Abstract: This document describes biochemical pathways for producing 1,3-butanediol using a polypetide having ?-ketothiolase activity to form a 3-oxo-5-hydroxypentanoyl-CoA intermediate that can be enzymatically converted to 1,3-butanediol, as well as recombinant hosts producing 1,3-butanediol.

Abstract: A method for producing tagatose comprises: a) performing epimerization of fructose using hexuronate C4-epimerase to obtain an epimerized product comprising tagatose; b) purifying the epimerized product; and c) crystallizing the purified epimerized product. The hexuronate C4-epimerase is an enzyme derived from Thermotoga maritima, Thermotoga neapolitana, Thermotoga thermarum or mutants thereof. The hexuronate C4-epimerase is produced from strains Escherichia. coli, Corynebacterum glutamicum, Aspergillus oryzae, or Bacillus subtilis.

Abstract: The present invention provides a method for decreasing pyruvate catabolism and increasing the accumulation of pyruvate in microbes. By overexpressing wild type dihydrolipoamide acetyltransferase or dihydrolipoamide acetyltransferase mutants which have mutations at conservative active sites, the present invention provide a method to decrease overall activity of pyruvate dehydrogenase complex and pyruvate catabolism, and thus increase the accumulation of extracellular pyruvate without killing the pyruvate-producing microbes. Overexpressing dihydrolipoamide acetyltransferase mutants is an effective way to increase pyruvate accumulation.

Abstract: The present invention provides various combinations of genetic modifications to a transformed host cell that provide increase conversion of carbon to a chemical product. The present invention also provides methods of fermentation and methods of making various chemical products.

Abstract: A yeast cell having a reduced level of activity of NAD dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has at least one exogenous gene encoding NADP dependent GAPDH and/or has up-regulation of at least one endogenous gene expressing NADP dependent GAPDH, wherein combined expression of the enzymes NADP dependent GAPDH, PDC, ALD, ACS, ACC* and MCR in said host cell increases metabolic flux towards 3-HP via malonyl-CoA compared to an otherwise similar yeast cell lacking said genetic modification.

Abstract: The present invention provides methods for enhancing ?-KG production in Yarrowia lipolytica, relates to the field of metabolic engineering. This invention successfully overexpresses the glutamate dehydrogenase in wild type strain Y. lipolytica WSH-Z06 to construct the recombinant Y. lipolytica WSH-Z06 which regulates the glutamate catabolism to synthesis ?-KG. L-methionine imine is added into the fermentation medium during the process to strengthen the supply of intracellular glutamate and inhibite the intracellular glutamine synthesis from glutamate metabolism and then enhance the accumunation of ?-KG. Therefor, the present invention provides an effective method for enhancing the accumunation of ?-KG through regulation of intracellular amino acid metabolism.

Abstract: The invention relates to a method for producing organic compositions comprising the method steps: A) providing an oxyhydrogen bacterium having an activity of an enzyme E1, which is increased by comparison with the wild type thereof and which can catalyse the conversion of 2 acetyl-CoA to acetoacetyl-CoA and CoA, in an aqueous medium; B) bringing the aqueous medium into contact with a gas containing H2, CO2 and O2 in a weight ratio from 20-70 to 10-45 to 5-35 and optionally C) purifying the organic composition.

Abstract: A production method of an optically active fluorolactic derivative according to the present invention includes asymmetrically reducing a fluoropyruvic acid derivative (or fluoropyruvic acid hydrate) with the use of an ?-keto acid dehydrogenase or ?-keto acid reductase. The optically active fluorolactic derivative can be obtained with high optical purity under mild reaction conditions by the asymmetric reduction reaction of the fluoropyruvic acid derivative with the specific enzyme.

Abstract: Sugar mixtures containing nonfermentable oligomers are fermented in the presence of certain enzymes that depolymerise the oligomers simultaneously with the fermentation process.

Abstract: At least one fatty acid and/or derivative thereof is produced from a gas containing H2, CO2, and O2 by providing a genetically modified hydrogen oxidizing bacterium in an aqueous medium; and contacting the aqueous medium with the gas containing H2, CO2 and O2 in a weight ratio of 20 to 70 (H2): 10 to 45 (CO2): 5 to 35 (O2); wherein the fatty acid contains at least 5 carbon atoms and wherein the hydrogen oxidizing bacterium is genetically modified relative to the wild type bacterium to increase the expression of enzyme E1 that is capable of catalyzing the conversion of acetyl CoA to acyl ACP via malonyl coA and to increase the expression of enzyme E2 that is capable of catalyzing the conversion of Acyl ACP to the fatty acid.

Abstract: A method for producing cathine ((1S,2S)-norpseudoephedrine), in which, in a first reaction step, benzaldehyde is reacted with an acetyl donor according to formula (1), where R?H or COOH, by way of an (S)-selective lease to yield an enantiomer mixture according to formulas (2) and (3) and, in a second step, the compound according to formula (3) is reacted with an amine donor by way of an (S)-selective transaminase to yield (1S,2S)-norpseudoephedrine.

Abstract: Methods and compositions for replication of threose nucleic acids (TNAs) are described. The described methods include a method for transcribing a DNA template into a TNA, and a method for reverse transcribing a threose nucleic acid into a cDNA.

Abstract: The instant invention relates to the field of protein production, and in particular to compositions and processes for controlling and limiting the heterogeneity of proteins expressed in host cells.

Abstract: The present invention relates to a method or process for controlling, inhibiting or reducing protein fucosylation in a eukaryote and/or a eukaryotic protein expression system. Said method comprises carrying out the protein expression and/or post-translational modification in the presence of an elevated total concentration of manganese or manganese ions.

Abstract: The present invention lies in the field of molecular biology, recombinant peptide and protein expression and relates to methods comprising nucleic acid sequences comprising allocrites of T1SSs or fragments thereof for the efficient production of recombinant Pe OIs and Pr OI. The allocrites or fragments thereof improve the expression of PeOI and Pr OI as IB and function as IB-tags.

Abstract: Methods and systems for purifying cells and/or viruses are provided. The sample is added to a well disposed in a medium. A potential is applied across the medium to cause the contaminants to enter one or more walls of the well, and retain the cells and/or viruses in the well. The cells and/or viruses can be removed from the well, and optionally adhered or fixed to a surface, or detected. In one embodiment, the cells and/or viruses may be retained in the well by embedding in the medium. The medium including the embedded cells and/or viruses may be excised or otherwise removed and transferred to a glass slide or other solid surface.

Abstract: The invention relates to a method of detection of Gram-negative bacteria periplasmic space and cell wall outer membrane proteins by mass spectrometry, wherein the periplasmic space and cell wall outer membrane proteins are extracted from the bacteria, and the proteins to be detected are stabilized by an inhibitor and/or a substrate of the given protein, the proteins are then dissolved, placed onto a MALDI-TOF plate, covered with matrix solution, measured by MALDI-TOF mass spectrometry, and the resulting spectra are compared to the reference peaks of the given protein. Preferably, the proteins are beta-lactamases and their detection can be used to quickly determine the bacterial resistance against beta-lactam antibiotics, minimizing the false-positive results.

Abstract: A method of determining the presence of Pseudomonas involves establishing a gaseous headspace over a surface suspected of containing at least one Pseudomonas strain and contacting at least a portion of the gaseous headspace with a capillary microextraction of volatiles (CMV) sampling device to absorb at least one component of the headspace by the CMV sampling device. The component loaded CMV sampling device is coupled to an injection port of an analytical device where the components are desorbed into the analytical device, where components are separated, detected, and identified to determine if one or more of the identified components is a biomarker for at least one Pseudomonas strain.

Abstract: A latent effervescent body comprising a selective agent is disclosed. A method of using the latent effervescent body in a method to selectively enrich a target microorganism is also disclosed. The method comprises providing a sample, a culture medium, and the latent effervescent body. The method further comprises contacting the sample, the culture medium, and the latent effervescent body under conditions to facilitate growth of the target microorganism. The method further comprises releasing the selective agent from the latent effervescent body. Optionally, the method includes detecting a microorganism.

Abstract: A method and instrument for detecting the presence or absence of a target organism in a test sample is provided. The instrument includes a carousel, a light source, alight detector, and a control system. The carousel is configured to hold a plurality of test sample containers, with each container held by the carousel at a container position. Each of the containers holds an admixture of a test mixture inoculated with the test sample. The light detector is operable to detect light emitted by the light source that has passed through the test sample disposed within the test container. The control system includes a processor. The control system is adapted to produce information indicative of the presence or absence of the target organism in the test sample using signals produced by the light detector.

Abstract: Methods are provided for performing antibotic susceptibility testing based on the detection of RNA, such as tmRNA, from microbial cells after exposure to antibiotics. In some embodiments, aliquots are obtained from a sample, one of which contains a selected antibiotic. The aliquots, which include growth media, are incubated under conditions suitable for microbial growth, and the microbial cells in each aliquot are removed and lysed, and the lysate is subjected to reverse transcription and amplification in infer the effect of the selected antibiotic on the microbial cells. In one embodiment, a sample containing microbial cells is incubated in the pressence of a selected antibiotic and a stimulus is provided to induce the production on m RNA within the microbial cells. The microbial cells are subsequently lysed without substantial degradation of the m RNA within the lysate, and the m RNA is detected to determine the effect of the antibiotic on the microbial cells.

Abstract: The present invention provides a protein comprising an amino acid sequence in which arginine at position 61 of a protein comprising the amino acid sequence represented by SEQ ID NO: 1 is substituted to an amino acid selected from the group consisting of glycine, alanine, valine, leucine, serine, threonine, proline, cysteine, methionine, asparagine, glutamine, and aspartic acid; and a method for measuring a glycated hemoglobin in a sample, wherein the method comprises reacting a glycated hemoglobin in a sample with a protease to produce a glycated hexapeptide, then reacting the produced glycated hexapeptide with the aforementioned protein, and measuring a substance produced or consumed by the reaction.

Abstract: The present invention provides methods for assessing efficacy of a methotrexate (MTX) dosing regimen in a patient.

Abstract: A system for determining usability of an analytical test strip includes a sample chamber to receive a fluid sample, a reagent in the sample chamber having a moisture-varying impedance, and two detection electrodes contacting the reagent. A test meter applies an AC waveform across the reagent via the detection electrodes while measuring an impedance of the reagent. A processor automatically determines whether the measured impedance of the reagent meets a dryness criterion. The meter includes a housing, a strip port connector, an impedance measurement circuit and the processor. A method for determining usability of a strip inserted in a hand held meter includes applying an AC waveform across a reagent of the strip and measuring a first electrical signal, and determining whether the strip meets the dryness criterion based on the first electrical signal. The test strip and ways of determining an analyte are also described.

Abstract: Presented herein are methods and compositions for the detection of specific beta-lactamases, including class A serine carbapenemases, metallo-beta-lactamases, AmpC beta-lactamases, and extended-spectrum beta-lactamases (ESBLs). The methods presented herein include methods that permit the detection of the presence of specific beta-lactamases in bacterial samples within as few as 2 to 10 minutes.

Abstract: Disclosed herein are compounds and methods for detecting enzyme activity. In some embodiments, the enzyme is a deacetylase enzyme such as HDAC. The compound of the invention comprises a detectable label, a linker, and an enamide group. The compound can be enzymatically cleaved by the enzyme of interest to produce a nucleophilic fragment that includes the detectable label. Measurement of a signal generated by the detectable label can indicate enzyme activity. The compounds can be used as either in vivo or in vitro enzyme probes.

Abstract: Method for identifying a modulator of Sirt6, PfSir2a, or Sirt7 deacylase activity, wherein a fatty-acylated substrate containing an acyl-lysine moiety and an indicator moiety is contacted with Sirt6, PfSir2a, or Sirt7 in the presence of a candidate compound under conditions for Sirt6, PfSir2a, or Sirt7 to deacylate the substrate, wherein the acyl is a hydrophobic fatty acyl group containing a hydrocarbon group having at least three carbon atoms connected by carbon-carbon bonds; contacting the deacylated substrate with a cleavage agent that cleaves the linkage between the lysine and indicator moiety to generate a detectable signal; and correlating a quantified Sirt6, PfSir2a, or Sirt7 deacylase activity therefrom. Modulating compounds of Sirt6, PfSir2a, or Sirt7 deacylase activity are also described, as are pharmaceutical compositions thereof, methods of treatment by administration of the modulating compounds, and kits for practicing the method.

Abstract: Methods, compositions and kits for selectively altering and detecting modified cytosine residues are provided.

Abstract: To provide a method for selectively detecting the methylation of particular cytosines in genomic DNA using a methylcytosine detection method using an anti-methylcytosine antibody to improve quantitativity and reliability. A method for detecting the methylated state of cytosine at a specific position contained in a nucleic acid, includes fragmenting the nucleic acid using a restriction enzyme; forming a double-stranded nucleic acid between the fragmented nucleic acid and a single-stranded nucleic acid having a base sequence capable of hybridizing with the fragmented nucleic acid but incapable of resulting in the formation of a base pair with cytosine at a specific position in the fragmented nucleic acid and a solid phase-binding site; binding the double-stranded nucleic acid on a solid phase using the solid phase-binding site; and measuring the amount of an antibody binding to the double-stranded nucleic acid on the solid phase.

Abstract: Provided is a method comprising (A) fragmenting genomic DNA in a state where the interaction of the genomic DNA and molecules interacting therewith is maintained, and (B) bringing genomic DNA into contact with an exogenous molecule capable of binding to a specific endogenous DNA sequence in the genomic DNA. According to the method, with the use of an endogenous DNA sequence present inside or in the vicinity of a target genomic region in cells to be analyzed, any genomic region can be specifically isolated in a state where the interaction of the genomic region and molecules interacting therewith is maintained, without the need of inserting a recognition sequence of an exogenous DNA-binding molecule into the vicinity of the target genomic region in the cells to be analyzed.

Abstract: The present invention provides miniaturized instruments for conducting chemical reactions where control of the reaction temperature is desired or required. Specifically, this invention provides chips and optical systems for performing and monitoring temperature-dependent chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost amplification of nucleic acids.

Abstract: A method of determining whether or not a nucleic acid having an expected sequence or one or more variants of the expected sequence are present in a sample containing nucleic acids after replication, transcription or editing (or other transformation) of a substrate nucleic acid. The method involves deciding an expected sequence likely to be formed in the sample upon the replication, transcription or editing of the substrate nucleic acid, and possible variants of the expected sequence, providing primer pairs for a polymerase chain reaction, reverse transcriptase polymerase chain reaction or ligase chain reaction, carrying out the polymerase chain reaction or reverse transcriptase polymerase chain reaction in one or more steps to form amplicons, and analyzing the amplicons to determining whether or not a nucleic acid having the expected sequence and/or variants are present in the sample.

Abstract: A cartridge set includes: a first package; a cleaning container that is accommodated and sealed in the first package while accommodating and sealing a cleaning solution for cleaning a nucleic acid-binding solid-phase carrier to which nucleic acid adheres; an elution container that is accommodated and sealed in the first package while accommodating and sealing an elution solution which elutes the nucleic acid from the nucleic acid-binding solid-phase carrier; a second package; and a reaction container that is accommodated and sealed in the second package while accommodating and sealing a reagent for performing a nucleic acid amplification reaction. The first package has water permeability that is lower than that of the cleaning container and the elution container. The second package has water permeability that is lower than that of the reaction container.

Abstract: A cartridge set includes: a first package; a cleaning container that is accommodated and sealed in the first package while accommodating and sealing a cleaning solution for cleaning a nucleic acid-binding solid-phase carrier to which nucleic acid adheres; a second package; an elution container that is accommodated and sealed in the second package while accommodating and sealing an elution solution which elutes the nucleic acid from the nucleic acid-binding solid-phase carrier; a third package; and a reaction container that is accommodated and sealed in the third package while accommodating and sealing a reagent for performing a nucleic acid amplification reaction, in which the first package has water permeability that is lower than that of the cleaning container, the second package has water permeability that is lower than that of the elution container, and the third package has water permeability that is lower than that of the reaction container.

Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

Abstract: This invention provides methods, compositions and kits for gene expression analysis and gene expression profiling. The methods of the invention are highly sensitive; have a wide dynamic range; are rapid and inexpensive; have a high throughput; and allow the simultaneous differential analysis of a defined set of genes. The methods, compositions and kits of the invention also provide tools for gene expression data collection and relational data analysis.

Abstract: Described herein are primers and probes useful for detecting, screening, isolating, and sequencing of the vancomycin resistance genes and vancomycin resistant Enterococci and methods of using the described primers and probes.

Abstract: The present invention relates to an assay for use in a method of determining the oral health status of a canine animal by identifying certain bacteria present or absent in a sample taken from the animal, and applying the information set out herein for each identified bacteria to statistical models in order to determine the oral health status of the animal.

Abstract: This application pertains to methods for the whole-cell analysis of intracellular bacteria. The methods are capable of making a determination of whether or not a sample (e.g. a clinical sample) comprises one or more select bacteria within host cells, for example, predatory host cells such as phagocytic cells. The method is performed on substantial intact bacteria and may be performed without the use of permeabilising or lysis reagents and using PNA probes. Furthermore, the application pertains to in situ hybridization methods for Gram-positive bacteria performed using buffered saline for hybridization.

Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.

Abstract: Photoblocked probes are disclosed including a specific hydrolysis probe having a first nucleic acid sequence complementary to a target having a second nucleic acid sequence, a first and a second interactive labels, a 5? end and a 3? end, and one or more photocleavable moieties coupled to one or more nucleotides of the specific hydrolysis probe, wherein the photocleaveable moiety interferes with the hybridization of the specific hydrolysis probe with the region of the amplification product. Also disclosed are PCR methods for the detection of the presence or absence of a target nucleic acid in a sample utilizing the photoblocked probes, as well as kits.

Abstract: Methods and apparatus for direct detection of chemical reactions are provided. Electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal.

Abstract: The present invention relates to methods for the differentiation of a 5-hydroxymethyl modification of a cytosine residue of interest in a nucleic acid molecule from (i) a 5-methyl modification of said cytosine residue of interest o,r (ii) said unmodified cytosine residue of interest, said methods making use of the capability of transcription-activator-like effector (TALE) proteins to preferentially bind with strong affinity to nucleic acid sequences containing non-modified cytosine residues or 5-methyl modified cytosine residues, and to bind, if at all, with only strongly reduced affinity to nucleic acid sequences containing 5-hydroxymethyl modified cytosine residues. The present invention further relates to respective uses of TALE proteins for the differentiation of a 5-hydroxymethyl modification of a cytosine residue of interest in a nucleic acid molecule from (i) a 5-methyl modification of said cytosine residue of interest or (ii) said unmodified cytosine residue of interest.

Abstract: A molecular manipulation system for investigating molecules, having a sample holder constructed to hold a sample comprising a plurality of molecules attached on one side to a surface in the sample holder and on another side attached to a microbead of a plurality of microbeads. The system having; an acoustic wave generator to generate an acoustic wave exerting a force on the microbeads in the sample; and a detector device to detect a response of the plurality of microbeads in the sample on the force exerted by the acoustic wave to investigate the molecules attached to the microbeads.

Abstract: The present invention relates a kit for detecting a nucleic acid and a method of detecting a nucleic acid for enabling a multiplexed-detection and real-time detection of a target nucleic acid by using properties of a graphene oxide.

Abstract: Provided is a rapid and simple method of detecting methylated DNA. The method of detecting methylated DNA includes the following steps of: (1) treating sample DNA with a hydrogen sulfite; (2) amplifying the sample DNA treated with the hydrogen sulfite by PCR; and (3) subjecting the resultant PCR amplification product to ion-exchange chromatography.

Abstract: A container accommodation body includes: a package; a container that is accommodated and sealed in the package while accommodating and sealing a reagent for performing a nucleic acid amplification reaction; and a drying agent that is accommodated and sealed in the package.

Abstract: Methods and systems for detecting a target nucleic acid using the quantitative capabilities of real-time nucleic acid amplification systems and the multiplexing capabilities of hybridization systems, comprising: identifying a conservative sequence and a distinctive sequence within each target nucleic acid sequence; simultaneously amplifying the conservative region and the distinctive region; monitoring the amplification of the conservative region in real-time; identifying the distinctive region amplicon via multiplexed identification; and performing quantitative multiplexing analysis of the target by combining the real-time monitoring information with the multiplexed identification of the target nucleic acid.

Abstract: The present invention relates to a novel method for analyzing nucleic acid sequences based on real-time detection of DNA polymerase-catalyzed incorporation of each of the four nucleotide bases, supplied individually and serially in a microfluidic system, to a reaction cell containing a template system comprising a DNA fragment of unknown sequence and an oligonucleotide primer. Incorporation of a nucleotide base into the template system can be detected by any of a variety of methods including but not limited to fluorescence and chemiluminescence detection. Alternatively, microcalorimetic detection of the heat generated by the incorporation of a nucleotide into the extending template system using thermopile, thermistor and refractive index measurements can be used to detect extension reactions.

Abstract: The present invention provides technology that uses current measurements to identify nucleotides and determine a nucleotide sequence in polynucleotides. The present invention calculates a modal value of a tunnel current that arises when a nucleotide or polynucleotide for analysis passes through between electrodes, and then employs the calculated modal value. The present invention accordingly enables direct rapid implementation to identify nucleotides and to determine a nucleotide sequence in a polynucleotide without marking.