Abstract: Methods are described for selecting or producing a cereal plant comprising a functional restorer gene for wheat G-type cytoplasmic male sterility and nucleic acids for use therein.

Abstract: Disclosed are methods for the ex-vivo genetic modification of an immune cell comprising delivering to the immune cell, (a) a nucleic acid or amino acid sequence comprising a sequence encoding a transposase enzyme and (b) a recombinant and non-naturally occurring DNA sequence comprising a DNA sequence encoding a transposon.

Abstract: Recombinant expression vectors are disclosed that include a control sequence for recombinant expression of proteins of interest; the control sequence combines a mCMV enhancer sequence with a rat EF-1alpha intron sequence. Some of the vectors are useful for tetracycline-inducible expression. Some of the vectors contain a 5? PiggyBac ITR and a 3? PiggyBac ITR to promote genomic integration into a host cell chromosome. A method of selecting a stable production cell line for manufacturing a protein of interest is also disclosed. Also disclosed are mammalian host cells comprising the inventive recombinant expression vectors and a method of producing a protein of interest, in vitro, involving the mammalian host cell.

Abstract: The invention provides delivery methods and compositions for antiviral therapeutics. Methods and compositions are provided for targeted delivery of antiviral therapeutics into cells of interest using, for example, viral vectors such as adenovirus, AAV, and replication incompetent HSV. These and other delivery systems can be used as vehicles to deliver DNA vectors encoding a nuclease or a cell-killing gene. These delivery methods can also be used to deliver naked DNA or RNA, protein products, plasmids containing a promoter that is active only in a latent viral state which drives a cell-killing gene, or other therapeutic agents.

Abstract: Some aspects of this disclosure provide compositions, methods, systems, and kits for controlling the activity of RNA-programmable endonucleases, such as Cas9, or for controlling the activity of proteins comprising a Cas9 variant fused to a functional effector domain, such as a nuclease, nickase, recombinase, deaminase, transcriptional activator, transcriptional repressor, or epigenetic modifying domain. For example, the inventive proteins provided comprise a ligand-dependent intein, the presence of which inhibits one or more activities of the protein (e.g., gRNA binding, enzymatic activity, target DNA binding). The binding of a ligand to the intein results in self-excision of the intein, restoring the activity of the protein.

Abstract: The present invention provides a process for producing one or more products for use as a transportation or heating fuel. In various embodiments the process comprises treating a cellulosic feedstock in one or more processing steps that release extractives from the feedstock. A solids-liquid separation is subsequently conducted on the process stream comprising the extractives and solids. An aqueous stream comprising one or more of the extractives may be fed to an anaerobic digester to produce crude biogas from which one or more impurities may optionally be removed. In various embodiments the process further comprises providing a solids stream to a thermal process. A product produced or derived from the thermal process may displace a product made from fossil fuel. One or more products obtained or derived from at least one of the foregoing process steps are provided for use as a transportation or heating fuel. In various embodiments the process enables advantaged fuel credit generation.

Abstract: A dry-milling process for the production of dried distiller's grains with solubles (“DDGS”) includes the steps of dry-milling corn kernels to form a corn flour comprising corn fiber; combining the corn flour with water to form a mash; separating the corn fiber from the mash; treating the separated corn fiber with a composition; combining the treated corn fiber with the mash having the corn fiber separated therefrom to form a slurry; fermenting the slurry to produce beer and carbon dioxide; distilling the beer to produce ethanol and whole stillage; and processing the whole stillage to produce DDGS. The composition includes an alkanesulfonic acid, water, an enzyme, and optionally a surfactant.

Abstract: Provided are methods and systems of propagating a microorganism on a stillage composition. The methods involve growing microorganisms in a propagation medium formed from a polysaccharide-containing stillage composition with the majority of the of the polysaccharides in the propagation medium coming from the stillage composition. The propagation medium also includes cellulases and/or amylases to form monosaccharides from the polysaccharides. A first cell mass is grown in the propagation medium to form a second cell mass which is greater than the first cell mass.

Abstract: The present disclosure provides a process for forming a biogenic carbon-based fuel or a fuel intermediate from biogenic carbon dioxide and hydrogen. At least a portion of the biogenic carbon dioxide and hydrogen is subjected to a reverse water gas shift reaction that produces at least carbon monoxide. The carbon monoxide so produced, the biogenic carbon dioxide and the hydrogen are introduced, together or separately, to a biologic or chemical conversion process to produce the fuel or fuel intermediate.

Abstract: The invention provides genetically engineered microorganisms and methods for the biological production of ethylene glycol and precursors of ethylene glycol. In particular, the microorganism of the invention produces ethylene glycol or a precursor of ethylene glycol through one or more of 5,10-methylenetetrahydrofolate, oxaloacetate, citrate, malate, and glycine. The invention further provides compositions comprising ethylene glycol or polymers of ethylene glycol such as polyethylene terephthalate.

Abstract: Methods for the production of L-glufosinate (also known as phosphinothricin or (S)-2-amino-4-(hydroxy(methyl)phosphonoyl)butanoic acid) are provided. The methods comprise a two-step process. The first step involves the oxidative deamination of D-glufosinate to PPO (2-oxo-4-(hydroxy(methyl)phosphinoyl)butyric acid). The second step involves the specific amination of PPO to L-glufosinate, using an amine group from one or more amine donors. By combining these two reactions, the proportion of L-glufosinate in a mixture of L-glufosinate and D-glufosinate can be substantially increased.

Abstract: The present invention makes available novel L-lysine excreting bacteria of the species Corynebacterium glutamicum, having the ability to excrete L-lysine, containing in their chromosome a polynucleotide encoding a polypeptide having the activity of a malate:quinone reductase wherein the amino acid at position 228 of the amino acid sequence of the polypeptide contains any proteinogenic amino acid different from valine and a method for producing L-lysine using such bacteria.

Abstract: The invention is in the field of enzymology. More in particular, it provides a method for the isomerization of glucose into fructose wherein the glucose is derived from lignocellulosic material. More in particular, it provides a method for converting glucose into fructose comprising the steps of: providing a composition comprising water, glucose and lignin, enzymatically converting the glucose to fructose in the presence of a glucose isomerase, and optionally purifying the fructose from the solution, wherein the glucose isomerase comprises an amino acid sequence that is at least 90% identical with the sequence according to SEQ ID NO: 1 or SEQ ID NO: 2.

Abstract: The invention is in the field of enzymology. More in particular, it provides a method for the isomerization of xylose into xylulose wherein the xylose is derived from lignocellulosic material.

Abstract: Compositions are disclosed herein comprising a graft copolymer that comprises: (i) a backbone comprising dextran that has been modified with about 1%-25% alpha-1,2 branches, and (ii) one or more alpha-1,3-glucan side chains comprising at least about 50% alpha-1,3 glycosidic linkages. Further disclosed are reactions for producing such graft copolymers, as well as their use in derivatives, films and various other applications.

Abstract: The present invention relates to a method for producing a food product comprising hydrolysed starch, as well as to products obtainable by the method. The method has the advantage of reducing the amount of sugar (i.e. maltose) produced by hydrolysis as compared to conventional methods of starch hydrolysis and present the additional advantage of providing good processability for the food product.

Abstract: This invention relates to DNA-Mn hybrid particles and a method of manufacturing the same, the method including producing a circular DNA template for replication and forming particles in which DNA and Mn are bound to each other using Mn during the synthesis of a new strand of DNA from the circular DNA template for replication using a DNA polymerase, thus promoting the activity of the DNA polymerase using the coenzyme function of Mn and broadening the range of application fields of DNA as a biomaterial.

Abstract: The invention provides compositions, treatment means and protocols for induction of regenerative processes by administration of noble gases. In one particular embodiment the invention provides the stimulation of production of factors associated with augmentation of hematopoiesis, angiogenesis, and wound healing by exposure of cells, organs, or mammals to a noble gas. In a particular embodiment the invention provides the administration of argon as a noble gas capable of upregulating production of VEGF and angiopoietin.

Abstract: The present invention relates to the field of protein production, and in particular to methods and compositions for modulating glycosylation of proteins expressed in host cells.

Abstract: The present invention provides for novel fucosidase mutants that server as fuco-ligases for core fucosylation of a range of biological glycopeptides and glycoproteins including intact therapeutic antibodies. Several mutants with mutation at the general acid/base residue E274 of the Lactobacillus casei ?1,6-fucosidase, including E274A, E274S, and E274G, were able to efficiently fucosylate a wide variety of complex N-glycopeptides and intact glycoproteins. The site specific mutants enable the transfer of fucose to a core GlcNAc-Asn residue and useful for drug delivery and vaccine development.

Abstract: The present disclosure discloses a method for producing 9?-hydroxy androstane-4-alkene-3,17-diketone by enzymatic conversion, and belongs to the fields of gene engineering and enzyme engineering. According to the present disclosure, oxidation subunit KshA, reduction subunit KshB and unknown active subunit KshC of 3-ketosteroid-9?-hydroxylase sourcing from Mycobacterium sp. Strain VKM Ac-1817D are successfully expressed in E. coli BL21, and KshC is identified as an oxidation subunit, the enzyme activity of which is far higher than that of KshA. BL21/pET-28a(+)-fdh constructed in the laboratory is used for expressing formate dehydrogenase (FDH), and by using crude enzyme liquid of KSH (KshB+KshC) and FDH engineering bacteria as a biocatalyst and a steroidal compound (AD) as a substrate, optimum reaction temperature is determined as 30° C. and optimum pH is determined as 7.0. In optimum conditions, AD is converted to produce a product 9-OH-AD, and within 20 hours, the output of 9-OH-AD is 4.

Abstract: The present invention is broadly concerned with new in vitro glycosylation methods that provide rational approaches for producing glycosylated proteins, and the use of glycosylated proteins. In more detail, the present invention comprises methods of glycosylating a starting protein having an amino sidechain with a nucleophilic moiety, comprising the step of reacting the protein with a carbohydrate having an oxazoline moiety on the reducing end thereof, to covalently bond the amino sidechain of the starting protein with the oxazoline moiety, wherein the glycosylated protein substantially retains the structure and function of the starting protein. Target proteins include oxidase, oxidoreductase and dehydrogenase enzymes. The glycosylated proteins advantageously have molecular weights of at least about 7500 Daltons. In a further embodiment, the present invention concerns the use of glycosylated proteins, fabricated by the methods disclosed herein, in the assembly of amperometric biosensors.

Abstract: Provided is a sample processing method that liquefies a medium solution by making a liquid that liquefies the medium solution act on a sample formed by gelating or solidifying the medium solution that is supported by a substrate while an observation subject is included therein, while maintaining a state in which the medium solution is supported by the substrate while the observation subject is included therein.

Abstract: Bacterial systems for analyzing ubiquitination of proteins is disclosed herein. Kits for analyzing the ubiquitination and methods for carrying out the analysis are also disclosed.

Abstract: The purpose of the present invention is to provide a cell creation method that enables a reduction in cost and time, that is highly safe, and that has great potential for being industrially applied. Provided by the present invention is a method for inducing differentiation of pluripotent cells in vitro into cells having a same phenotype and function as information-presentation cells, the method comprising co-culturing pluripotent cells or a cellular fraction having said pluripotent cells concentrated therein, together with damaged cells or dead cells derived from information-presentation cells, or together with a portion of the damaged cells or dead cells derived from information-presentation cells.

Abstract: A mutated tryptophan oxidase suitable for practical implementation is described herein. Specifically, a mutated tryptophan oxidase wherein at least one amino acid residue of a wild-type tryptophan oxidase is mutated and, as a result, has higher tryptophan oxidase activity and/or stability as compared to the wild-type tryptophan oxidase. The mutated tryptophan oxidase can be derived from a wild-type tryptophan oxidase having at least one of Motifs (2), (3), (5), (7), (9), (11), (13), and (14), and at least one amino acid residue in any of these motifs can have mutation. The mutated tryptophan oxidase also can have a mutation of one or more amino acid residues in an amino acid sequence represented by SEQ ID NO: 2 and a sequence homologous thereto.

Abstract: In a first aspect, there is provided an isolated polypeptide substrate for a disintegrin-like and metallopeptidase with thrombospondin type-1 motif, 13 (ADAMTS13) that is from 45 to 70 amino acids in length and has an amino acid sequence that is substantially similar to part of the von Willebrand factor A2 domain sequence set forth in SEQ ID NO: 2, with one or more of the following modifications: (i) the amino acid corresponding to position 1599 of SEQ ID NO: 2 is mutated from Q to K; (ii) the amino acid corresponding to position 1610 of SEQ ID NO: 2 is mutated from N to C; and (iii) the amino acids corresponding to Q1624 to R1641 of SEQ ID NO: 2 are deleted.

Abstract: Kinases can be engineered to utilize an ATP analog that is not readily utilized by wild-type kinases by introducing a mutation in the ATP-binding pocket. However, application of this method has been limited by the membrane impermeability of the ATP analog. Provided herein are methods for in situ visualization of substrates of an analog-sensitive kinase, the method comprising a mild fixation step. Also provided herein are kits comprising a fixative, an ATP analog, and an agent for detecting the substrates modified by the ATP analog.

Abstract: Provided is a method of continuous glucose monitoring (CGM) comprising using an FAD-GDH. The FAD-GDH is capable of retaining initial activity over a certain period of time. Also provided is a method for screening for an FAD-GDH suitable for use in CGM as well as a CGM device comprising an FAD-GDH.

Abstract: A polynucleotide encoding a modified luciferase polypeptide. The modified luciferase polypeptide has at least 60% amino acid sequence identity to a wild-type Oplophorus luciferase and includes at least one amino acid substitution at a position corresponding to an amino acid in a wild-type Oplophorus luciferase of SEQ ID NO:1. The modified luciferase polypeptide has at least one of enhanced luminescence, enhanced signal stability, and enhanced protein stability relative to the wild-type Oplophorus luciferase.

Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples.

Abstract: Methods for detecting presence or absence of at least two known gene fusions in isolated genomic DNA comprise subjecting isolated genomic DNA to multiplex PCR. For each known gene fusion, the multiplex PCR employs one or a plurality of forward primers which hybridize to a first gene adjacent its fusion breakpoint location, and one or a plurality of reverse primers which hybridize to a second gene adjacent its fusion breakpoint location. The primers hybridize to the respective gene at consecutive respective positions separated from one another by a plurality of base pairs. Amplified products are detected and respectively represent the presence of a gene fusion. Amplified products may be Sanger sequenced to determine the fusion breakpoints. The identified specific fusion is monitored by a designed fusion PCR. Drug-resistant mutations are detected using multiplex mutation real-time PCR in patient plasma cell-free DNA during targeted therapy, for example, tyrosine kinase inhibitor-targeted therapy.

Abstract: Improved methods for use in nucleic acid amplification, including multiplex amplification, where the amplification is carried out in two or more distinct phases are disclosed. The first phase amplification reaction preferably lacks one or more components required for exponential amplification. The lacking component is subsequently provided in a second, third or further phase(s) of amplification, resulting in a rapid exponential amplification reaction. The multiphase protocol results in faster and more sensitive detection and lower variability at low analyte concentrations. Compositions for carrying out the claimed methods are also disclosed.

Abstract: A method for quantifying an ADAMTS5 gene, the method includes: measuring an amount of the ADAMTS5 gene in a sample through a quantitative PCR, wherein a primer consisting of a nucleotide sequence set forth in SEQ ID NO: 2 and a primer consisting of a nucleotide sequence set forth in SEQ ID NO: 3 are used as an amplification primer pair for amplifying a region including the ADAMTS5 gene.

Abstract: The invention provides methods and compositions for detecting a mutation in a target gene in a sample of blood or a fraction thereof, including in certain examples, a fraction that includes circulating tumor DNA. The methods can include a tiling PCR reaction, for example a one-sided multiplex tiling reaction. Virtually any type of mutation can be detected with the methods and compositions. In certain embodiments, gene fusions are detected. Improved PCR methods, especially for performing nested multiplex PCR reactions are provided.

Abstract: It is disclosed a method for amplification of nucleic acids in which substantially use is made of the fact that a pre-defined nucleic acid chain (target sequence) can be multiplied/amplified in the presence of a target sequence-specific activator oligonucleotide. The target sequence-specific activator oligonucleotide causes the separation of re-synthesized complementary primer extension products by means of strand displacement, so that a new primer oligonucleotide can attach to the respective template strand. The thus formed complex of a primer oligonucleotide and a template strand can initiate a new primer extension reaction. The thus formed primer extension products in turn function as templates, so that an exponential amplification reaction results. Here, the activator oligonucleotide itself does not function as a template and preferably is inert over a primer extension reaction.

Abstract: The present disclosure relates to methods and devices for amplifying a plurality of targets in a single PCR run while distinguishing between clinically relevant amplification and amplification from other sources such as from background contamination. The methods and devices further enable discrimination between gram-positive, gram-negative and fungal infections as wells as identify antimicrobial resistance genes. When applying the methods and devices of the invention, the species or genus of an infection(s), and genus of a fungal co-infection(s) or category of bacterial (gram-positive or negative) co-infection(s) are identified. Species identification of co-infections can also be achieved. Further, when applying the methods and devices of the invention, organisms which are likely to be contaminating organisms from a blood draw are identified.

Abstract: The invention includes methods and apparatus for separating mutations, especially rare and unknown mutations, using heteroduplex binding proteins. Nucleic acids may optionally be nicked at or near the mutation in order to promote heteroduplex binding protein recognition and binding. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.

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: The present application relates to new coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA.

Abstract: The current document relates generally to the field of nucleic-acid detection and, in particular, to a highly sensitive and specific nucleic-acid-detection method that includes hybridization of a specific nucleic-acid target to a recognition probe, subsequent specific cleavage of the double-stranded target-probe helix at a specific restriction site, and exponential amplification of the enzymatic cleavage accompanied by release of a molecular marker.

Abstract: Various method of isolating a modified polynucleotide having the formula A-P-B from a crude mixture of modified polynucleotides also including those having the formulae A-P-A and B-P-B, wherein P is a polynucleotide region and A and B are different modifying moieties or nucleotide sequences are provided. The methods include the steps of (a) reacting the crude mixture concurrently or consecutively with beads of one type capable of binding to moiety A but not B, and beads of a second type capable of binding to moiety B but not A; (b) fractionating the intermediate product based on the properties of each type of bead and of pairs of different types of bead conjoined by A-P-B polynucleotides, such that only or predominantly conjoined pairs of the two different types of bead are retained and (c) optionally, releasing one or both beads from such conjoined pairs such that the polynucleotide may be recovered.

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: Systems, methods, devices, and kits are described that can be used to distinguish cystic fibrosis patients from healthy individuals and from lung cancer patients. The systems, methods, devices, and kits utilize one or more serum biomarkers.

Abstract: The present invention relates to improved processes for production of closed linear deoxyribonucleic acid (DNA), in particular cell-free enzymatic production of closed linear DNA molecules, preferably using a closed linear DNA as a template for DNA synthesis. The invention further relates to a novel closed linear DNA species, suitable for use as a template in the improved processes for production of closed linear DNA. Further, the invention pertains to the intermediate products of the processes, since this enables the production of larger quantities of closed linear DNA from the template than with methods known in the art.

Abstract: A method for amplifying a CYP21A2 gene and/or a CYP21A2 gene chimera from a sample is provided. In some embodiments, the method may comprise amplifying a product from a sample comprising human genomic DNA by PCR using a forward primer that is complementary to a sequence that is duplicated in a bimodular human RCCX locus and a reverse primer that is complementary to a sequence that occurs only once in the bimodular human RCCX locus at a position that is downstream of the CYP21A2 gene. Methods for analyzing the amplification product are also provided.

Abstract: Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.

Abstract: This disclosure provides a biochip comprising a plurality of wells. The biochip includes a membrane that is disposed in or adjacent to an individual well of the plurality of wells. The membrane comprises a nanopore, and the individual well comprises an electrode that detects a signal upon ionic flow through the pore in response to a species passing through or adjacent to the nanopore. The electrode can be a non-sacrificial electrode. A lipid bilayer can be formed over the plurality of wells using a bubble.

Abstract: The invention provides methods and reagents for diagnosing prostate cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated.