Abstract: A DNA methylation editing kit comprises: (1) a fusion protein of inactivated CRISPR-associated endonuclease Cas9 (dCas9) having no nuclease activity and a tag peptide array in which plural tag peptides are linked by linkers, or an RNA or DNA coding therefor; (2) a fusion protein(s) of a tag peptide-binding portion and a methylase or demethylase, or an RNA(s) or DNA(s) coding therefor; and (3) a guide RNA(s) (gRNA(s)) comprising a sequence complementary to a DNA sequence within 1 kb of a desired site of methylation or demethylation, or a DNA(s) expressing the gRNA(s).

Abstract: The present disclosure relates to methods and compositions for reprogramming cells to a pluripotent state. In particular, it relates to an integration- and feeder cell-free method for reprogramming primary human fibroblast cells to induced pluripotent stem cells (iPSCs).

Abstract: The present invention provides a method for obtaining site-specific recombination in a eukaryotic cell, the method comprising providing a eukaryotic cell that comprises a first recombination attachment site and a second recombination attachment site; contacting the first and second recombination attachment sites with a prokaryotic recombinase polypeptide, resulting in recombination between the recombination attachment sites, wherein the recombinase polypeptide can mediate recombination between the first and second recombination attachment sites, the first recombination attachment site is a phage genomic recombination attachment site (attP) or a bacterial genomic recombination attachment site (attB), the second recombination site is attB or attP, and the recombinase is selected from the group consisting of a Listeria monocytogenes phage recombinase, a Streptococcus pyogenes phage recombinase, a Bacillus subtilis phage recombinase, a Mycobacterium tuberculosis phage recombinase and a Mycobacterium smegmatis pha

Abstract: Reduced graphene oxide is produced by adding graphene oxide and electrically active bacteria to a container. After a period of time reduced graphene oxide is produced by an interaction of the electrically active bacteria and the graphene oxide. The resulting composition of matter includes reduced graphene oxide and electrically active bacteria. The resulting composition of matter can be doped with a plurality of different elements.

Abstract: The present disclosure generally relates to methods of using microorganisms that comprise one or more polynucleotides coding for enzymes in one or more pathways that catalyze a conversion of a fermentable carbon source to butadiene and products and processes derived therefrom.

Abstract: The present invention relates to a genetically engineered yeast capable of manufacturing a fermentation product using sucrose as a fermentation substrate, and fermentation processes using such a yeast. In some embodiments, the fermentation product is ethanol.

Abstract: In one aspect, the present invention provides methods for preparing a fermentation product. The methods include pre-treating a mixture of biomass and ionic liquid, wherein the ionic liquid comprises a choline cation and the biomass comprises polysaccharide and lignin. The methods further include forming hydrolysates from the introduction of glycoside hydrolase to the pre-treated mixture at conditions sufficient to produce a sugar composition mixture for fermentation steps. The present invention provides methods for loading biomass mixtures in a batch-fed process, wherein the biomass slurries can be loaded into water or a concentrated sugar composition for hydrolysate production. The methods can be performed in a one-pot process, wherein the ionic liquids are present in the mixtures throughout each step. Aspects of the invention provide compositions of sugar composition mixtures and fermentation product mixtures.

Abstract: The present invention relates to a genetically engineered yeast capable of manufacturing a fermentation product using sucrose as a fermentation substrate, and fermentation processes using such a yeast. The yeast has an exogenous invertase gene and has a deletion or disruption of the PDC activity gene. Accordingly, the yeast is useful for manufacturing fermentation products other than ethanol from fermentation substrates containing sucrose.

Abstract: In alternative embodiments, provided are genetically or recombinantly engineered nitrogen-fixing, nitrogenase-expressing bacteria capable of enzymatically synthesizing hydrocarbons and generating hydrogen and carbon monoxide, and for carbon dioxide and/or carbon monoxide recycling, and compositions (e.g., bioreactors and devices) for using them, and methods for making and using them. In alternative embodiments, the genetically or recombinantly engineered nitrogen-fixing, nitrogenase expressing bacteria used to practice embodiments provided herein include nitrogen-fixing diazotrophs such as nitrogen-fixing bacteria of the family Pseudomonadaceae, or the genus Azotobacter, including Azotobacter vinelandii, for the whole cell synthesis of hydrocarbons and generating hydrogen and carbon monoxide, and for the recycling of carbon dioxide and/or carbon monoxide.

Abstract: Compositions and methods for a hybrid biological and chemical process utilizing chemotrophic microorganisms that converts syngas and/or gaseous CO2 and/or a mixture of CO2 gas and H2 gas into one or more desaturated hydrocarbons, unsaturated fatty acids, hydroxy acids, or diacids.

Abstract: The invention relates to an engineered eukaryotic microorganism into which a gene encoding an acyl-CoA dehydrogenase is introduced and a method for producing methacrylic acid esters such as MMA and MMA-CoA and precursors thereof using the microorganism.

Abstract: The present invention provides a novel polyhydroxyalkanoic acid having a functional group at a terminal carboxy group, which being capable of being chemically modified and easily controlled in reaction, and a method for production the same. The present polyhydroxyalkanoic acid includes a specific alkyne group, alkene group, thiol group, azide group or allyl group introduced at a terminal carboxy group. Further, the present production method comprises culturing a microorganism capable of producing a polyhydroxyalkanoic acid with use of an alcohol having an alkyne group, an alkene group, a thiol group, an azide group or an allyl group.

Abstract: A method of producing a polyunsaturated fatty acid in a transgenic bacterium, includes: introducing a recombinant plasmid into a bacteria cell to obtain the transgenic bacterium, wherein the recombinant plasmid comprises a polynucleotide encoding one or more elongase and one or more desaturase; incubating the transgenic bacterium in a medium containing a fatty acid substrate; harvesting the transgenic bacterium, and extracting the polyunsaturated fatty acid from the transgenic bacterium. A method of converting linoleic acid to arachidonic acid and a cassette and recombinant plasmid comprising nucleic acid sequences for the above methods are also provided.

Abstract: The present disclosure provides engineered polypeptides having imine reductase activity, polynucleotides encoding the engineered imine reductases, host cells capable of expressing the engineered imine reductases, and methods of using these engineered polypeptides with a range of ketone and amine substrate compounds to prepare secondary and tertiary amine product compounds.

Abstract: The present invention relates to a method for producing L-methionine in which a microorganism is cultured in the presence of L-homoserine and methyl mercaptan, a salt of the same or dimethyl disulfide whereby the L-methionine is accumulated in the culture medium.

Abstract: The present invention belongs to microbial technology field and relates to a strain producing toluene o-xylene monooxygenase (Arthrobacter woluwensis) HW-1 and its application in preparation of 5-methylpyrazine-2-carboxylic acid by microbial fermentation. The present invention providing a new strain HW-1 which could produce toluene o-xylene monooxygenase, and the strain is identified as Arthrobacter woluwensis. The strain is firstly found to convert 2, 5-dimethylpyrazine by bio-fermentation to obtain the medicine intermediate 5-methylpyrazine-2-carboxylic acid. The concentration of accumulated product could reach 34.19 g/L and the yield rate is 81.4% by shake flask fermentation. Compared with 20.41 g/L reported in the literature, this method has a greater advantage and could be industrialized. The conditions to prepare 5-methylpyrazine-2-carboxylic acid provided in the present invention is mild, the reaction process is controllable and has good performance in environmental protection and energy saving.

Abstract: The present invention relates to isolated polypeptides having catalase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Abstract: An object of the present invention is to provide an ?-glucan mixture in a preferable molecular weight range, which can be made into a transparent film with advantageous strength and water solubility when an edible film is made by using the ?-glucan mixture without adding any plasticizer. The above object is solved by providing an ?-glucan mixture, which is obtainable by a process comprising the steps of gelatinizing waxy starch and liquefying the resulting gelatinized waxy starch by allowing an amylase to act on it, having the following characteristics (1) and (2): (1) having the weight average molecular weight (Mw) in a range of 150 kDa to 3,000 kDa; and (2) having the value of dividing weight average molecular weight (Mw) with number average molecular weight (Mn), Mw/Mn, of 35.1 or lower.

Abstract: The invention relates to a process for inactivating proteases by repeatedly changing the pH in the cell culture supernatant at the start of the process for the purification of biopharmaceuticals. The pH is adjusted first to 3-5, and then to 7-9.

Abstract: The present invention is directed to methods and compositions for the production of Fc-containing polypeptides having improved properties and comprising mutations at positions 243 and 264 of the Fc region.

Abstract: The present invention relates to binding fusion protein compositions comprising targeting moieties linked to extended recombinant polypeptide (XTEN), binding fusion protein-drug conjugate compositions, and XTEN-drug conjugate compositions, isolated nucleic acids encoding the compositions and vectors and host cells containing the same, and methods of using such compositions in treatment of diseases, disorders, and conditions.

Abstract: The invention relates to methods for producing mogrosides with the aid of enzymes. In particular the invention proposes various biosynthetic pathways useful for mogroside production and enzymes useful for mogroside production are provided. Furthermore, the invention provides recombinant hosts useful in performing the methods of the invention.

Abstract: This application describes consortium between fungi and algae, where the algae are incorporated within hyphae of the fungi. The fungi, the algae, or both can be modified to express heterologous lipid synthesizing enzymes. Incorporation of algae into fungi facilitates harvesting of the algae and products produced by the consortia. Such consortia are robust. For example, the fungi and algae can symbiotically provide nutrients to each other and are tolerant of environmental stresses.

Abstract: According to the present invention a method of determining a concentration of sulfate reducing bacteria (SRB) comprising is provided. The method comprises preparing a standard growth medium in a group of test vials, adding ferrous chloride tetrahydrate (FCTH) to the each of the test vials, adding a sample portion to a first of the group of test vials, sequentially diluting the sample portion by injecting succeeding vials in the test group with fluid from sequentially previous vials and incubating the group of test vials, wherein blackening of fluid in an incubated test vial indicates a presence of a threshold number of SRB.

Abstract: Provided is a device for determining the live/dead bacterial state, with which it is possible to ascertain the accurate state of live bacteria/dead bacteria via a captured image in a relatively easy operation with which ascertaining the state of a bacterial cell is more accurate than conventional methods. This device for determining the live/dead bacterial state comprises: a case body in which a measurement mechanism is housed; an opening/closing lid body that allows a fungus base insertion port formed in the case body to be opened and closed; and the measurement mechanism, which is housed in the case body and is configured to measure the number of bacteria.

Abstract: The present invention provides a high throughput method to quantify and characterize the size and integrity of viruses and viral molecules. In one embodiment, the present invention provides a method to quantify and characterize size and integrity of Foot and Mouth Disease virus (FMDV) using chromatographic system and in-line Dynamic Light Scattering (DLS) technique. In one embodiment, the present invention further comprises a column-switching system for running multiple analyses simultaneously. The present invention also provides a method to develop and evaluate FMDV containing products for preventing Foot and Mouth Disease (FMD). In one embodiment, the methods described herein assess the stability of FMDV. In another embodiment, the methods described herein serve as in-process quality control for a manufacturing process of FMD vaccine.

Abstract: Methods of detecting actively growing host organisms, including bacterial organisms, involving the detection of ribonucleic acid (RNA) products produced by unmodified infectious bioagents that infect the host organisms are provided. Related methods of assessing drug susceptibility and resistance are further provided. In addition to these surrogate detection methods, related reaction mixtures, kits, systems, and microfluidic cards are also provided.

Abstract: Methods of detecting a local infection, critical colonization, or infection in a wound, predicting wound healing in a wound, and detecting bacterial pathogenesis in a wound are provided.

Abstract: The measurement of Factor Xa (FXa) enzymatic activity using novel fluorogenic peptide substrates that have a C-terminus cleavable fluorophore and optionally the ability to attach to a solid support. Fluorogenic measurements increase sensitivity and flexibility of measurements of enzymatic reactions over traditional absorbance-based approaches. The measurement of FXa generation is applicable to a range of biological reactions.

Abstract: This invention provides a substrate solution for measuring lipase activity, a reagent for measuring lipase activity, and an emulsion solution excellent in storage stability. This invention also provides a method for measuring lipase activity in a sample that enables accurate measurement over a long period of time. This invention further provides a method for improving storage stability of a substrate solution for measuring lipase activity and an emulsion solution. To this end, a substrate solution for measuring lipase activity comprising the emulsion solution comprising micelle particles of 1,2-o-dilauryl-rac-glycero-3-glutaric acid (6?-methylresorufin) ester and side-chain-type nonreactive polyether-modified-type modified silicone oil is used.

Abstract: Provided herein is a nanostructure comprising a nucleic acid scaffold and at least one functional core. The nanostructure is of any two-dimensional or three-dimensional shape such as a sheet, square, rectangle, nanotube, cylinder, ring, disc, ribbon, box, cube, pyramide and rod formed by a DNA and/or RNA scaffold and may have various catalytic activities.

Abstract: Methods for preparing concatenated nucleic acid molecules are provided. The methods herein include adaptors with complementary sequences for preparation of concatenated nucleic acid molecules, and methods of sequencing such nucleic acids.

Abstract: The present invention refers to a method for immuno-histochemical staining of a formalin-fixed, paraffin-embedded tissue section comprising the steps of a) providing a solid support, b) mounting the formalin-fixed, paraffin-embedded tissue section onto the solid support, c) removing the paraffin from the formalin-fixed, paraffin-embedded tissue section, d) heating the tissue section mounted on the solid support to retrieve epitopes at 50 to 70° C. for 12 to 24 h, and e) staining the tissue section mounted on the solid support, wherein at least step e) is performed in the presence of 0.5 to 3.0 M sodium chloride. The present invention further refers to a kit for performing the method.

Abstract: A parallel processing system for processing samples is described. In one embodiment, the parallel processing system includes an instrument interface parallel controller to control a tray motor driving system, a close-loop heater control and direction system, a magnetic particle transfer system, a reagent release system, a reagent pre-mix pumping system and a wash buffer pumping system.

Abstract: Aspects of the disclosure relate to primer compositions and multiplex methods for detecting the presence of Listeria. The primer composition includes a first primer sequence operable to amplify a first polymerase chain reaction (PCR) product (e.g., a nucleic acid, a fragment thereof, a complement thereof, or a gene). The first primer sequence is specific for the Listeria genus. The primer composition also includes at least one additional primer sequence operable to amplify at least one additional PCR product. The additional primer sequence(s) are specific for one or more species or subspecies of Listeria. The multiplex method includes contacting a sample with the primer composition to substantially simultaneously detect the presence of the Listeria genus and differentiate between species of Listeria present in the sample.

Abstract: The disclosure provides methods and kits for preparing sequencing library to detect chromosomal abnormality using cell-free DNA (cfDNA) without the need of first isolating the cfDNA from a liquid fraction of a test sample. In some embodiments, the method involves reducing the binding between the cfDNA and nucleosomal proteins without unwinding the cfDNA from the nucleosomal proteins. In some embodiments, the reduction of binding may be achieved by treating with a detergent or heating. In some embodiments, the method further involves freezing and thawing the test sample before reducing the binding between the cfDNA and the nucleosomal proteins. In some embodiments, the test sample is a peripheral blood sample from a pregnant woman including cfDNA of both a mother and a fetus. In other embodiments, the test sample is a peripheral blood sample from a patient known or suspected to have cancer.

Abstract: Methods for detecting presence of one or more of Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Toxoplasma gondii, Moraxella catarrhalis, Escherichia coli, Shigella, Staphylococcus aureus, Pneumocystis jirovecii, Chlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Ureaplasma spp., Bartonella spp., Streptococcus agalactiae, and Neisseria meningitidis nucleic acids in a sample, such as a biological sample obtained from a subject, or an environmental sample, are provided. This disclosure also provides probes, primers, and kits for detecting one or more of Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Toxoplasma gondii, Moraxella catarrhalis, Escherichia coli, Shigella, Staphylococcus aureus, Pneumocystis jirovecii, Chlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Ureaplasma spp., Bartonella spp., Streptococcus agalactiae, and Neisseria meningitidis in a sample.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

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 compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to improved, stable nanoreporter probes that are capable of binding to and identifying target molecules based on the probes' uniquely detectable signal. Methods for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. Polynucleotide sequences of certain nanoreporter components are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

Abstract: The present invention is directed methods for identifying, in a sample, one or more target nucleotide sequences differing from other nucleotide sequences in the sample by one or more nucleotides, one or more copy numbers, one or more transcript sequences, and/or one or more methylated residues, using ligation detection reactions, polymerase mediated extension reactions, and/or cleavage reactions. The present invention is also directed to methods for identifying, in a sample, one or more nucleotides in a target nucleotide sequence.

Abstract: Methods for detecting DNA or RNA target nucleic acids are provided. Such methods are based on isothermal amplification of nucleic acids mediated by cooperative hybridization, designated as exponential CHAMP. Kits for implementing methods for detecting DNA or RNA target nucleic acids based on isothermal amplification of nucleic acids mediated by cooperative hybridization are also provided.

Abstract: Described are methods for detecting and quantifying biomolecules such as polynucleotides or polypeptides in an electrophoresis matrix using ion concentration polarization and nanoparticle aggregation.

Abstract: Method and system for quantifying target nucleic acids using real-time amplification and internal calibration adjustment. The invention employs dual reference calibration curves for approximating a complete calibration curve from only a single adjustment calibrator amplified on the instrument that is to be calibrated.

Abstract: Described herein are methods and systems relating to high throughput, genome-wide translocation sequencing (HTGTS) and/or detection of double-stranded DNA break (DSB) locations. The methods described herein can comprise generating DSBs in a nucleic acid sequence and performing nested PCR with the primers described herein. Described herein is an enhanced HTGTS approach. The assays and methods described herein permit the measurement of various DNA double-strand break (DSB) activities either intrinsic to the biological system or from outside agents.

Abstract: The present invention relates to a nucleic acid sequencing method that determines the sequence of a template nucleic acid by electrochemical means via the depletion of metal ions as a result of its binding to and/or precipitation with pyrophosphate.

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.

Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

Abstract: Methods of detecting a mutation associated with a genetic eye disease in a subject, using target enrichment and next generation sequencing.