Abstract: The present invention relates to a method for preparing bioethanol from lignocellulosic biomass. The method of the present invention is capable of: minimizing the impurity content of an enzymatic saccharification raw material, by extracting biomass using hot water, before pretreatment, and removing extractable substances such as inorganic salts; suppressing, to the greatest extent, the production of overdecomposition products of sugar, by pretreating the biomass, from which the hot water extractable substances have been removed, in a condition for maximizing xylan yield; preparing fermentable sugar at a low cost, without washing a pretreated solid obtained from subsequent solid-liquid separation, but by only concentrating a sugar solution obtained after enzymatic saccharification, using a separation film; and preparing bioethanol therefrom in high yield.

Abstract: The invention relates to the fields of bacterial metabolism and the utilization or consumption of short-chain carboxylic acids to reduced products. Specifically, it relates to syngas fermentations using monocultures of syngas-utilizing homoacetogenic bacteria for the production of alcohols using native alcohol dehydrogenase.

Abstract: A method of producing 2,3-butanediol includes the steps of: culturing a microorganism belonging to the genus Zymobacter in a fermentation feedstock containing a carbon source (Step A); and purifying 2,3-butanediol from culture liquid obtained in this step (Step B). In this method, the carbon source contains pentose, and the microorganism belonging to the genus Zymobacter has a capacity to metabolize pentose.

Abstract: Provided are engineered microorganisms capable of producing fatty dicarboxylic acids and products expressed by such microorganisms. Also provided are biological methods for producing fatty dicarboxylic acids.

Abstract: The present disclosure relates to a hydrolysate of a mixture of lignocellulosic biomass and seaweed biomass. By mixing seaweed biomass with lignocellulosic biomass and then preparing a hydrolysate, lignocellulosic biomass-derived acetic acid is consumed together with seaweed biomass-derived mannitol. As a result, high sugar productivity can be maintained while reducing fermentation inhibitors. Because the present disclosure can solve the problem of lignocellulosic biomass of decreased fermentation efficiency due to lignocellulose-derived fermentation inhibitors and the problem of seaweed biomass of very low productivity in spite of long fermentation time, the hydrolysate according to the present disclosure may be used to produce biofuels and biochemicals economically.

Abstract: Biomass (e.g., plant biomass, animal biomass, microbial, and municipal waste biomass) is processed to produce useful products, such as food products and amino acids.

Abstract: The present invention relates to isolated phospholipid:diacylglycerol acyltransferases (PDAT) and polynucleotide sequences encoding the PDAT enzymes; polynucleotide constructs, vectors and host cells incorporating the polynucleotide sequences; and methods of producing and using same. Also provided are transformed cells and transgenic plants with enhanced oil accumulation and quality.

Abstract: The present invention relates to a fermenting method for enriching biomass of Thraustochytrium genus microalgae, specifically Schizochytrium sp. or Schizochytrium mangrovei, with docosahexaenoic acid (or DHA), by controlled addition of oxygen.

Abstract: Provided is a means for producing an acetylated sphingoid base using modified microorganism in the genus Starmerella, particularly Starmerella bombicola. A method for producing an acetylated sphingoid base comprising culturing a microorganism in the genus Starmerella to which a xenogeneic gene encoding a polypeptide having an activity to acetylate a sphingoid base is introduced.

Abstract: The present invention is a method for the biosynthesis of hundreds of compounds, mainly found in the cannabis plant. The starting material for these compounds can be any biological compound that is used/produced in a biological organism from the sugar family starting materials or other low cost raw materials processed via enzymes or within organisms to give final products. These final products include, but are not limited to: cannabinoids, terpenoids, stilbenoids, flavonoids, phenolic amides, lignanamides, spermidine alkaloids, and phenylpropanoids. Specifically, the present invention relates to the regular/modified/synthetic gene(s) of select enzymes are processed and inserted into an expression system (vector, cosmid, BAC, YAC, phage, etc.) to produce modified hosts. The modified host is then optimized for efficient production and yield via manipulation, silencing, and amplifying inserted or other genes in the host, leading to an efficient system for product.

Abstract: This disclosure relates to modified tryptophan synthase and more particularly to modified beta-subunits of tryptophan synthase. The disclosure further relates to cells expressing such modified subunits and methods of producing non-canonical amino acids.

Abstract: The present invention provides for a genetically modified host cell capable of producing 1-deoxyxylulose 5-phosphate or 1-deoxy-D-xylulose 5-phosphate (DXP) (12), and optionally one or more DXP derived compounds, comprising: (a) a mutant RibB, or functional variant thereof, capable of catalyzing xylulose 5-phoshpate and/or ribulose 5-phospate to DXP, or (b) a YajO, or functional variant thereof, and a XylB, or functional variant thereof.

Abstract: The present invention relates to methods for increasing hydrolysis of a cellulosic material, comprising: hydrolyzing the cellulosic material with an enzyme composition in the presence of a combination of an AA9 polypeptide and one or more oxidoreductases selected from the group consisting of a catalase, a laccase, and a peroxidase.

Abstract: Provided are an apparatus and method for reducing the phenol concentration in a commercial enzyme solution and/or feedstock.

Abstract: The present invention relates to the expression and optimisation of enzymes involved in the breakdown of lignocellulosic biomass. The present invention relates more specifically to variants of Trichoderma reesei endoglucanase I, and the use of said variants having an improved performance in methods of breaking down cellulose and producing biofuel.

Abstract: The present compositions and methods relate to a beta-glucosidase from Melanocarpus albomyces, polynucleotides encoding the beta-glucosidase, and methods of making and/or using the same. Formulations containing the beta-glucosidase are suitable for use in numerous applications, including hydrolyzing lignocellulosic biomass substrates.

Abstract: Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

Abstract: Provided is a method for preparing rebaudioside M by using an enzyme method. In the method, rebaudioside A or rebaudioside D is used as a substrate; and in the existence of a glucosyl donor, rebaudioside M is generated by means of reaction of the substrate under the catalysis of UDP-glucosyl transferase and/or recombinant cells containing the UDP-glucosyl transferase.

Abstract: The present invention relates to a method of producing riboflavin in a genetically modified organism of the genus Eremothecium, wherein said genetic modification is linked to the fatty acid uptake and/or beta-oxidation pathway of said organism, comprising growing said organisms in a culture medium and isolating riboflavin from the culture medium. The invention further relates to a method of providing a riboflavin accumulating organism belonging to the genus Eremothecium by genetically modifying said organism, to organisms obtained by such a method, as well as the use of such genetically modified organisms for increasing the accumulation of riboflavin.

Abstract: A method of noninvasively detecting plant pathogenic virus and an electronic apparatus thereof are provided. The method is adapted to the electronic apparatus for detecting pathogenic virus in plants. The method includes the following steps. An excitation light beam is projected to the plant, and a reaction light emitted by the plant in response to the excitation light is received. An analytic optical spectrum corresponding to the reaction light is obtained, and whether the plant has the pathogenic virus or not is determined according to the analytic optical spectrum.

Abstract: The invention relates to a method for determining the presence and/or amount of viable cells in a cell containing sample, for example, a fluid sample, using a dye precursor selected from the group consisting of a bioactivatable tetrazolium dye and a bioactivatable esterase dye, where the dye precursor is converted into a fluorescent label by a viable cell.

Abstract: The invention relates to a method for distinguishing between and enumerating strains of lactic acid bacteria or Bifidobacteria present in a food product. This method implements various agar culture media and/or selective culture conditions, combined with various chromogenic substrates.

Abstract: The invention relates to methods and instruments for determining the resistances of microbes to antibiotics, in particular those microbes which produce beta-lactamases. The method determines the resistance of the microbes in less than an hour by incubating a tiny quantity of the microbes on a mass spectrometric sample support plate after they have been combined with a dosed quantity of a suitable antibiotic, for example the beta-lactam antibiotic imipenem, and by direct mass spectrometric measurement of the breakdown of the antibiotic by the microbial enzymes.

Abstract: The present invention addresses a need for improved methods of treating M. tuberculosis infection using enhancers of respiration, and compositions for treating tuberculosis as well as assays for identifying novel agents for treating M. tuberculosis infection.

Abstract: Reagents, methods, and kits for assaying enzymes associated with lysosomal storage diseases MPS-I, MPS-II, MPS-IIIA, MPS-IIIB, MPS-IV A, MPS-VI, and MPS VII. In one aspect, the invention provides methods for assaying one or more enzymes associated with a lysosomal storage disease. In a first embodiment, the method includes: (a) contacting a sample with a first solution to provide a solution comprising one or more lysosomal enzymes; (b) contacting the one or more lysosomal enzymes in solution with an enzyme substrate for each lysosomal enzyme to be analyzed and incubating the substrates with the enzymes for a time sufficient to provide a solution comprising an enzyme product for each lysosomal enzyme present in the sample.

Abstract: Conjugates of 2,3-dihydroxynaphthalene and its derivatives with enzyme cleavable groups are chromogenic substrates that form coloured compounds when complexed with metal ions, e.g. iron ions, on cleavage by enzymes, and are useful in microbial detection and identification. The cleavage products form purple or red-brown coloured complexes, that can easily be observed by the naked eye. Microbes can be grown in the presence of the substrates and the metal salts that provide the metal ion for complexing with the 2,3-dihydroxynaphthalene product. Substituents in the naphthalene ring may affect the solubility of the substrates and also the diffusibility and colour of the metal complexes. Some of the substrates yield soluble complexes on cleavage and are of particular value in liquid growth media. Other substrates produce less soluble complexes that are more suitable for use in solid agar media. Methods of synthesising the substrates are described.

Abstract: A rapid, infrared spectroscopic method has been developed to assess the efficacy of targeted chemotherapeutics against the structure of the polypeptide target, based on the effect of natural polymorphic sequence variation on the conformation of the protein. This method has an advantage over the current genomics-based screening, as the new method provides a direct readout of the structural, and hence functional, outcome of polymorphisms to the protein region targeted by drugs. It allows rapid measurement of a protein's susceptibility to therapeutic targeted agents, prior to using the drug as treatment in the patient. This method can be used to identify biomarkers for a response for a protein to a drug which can be readily tested, interpreted, and used in a clinical setting.

Abstract: Methods are provided for detecting enzymatic activity of various lysosomal storage enzymes using substrates that include: a sugar moiety; a linker moiety allowing the conjugation of sugar moiety with the remaining structure of the substrate; and two or more fatty acid chains or derivatives thereof at least one of which is sufficiently structured to provide improved solubility in aqueous or organic solvent systems. Also provided are internal standards, and inhibitors for use in detecting or reducing enzymatic activity using the inventive substrates.

Abstract: A linearity standard includes a plurality of calibration solutions, each calibration solution having a different level of a reactant having a known response in a test strip and meter combination, and an electronic storage medium for storing calibration instructions and known responses for each solution of the plurality of calibration solutions.

Abstract: There has been a demand for a codon-optimized gene for the mutated catalytic domain of Oplophorus luciferase, which is capable of efficiently expressing a protein both in a cultured animal cell and Escherichia coli. There has also been a demand for a substrate coelenterazine analogue showing a higher activity than that of native 19 kDa protein. The invention provides a polynucleotide comprising a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 2. According to the invention, bis-coelenterazine is used as a substrate coelenterazine analogue suitable for the photoprotein encoded by the polynucleotide comprising the polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 2.

Abstract: An adaptor for use in amplifying all linear, double-stranded nucleic acid molecules of unknown sequences in a sample is disclosed. The adaptor consists of: (1) the first oligonucleotide (P-oligo) with a phosphate at the 5? end and without an additional thymine nucleotide at the 3? end; and (2) the second oligonucleotide (T˜oligo) with an extra 3?-T and without a 5?-phosphate. The P-oligo and T-oligo are complementary to each other except at the 3?-T (thymine) in the T-oligo. The adaptor is ligated to nucleic acids of unknown sequences which have an extra A in the 3? end (3?˜A overhang) to form adaptor-ligated target nucleic acids. The T-oligo is then employed as a single primer for T-oligo-primed polymerase chain reaction (TOP-PCR) and amplifies the nucleic acids of unknown sequences in full-length.

Abstract: The present application relates to a continuous droplet flow microfluidic system, including a microfluidic chip including an optical detection section; a stage assembly including a microfluidic chip holder configured to receive the microfluidic chip and a plurality of heating elements arranged to heat a plurality of separate sections of the microfluidic chip to a corresponding plurality of different temperatures; and an optical detection system arranged to detect fluorescent light emitted from said optical detection section of the microfluidic chip.

Abstract: The present invention provides DNA polymerases and their use in various applications. The present invention also relates to uses and methods utilizing the DNA polymerase of the present invention for discriminating between matched and mismatched primers or detecting SNP or methylated cytosine. The present invention also relates to kits comprising such DNA polymerases.

Abstract: Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention.

Abstract: The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.

Abstract: Disclosed are biomolecule based bioprobes that exhibit improved water solubility and mono layer-forming properties with substantially little or no aggregation that can appreciably interfere with binding of the bioprobes to a target nucleotide. The bioprobes may be used in conjunction with a suitable reporter system to detect very small quantities of biological markers. The bio-probes comprise a nucleobase sequence capable of hybridizing to a target nucleotide; and at least one charged functional group attached to said nucleobase sequence. Also disclosed are biosensors, and sensing devices that comprise the bin-probe. Further disclosed are suitable electrochemical reporter systems for use with the bioprobes. Methods of use of these devices and probes, including for the detection of target biomarkers, including biomarkers for cancer cells or pathogens, are also included.

Abstract: A method and kits are provided for nucleic acid quantification and discrimination using surface plasmon resonance (SPR). The method provided is able to significantly enhance the detection limit and multiplex the discrimination assay using the melting properties of the target DNA on top of standard PCR reaction. By using the heating and cooling cycles of the polymerase chain reaction (PCR) or Ligation chain reaction (LCR), DNA is melted and hybridized onto the SPR sensor surface together with a nanoparticle label. Thus, during every cycle of DNA amplification, the quantity and type of target DNA can be monitored.

Abstract: A method for labeling target molecules coupled to particles for the detection of the target molecules using a microarray chip, comprises: providing a functionalized microparticle, wherein the microparticle is coated with one or more functional group; providing a modification group on each of the target molecules to be detected to form modified target molecules; contacting the functionalized microparticle with the modified target molecules; coupling a luminophore to the complex between the functionalized microparticle and the modified target molecules, thereby directly or indirectly labeling each modified target molecules with the luminophore. By directly or indirectly labeling the target molecules with the luminophore, the method reduces the cost of fluorescence detection, and avoids PCR inhibition derived from traditional fluorescence labeling molecules.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: A kit for detecting live cells of a microorganism in a test sample by distinguishing the live cells from dead cells or injured cells by a nucleic acid amplification method includes the following components: 1) an agent capable of covalently binding to DNA or RNA of the microorganism by irradiation with light having a wavelength of 350 nm to 700 nm; 2) an agent for suppressing a nucleic acid amplification inhibitory substance; and 3) a primer or primers for amplifying a target region of the DNA or RNA of the microorganism to be detected by a nucleic acid amplification method. The agent for suppressing a nucleic acid amplification inhibitory substance is one or more selected from albumin, dextran, T4 gene 32 protein, acetamide, betaine, dimethyl sulfoxide, formamide, glycerol, polyethylene glycol, soybean trypsin inhibitor, ?2-macroglobulin, tetramethylammonium chloride, lysozyme, phosphorylase and lactate dehydrogenase.

Abstract: The present invention relates to methods and uses for the detection or quantification of newly-synthesized double-stranded target nucleic acid molecules in a sample during quantitative real-time polymerase chain reaction (qPCR) amplification. According to the invention, an intercalating dye recognizing double-stranded DNA molecules with higher affinity than single-stranded DNA molecules and a fluorophore-labeled oligonucleotide-probe being sequence specific for a target nucleic acid molecule are simultaneously employed, thus enabling quantification a specific target and total amount of a mixed nucleic acid population, and enabling assessing the cause of suboptimal PCR performance.

Abstract: A high-throughput sequencing method for detecting methylated CpG islands includes: processing a DNA sample by using a modifier, and converting cytosine in the DNA sample into uracil, and keeping 5?methylcytosine unchanged; amplifying the obtained segment by using a primer A and DNA polymerase, to obtain a segment having one end being capable of anchoring a junction primer C; amplifying the obtained segment by using a primer B and DNA polymerase, to obtain a segment gathering methylated CpG islands and having two ends being capable of separately anchoring junction primers C and D; amplifying the obtained segment at a PCR exponent by using the junction primers C and D and the DNA polymerase, to obtain the amplified product; and separating and purifying the amplified product, to form a high-throughput sequencing library and perform computer sequencing, and data analysis.

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: A system and method for determining the exact pair of alleles corresponding to polymorphic genes from sequencing data and for using the polymorphic gene information in formulating an immunogenic composition. Reads from a sequencing data set mapping to the target polymorphic genes in a canonical reference genome sequence, and reads mapping within a defined threshold of the target gene sequence locations are extracted from the sequencing data set. Additionally, all reads from the set data set are matched against a probe reference set, and those reads that match with a high degree of similarity are extracted. Either one, or a union of both these sets of extracted reads are included in a final extracted set for further analysis. Ethnicity of the individual may be inferred based on the available sequencing data which may then serve as a basis for assigning prior probabilities to the allele variants. The extracted reads are aligned to a gene reference set of all known allele variants.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Abstract: The present invention relates generally to the fields of cell biology and laboratory diagnostics, and particularly to general compositions and of uniquely tagged particles linked to moieties of known properties and methods of making tagged, functionalized particles. Additionally, the invention relates to methods of screening a collection of tagged functionalized particles.

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention; incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Abstract: A method for identifying a cluster or sub-cluster of microRNAs (miRNAs) that provides a signature profile for differentiating cells grown in one type of culture model from cells grown in another type of culture model. Also, kits and methods for evaluating, selecting, and/or characterizing tissue culture models using the miRNA profiles and a cluster or sub-cluster of miRNAs that provides the signature profile. Also, a method for identifying a putative mRNA target of a miRNA for evaluating and targeting with a drug candidate by using the cluster or sub-cluster of miRNAs and a method for selecting a culture model for use as a drug platform for screening a candidate molecule for activity against tumor cells in tumor stroma.

Abstract: The present invention relates to methods for assessing an individual's susceptibility to treatment of an inflammatory disease with a dietary supplement. The invention describes the recognition that the sensitivity of an individual to the inflammation suppressing effects of fish oil on TNF-? production is linked both to genetic variation encoded by, or associated with, TNF-?, LT-? and/or IL-6 single nucleotide polymorphisms and to the inherent level of production of TNF-? by cells.

Abstract: Methods and kits for diagnosing and treating type I diabetes based upon the expression of macrophage-specific Chymotrypsin-Like Elastase Family, Member 3B, either alone or in combination with sialic acid-binding immunoglobulin-like lectin-1, are provided.