof. Hence, host cells comprising the latter enzyme can be used, via the formation of intra- or inter-molecular ester-bounds, to produce, for example, lactonized sophorolipids or polymers of acidic sophorolipids. On the other hand, host cells having lost their capability to produce a functional enzyme disclosed herein can be used to produce 100% acidic sophorolipids.

Abstract: The isolation and characterization of a glucosyltransferase gene from Candida bombicola is disclosed. Use of the glucosyltransferase enzyme for the production of glucosylated sterol and hydroxyl-fatty acid substrates is also disclosed. This enzyme has broad-specificity and is useful for the production of sophorolipids both in-vivo and in-vitro.

Abstract: Provided herein are kits and methods suitable for enhancing in vitro translation of a nuclei acid sequence of interest.

Abstract: A method for engineering and utilizing large DNA vectors to target, via homologous recombination, and modify, in any desirable fashion, endogenous genes and chromosomal loci in eukaryotic cells. These large DNA targeting vectors for eukaryotic cells, termed LTVECs, are derived from fragments of cloned genomic DNA larger than those typically used by other approaches intended to perform homologous targeting in eukaryotic cells. Also provided is a rapid and convenient method of detecting eukaryotic cells in which the LTVEC has correctly targeted and modified the desired endogenous gene(s) or chromosomal locus (loci) as well as the use of these cells to generate organisms bearing the genetic modification.

Abstract: The present invention relates to methods for mammalian cell culture. The methods make use of independent tyrosine and cystine feed streams.

Abstract: A system and method for processing samples. The system can include a loading chamber, a detection chamber positioned in fluid communication with the loading chamber, and a fluid path defined at least partially by the loading chamber and the detection chamber. The system can further include a filter positioned such that at least one of its inlet and its outlet is positioned in the fluid path. The method can include positioning a sample in the loading chamber, filtering the sample in the fluid path to form a concentrated sample and a filtrate, removing the filtrate from the fluid path at a location upstream of the detection chamber, moving at least a portion of the concentrated sample in the fluid path to the detection chamber, and analyzing at least a portion of the concentrated sample in the detection chamber for an analyte of interest.

Abstract: Methods and materials are disclosed for use in an enzyme fragment complementation assay using complementary fragments of ?-galactosidase to study the trafficking of proteins in a cell. Compounds that bind to a target peptide have been found to affect protein folding and therefore trafficking. ?-Galactosidase fragments, an enzyme donor (ED) and an enzyme acceptor (EA), are fused to a target peptide and to an intracellular compartment protein, wherein the compartment is involved in intracellular trafficking. Contacting the cell with a compound that binds to the target peptide results in enhanced movement of the protein through the cellular trafficking pathway comprised of the endoplasmic reticulum, Golgi apparatus, the plasma membrane, endosomes, etc. Using this approach, compounds that bind to a target peptide and alter its ability to traffic through the normal cellular pathway can be readily detected.

Abstract: The present invention includes compositions and methods for fluorescence-based multiplex probe to simultaneously detect one or more enzymatic activities comprising: a first enzymatic target having a first end and a second end, wherein the first end of the first enzymatic target is attached to a central body and the second end of the first enzymatic target is attached to a first fluorophore; a second enzymatic target having a first end and a second end, wherein the first end of the second enzymatic target is attached to the central body and the second end of the second enzymatic target is attached to a third fluorophore; wherein the central body comprises at least one second fluorophore; wherein the first enzymatic target comprises a specific cleavage site of a first enzyme that cleaves the first enzymatic target; and wherein the second enzymatic target comprises a specific cleavage site of a second enzyme.

Abstract: Described are methods and systems for testing lumens of cannulated delivery components or assemblies thereof that may be used to deliver cells to a patient. Test cells are contacted with walls of the lumens and/or liquids that contact walls of the lumens, potentially over an incubation period. The test cells are then assessed for an effect of the wall contact, or the liquid contact, on at least one and preferably multiple characteristics of the test cells such as innate immune response, metabolic activity, viability, cytotoxic response, and/or motility. Methods and systems as described can be used in the development and/or manufacture of cannulated delivery devices, for example providing specifications for design or process inputs or outputs, design or process validations, and/or device lot approvals. Also described are devices or products produced in accordance with such methods and systems.

Abstract: The present invention relates to a method for determining the highest temperature that is suitable for performing accelerated protein stability studies, as well as to a method for modeling real-time protein stability from accelerated stability data generated at said temperature.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.

Abstract: Provided is a method for producing a nucleic acid probe that can detect a target substance with good sensitivity. A method for producing a nucleic acid probe, comprising: a 3?-terminal addition step of adding at least one nucleoside triphosphate derivative having a glutamine (Gln) residue or a lysine (Lys) residue to the 3?-terminal of a nucleic acid using a 3?-terminal addition enzyme which adds a nucleotide to the 3?-terminal of a nucleic acid, and a labeling compound binding step of either binding a labeling compound having a lysine (Lys) residue and containing a labeling moiety to the glutamine (Gln) residue using a transglutaminase (TGase), or binding a labeling compound having a glutamine (Gln) residue and containing a labeling moiety to the lysine (Lys) residue using a transglutaminase (TGase).

Abstract: A double-stranded nucleic acid hybridization probe and methods of using the same are described. The probe described is particularly suited for real-time RT-PCR reactions and has high tolerance to mismatches.

Abstract: The invention provides methods and compositions for performing a stringent wash step in a hybridization assay between at least one molecule and a target. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in the stringent wash step. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature non-complementary sequences in a hybridization product.

Abstract: Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.

Abstract: This invention provides methods, systems, and compositions for detecting low abundance microbial DNA in a sample by PCR. Methods of the present invention are based on a strategy that tags the 5?-end of the target DNA templates with a non-bacterial tagging sequence so as to set the templates apart from the endogenous contaminants present in the PCR reagents. There is also provided fusion probes for tagging the templates and primer sets to amplify the tagged templates. Systems and kits for facilitating and automating methods of the present invention are also provided.

Abstract: The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The allele specific oligonucleotides may be attached to a solid support such as a chip or a bead.

Abstract: The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the to presence or absence of a polymorphism.

Abstract: Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.

Abstract: Polymer sequencing is facilitated. According to an example embodiment of the present invention, a polymer sequencing approach is implemented using a multitude of polymer specimens for a particular polymer type is implemented. For each step in a polymer sequencing test, non-idealities are categorized using data obtained from the polymer sequencing test, and in response to the categorized non-idealities, a polymer sequence is identified for a corresponding step of the polymer sequencing test. With this approach, read lengths achieved with a particular polymer sequencing method can be improved.

Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.

Abstract: The invention provides modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3?-OH blocking group covalently attached thereto, such that the 3? carbon atom has attached a group of the structure —O—Z wherein Z is any of —C(R?)2-O—R?, —C(R?)2-N(R?)2, —C(R?)2-N(H)R?, —C(R?)2-S—R? and —C(R?)2-F, wherein each R? is or is part of a removable protecting group; each R? is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group; or (R?)2 represents an alkylidene group of formula ?C(R??)2 wherein each R?? may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and wherein said molecule may be reacted to yield an intermediate in which each R? is exchanged for H or, where Z is —C(R?)2-F, the F is ex

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. In some cases, this disclosure provides methods for the generation of polynucleotide barcode libraries, and for the attachment of such polynucleotides to target polynucleotides.

Abstract: Modulation of mRNA activity is achieved with precursor miRNAs (ta-RNAs). ta-RNAs, primarily pre-miRNAs and pri-miRNAs, including truncated and mutated ta-RNAs, are employed for modulation of mRNA expression where it is found that pri- and pre-miRNA have activity independently of the presence of functional mature miRNAs. Modification of at least one of the stem and loop of the ta-RNAs to enhance binding of the ta-RNA to the target mRNA is employed. The modification may be enhanced complementarity between the ta-RNA and the target mRNA and/or improved thermodynamic efficiency in binding of the ta-RNA to the target.

Abstract: A biochip used for quantitative analysis of a target DNA contained in a sample. The biochip includes a type I chamber that includes a primer designed to bind to the target DNA, an internal standard DNA of a first amount that has a sequence different from a sequence of the target DNA, and is amplifiable with the primer, and a fluorescent probe that is designed to bind to a part of a PCR product of the target DNA and to a part of a PCR product of the internal standard DNA. The fluorescent probe fluoresces differently for the PCR product of the target DNA and the PCR product of the internal standard DNA. The biochip also includes a type II chamber that includes the internal standard DNA of a second amount, the primer, and the fluorescent probe. The first and second amounts are different.

Abstract: Diagnostic kit comprising an oligonucleotide probe for the mRNA encoding a polypeptide having an amino acid sequence substantially identical to that of SEQ ID NO: 2.

Abstract: The present invention provides a binding moiety which selectively binds to Sox11 protein and/or mRNA for imaging, diagnosis or prognosis of lymphomas, such as mantle cell lymphomas (MCL) and diffuse large B-cell lymphoma (DLBCL). Optionally, the moiety is an antibody or antigen-binding fragment thereof. Advantageously, moiety comprises a further, readily detectable moiety. The invention also provides methods of imaging lymphomas cells as well as methods of diagnosing or prognosing lymphomas in an individual. A further aspect of the present invention provides a method of identifying cells associated with lymphomas, the method comprising analyzing the pattern of gene expression in a sample of cells to be tested and comparing it to the pattern of gene expression in a sample of known lymphomas cells. Preferably, the cells to be tested are identified as lymphoma cells if the expression of Sox11 is upregulated compared to normal B-cells.

Abstract: The present invention provides non-small cell lung cancer markers and the use thereof in diagnosing and monitoring diseases in vitro. The non-small cell lung cancer markers include at least one of the 26 selected detectable mature microRNAs existing stably in human serum or plasma. The invention also provides probe combinations, a kit and biochip for detecting the non-small cell lung cancer markers. The invention further provides a method for detecting the said lung cancer markers. The method in the present invention enables extensive detection spectrum, high sensitivity, low cost, convenient sample taking and preservation. The method can be applied in the general survey of disease, solves problems of the low specificity and sensitivity encountered with previous single markers, and increases significantly the clinical detection rate of diseases; it forms an effective means for diagnosing diseases at an early stage.

Abstract: A method of detecting a predisposition to, or the incidence of, bladder cancer in a sample comprises detecting an epigenetic change in at least one gene selected from FOXE1 and GATA4. Detection of the epigenetic change is indicative of a predisposition to, or the incidence of, bladder cancer. The sample comprises nucleic acid molecules from bladder cells. The methods may be used to select treatments and patients for treatment. Related kits include primers allowing the methylation status of the genes to be determined.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: This invention relates to a rapid method for detection of Salmonella in a sample based on the presence of nucleic acid sequences, in particular, to a PCR-based method for detection, and to oligonucleotide molecules and reagents and kits useful therefore. In certain embodiments, the method is employed to detect Salmonella in a food or water sample. The present invention further relates to isolated polynucleotides, replication compositions, and kits for carrying out the method of the present invention.

Abstract: Provided are an oligonucleotide which realizes specific and highly sensitive detection of toxigenic C. difficile, and a method for detecting toxigenic C. difficile, the method employing the oligonucleotide. 1) A primer pair containing an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 1, and an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 2; or a primer pair having complementary sequences to the nucleotide sequences. 2) A primer pair containing an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 4, and an oligonucleotide having a nucleotide sequence represented by SEQ ID NO: 5; or a primer pair having complementary sequences to the nucleotide sequences.

Abstract: A method of and system for producing oil and valuable byproducts from grains, such as corn, in dry mills are disclosed. The method and system include dewater milling process after fermenting. Further, the method and system are able to produce oil without evaporating. Moreover, the method and system include one or more of the germ processing units, emulsion processing units, fiber processing units, high value protein producing units, and glycerol and inorganic salt producing units, such that high value byproducts are able to be generated.

Abstract: A steel gear includes a substantially cylindrical outer peripheral ring portion having a toothed shape formed on its outer peripheral surface; and a flange portion extended radially inward from an inner peripheral surface of the outer peripheral ring portion. The steel gear has a thermal history layer formed in the outer peripheral ring portion, and the depth of the thermal history layer in the direction inward from the tooth bottom of the toothed shape of the outer peripheral surface is greater in the first protruding portion and the second protruding portion than in the coupling portion with the flange portion, and is substantially the same between the first protruding portion and the second protruding portion. As a result, even if the “carburization/slow cooling/high-frequency quenching treatment” is used as a manufacturing method of the steel gear, the steel gear has high dimensional accuracy.

Abstract: A method comprises heating an aqueous solution of colloidal silver particles. A soluble noble metal halide salt is added to the aqueous solution which undergoes a redox reaction on a surface of the silver particles to form noble metal/silver halide SPs, noble metal halide/silver halide SPs or noble metal oxide/silver halide SPs on the surface of the silver particles. The heat is maintained for a predetermined time to consume the silver particles and release the noble metal/silver halide SPs, the noble metal halide/silver halide SPs or the noble metal oxide/silver halide SPs into the aqueous solution. The aqueous solution is cooled. The noble metal/silver halide SPs, the noble metal halide/silver halide SPs or noble metal oxide/silver halide SPs are separated from the aqueous solution. The method optionally includes adding a soluble halide salt to the aqueous solution.

Abstract: Disclosed are methods for recovering technetium from a highly alkaline solution. The highly alkaline solution can be a liquid waste solution from a nuclear waste processing system. Methods can include combining the solution with a reductant capable of reducing technetium at the high pH of the solution and adding to or forming in the solution an adsorbent capable of adsorbing the precipitated technetium at the high pH of the solution.

Abstract: A method of forming an article includes forming a layer of a mixture of at least two distinct metal powders selected such that when combined they are chemically in the proportions of a superalloy containing a gamma prime phase, and fusing the powders locally without diffusion to define the shape of a part of the article such that the materials of the distinct metal powders remain substantially chemically segregated forming regions of different chemical composition. The method further includes repeating the forming and fusing until the derived article is formed, and heat treating the finished article such that at least one of the distinct separate materials diffuses to form a gamma prime phase containing superalloy with the other.

Abstract: Methods for producing silver nanostructures with improved dimensional control, yield, purity, monodispersity, and scale of synthesis.