Abstract: The present disclosure provides cytomegalovirus vectors encoding fusion proteins comprising Mycobacterium tuberculosis (Mtb) antigens, nucleic acid molecules encoding the same, cytomegalovirus vectors comprising nucleic acid molecules, compositions comprising the same, and methods of eliciting an immune response against tuberculosis.

Abstract: The present invention relates to a method for transducing a target cell, the method comprising the step of contacting a target cell with a retroviral vector and a poloxamer having a molecular weight of 12.8 kDa to about 15 kDa. Further, the invention relates to the use of a poloxamer as defined herein, optionally in combination with a polycationic substance as defined herein, for transducing a target cell with a retroviral vector and a kit comprising a retroviral vector, a poloxamer as defined herein and, optionally, instructions for use.

Abstract: Provided herein are methods and kits for modulating genome editing of target DNA. The invention includes using small molecules that enhance or repress homology-directed repair (HDR) and/or nonhomologous end joining (NHEJ) repair of double-strand breaks in a target DNA sequence. Also provided herein are methods for preventing or treating a genetic disease in a subject by enhancing precise genome editing to correct a mutation in a target gene associated with the genetic disease. Further provided herein are systems and methods for screening small molecule libraries to identify novel modulators of genome editing. The present invention can be used with any cell type and at any gene locus that is amenable to nuclease-mediated genome editing technology.

Abstract: A system and process is disclosed for adding pre-fermentation separated non-fermentables, e.g., fiber, germ/oil, and/or protein, to a post-fermentation stream in a corn (or similar carbohydrate-containing grain) dry milling process for making alcohol and/or other biofuels/biochemical. The process includes mixing grain particles with a liquid to produce a slurry having starch and non-fermentables. The slurry is subjected to liquefaction to convert the starch in the slurry to complex sugars and produce a liquefied stream including the complex sugars and non-fermentables. After liquefaction but prior to fermentation of simple sugars resulting from conversion of the complex sugars, the non-fermentables are separated out to define a non-fermentables portion and an aqueous solution including the complex and/or simple sugars. The simple sugars are fermented to provide a fermented stream. Then, the separated non-fermentables portion is reincorporated back into the process into a post-fermentation stream.

Abstract: A method for producing arabitol may include providing a fermentation culture having a microorganism and a carbon source; allowing the microorganism to ferment the carbon source; monitoring a process condition of said step of allowing the microorganism to ferment the carbon source; and collecting a product from the fermentation culture after said step of monitoring a process condition indicates that a predetermined change in the process condition has occurred. Other methods may include steps of providing soybean-based lignocellulosic hydrolysate as a carbon source for a fermentation culture, and modifying the pH of one or more of the growth phase and the stationary phase of a fermentation process.

Abstract: The present invention relates to a method for the production of itaconic acid, which method comprises fermenting a recombinant cell capable of producing itaconic acid in a suitable fermentation medium, thereby to produce itaconic acid, wherein: (a) the recombinant cell: (i) overexpresses cis-aconitate decarboxylase; and (ii) overexpresses a part of the citric acid cycle and/or has reduced activity of a native metabolic route to acetate and/or lactate; and, optionally, (b) the fermentation is carried out under anaerobic conditions.

Abstract: The invention concerns a strain of Shizochytrium mangrovei filed on 22 Nov. 2012 with the CNCM as number 1-4702 having the ability to produce a high quantity of docosahexaenoic acid (or DHA) and palmitic acid, the methods for producing the corresponding biomass containing said lipid compounds of interest, and the biomass containing the products and compositions prepared from this strain.

Abstract: The invention provides a method of degrading or hydrolyzing a polysaccharide, preferably cellulose or chitin, comprising contacting said polysaccharide with one or more oxidohydrolytic enzymes, preferably a CBM33 family protein (preferably CBP21) or a GH61 family protein, wherein said degradation or hydrolysis is carried out in the presence of at least one reducing agent and at least one divalent metal ion. A method of producing an organic substance comprising said method is also provided.

Abstract: The present invention relates to a method for pretreating a softwood starting material comprising the following steps: a) pretreating the softwood starting material in a pretreatment process to form a slurry; b) measuring the concentration of glucose and the concentration of mannose in the slurry formed in step a); c) calculating a ratio glucose:mannose from the concentrations measured in step b) d) comparing the ratio calculated in step c) to a reference value and if the ratio calculated in step c) differs from the reference value, controlling at least one process parameter of the pretreatment process in response to the difference.

Abstract: This Invention relates to, for production of N-acetyl-D-glucosamine and D-glucosamine by microbial fermentation: A nongenetic recombinant strain, preserved in the General Microbiology Center of the China Committee for Culture Collection of Microorganisms; NJ090259, a strain of Bacillus subtilis, Preservation No. CGMCC10257; and NJ091195, a strain of Bacillus licheniformis, Preservation No. CGMCC10258 and Preservation Date Dec. 29, 2014. The beneficial effects of this Invention are: Provide a new strain for production of N-acetyl-D-glucosamine and D-glucosamine, and its production methods. By this method, it may achieve stable production and supply of N-acetyl-D-glucosamine, and may also achieve non-animal-derived, safety production of N-acetyl-D-glucosamine and D-glucosamine; the method is of short production phase and low cost, and is more environmentally-friendly.

Abstract: The invention relates to a method of nucleic acid synthesis comprising the use of 3?-O-azidomethyl blocked nucleotide triphosphates which comprises the step of adding a capping group to any uncleaved 3?-O-azidomethyl groups and to the use of kits comprising said capping groups in a method of nucleic acid synthesis. The invention also relates to capped nucleotide triphosphates and 3?-O-azidomethyl capping groups.

Abstract: The invention provides a construction method of spinosad heterologous expression strain, a spinosad heterologous expression strain obtained by the method and use thereof in preparing spinosad. The method utilizes a plurality of homologous recombination to replace the erythromycin synthetic gene cluster of Saccharopolyspora erythraea with the spinosad synthetic gene cluster and the rhamnose synthetic gene cluster, such that the Saccharopolyspora erythraea produces spinosad.

Abstract: The present invention relates to a method of using cells to produce a substance, and involves applying the cells to a polyimide porous film, culturing the cells and producing the substance by means of the cells.

Abstract: Disclosed are methods, systems, components, and compositions for cell-free synthesis of glycosylated proteins. The glycosylated proteins may be utilized in vaccines, including anti-bacterial vaccines. The glycosylated proteins may include a bacterial polysaccharide conjugated to a carrier, which may be utilized to generate an immune response in an immunized host against the polysaccharide conjugated to the carrier. The glycosylated proteins may be synthesized in cell-free glycoprotein synthesis (CFGpS) systems using prokaryote cell lysates that are enriched in components for glycoprotein synthesis such as oligosaccharyltransferases (OSTs) and lipid-linked oligosaccharides (LLOs) including OSTs and LLOs associated with synthesis of bacterial O antigens.

Abstract: The present invention relates to a method for preparing a recombinant Phe-free or Phe-low protein, the method comprising using B. subtilis or B. licheniformis as an expression system and/or a recombinant host cell into which a nucleotide encoding a recombinant Phe-free or Phe-low protein has been inserted into the genome.

Abstract: Disclosed are methods, systems, components, and compositions related to genomically recoded and engineered organisms. The disclosed genomically recoded and engineered organisms may be used to prepare extracts for use in platforms and methods for preparing sequence defined biopolymers in vitro. In particular, the methods, systems, components, and compositions relate to genomically recoded and engineered organisms comprising a strain deficient in release factor 1 (RF-1) or a genetic homolog thereof, wherein the genomically recoded organisms have been engineered to express a heterologous RNA polymerase that may be utilized to express a target protein from a transcription template comprising a promoter for the heterologous RNA polymerase, such as bacteriophage T7 RNA polymerase.

Abstract: A method of making an electrochemical sensor strip that includes: depositing a first electrode on a base; depositing a second electrode on the base; applying a first layer onto the first electrode; and applying a second layer onto the second electrode. The first layer includes an oxidoreductase and a mediator. The second layer includes a soluble redox species.

Abstract: Methods and compositions for the identification of functional C. difficile toxin, as among other things identifying individuals infected with toxigenic C. difficile and therefore in need of therapy. In specific embodiments, the methods and compositions provide colorimetric assays for cleavage activity of C. difficile toxin.

Abstract: Particular aspects provide a method of sampling, testing and validating test lots (e.g., single-unit production lots), comprising: assembling a plurality of product portions from each of a plurality of test lots and combining the collected product portions to provide a corresponding set of test lot samples (wherein each test lot sample is attributed to a particular corresponding test lot); enriching the set of test lot samples; removing equal portions of each enriched sample, and combining the removed portions to provide a modular composite sample; and testing of the modular composite sample for the target agent/organism, wherein where such testing is positive, individual test lots may nonetheless yet be validated by further testing of a respective enriched test lot sample and obtaining a negative test result. The methods have broad utility for monitoring all sorts of test lots (e.g., environmental lots, production lots, pharmaceutical lots, etc.

Abstract: The present invention provides a method for determining the presence of a microorganism in a sample using an electrochemically active reporter, wherein the method comprises (a) contacting the sample with an electrochemically active reporter, wherein the electrochemically active reporter is a conjugate comprising a sugar moiety and a redox active reporter moiety that are covalently linked such that the covalent bond can be enzymatically cleaved in the presence of the microorganism by an enzyme expressed by the microorganism, wherein the redox active reporter moiety is selected from the group consisting of resorufin and compounds of formula (I) as defined herein, under conditions that allow enzymatic cleavage of the covalent bond between the sugar moiety and the redox active reporter moiety and reduction of the redox active report moiety in the presence of the microorganism; (b) electrochemically determining the released redox active reporter moiety; and (c) determining the presence of the microorganism and, op

Abstract: A rapid screening process is provided for identification of bacterial resistance to antibiotics by utilizing LC-MS/MS to quantitate concentrations of parent drugs and also detect hydrolysis products which result from beta-lactamase activity. The susceptibility testing is accomplished in time periods as short as 90 minutes, which includes incubation of bacteria with antibiotics and LC-MS/MS analysis. The antibiotics can be multiplexed for incubation with bacteria to minimize analysis time. 23 different strains of E. coli have been evaluated by this method including ATCC reference (3) as well as clinical isolates (20) and achieved complete concordance with traditional methods. To date the following antibiotics have been tested: penicillin, ampicillin, amoxicillin, cloxacillin, piperacillin/tazobactam, and cefotaxime. All incubations are conducted in the absence and presence of tazobactam which acts as a control.

Abstract: Isolated antigen binding molecules that specifically binds to a molecule comprising an amino acid sequence selected from the group consisting of GSTSGSGKPGSGEGSTKG (SEQ ID NO: 1), GSGKPGSGEG (SEQ ID NO: 2), GKPGSGEG (SEQ ID NO: 3), SGKPGSGE (SEQ ID NO: 499) and KPGSG (SEQ ID NO: 500) are provided. The antigen binding molecules can be used in the methods provided herein.

Abstract: Method to perform a PCR assay that comprises the following steps: a. Obtaining a nucleic acid sample; b. Hybridizing that nucleic acid sample to one or more pair of primers where at least one primer consists of a single stranded DNA polynucleotide having a length of 60 or more nucleotides; c Subjecting said nucleic acid sample to a PCR, wherein the reaction mixture medium contains at least one of said primers; and d. Detecting the length of the amplified products. The amplified nucleic acid may contain any sequence or multiple sequences of STRs (short tandem repeats), genes or any coding region having a defined location on a genome. The preferred nucleic acid samples to be amplified are degraded or fragmented and contain one or more genetic markers.

Abstract: The present invention generally relates to droplet-based microfluidic devices, including systems, methods, and kits for amplifying or cloning within droplets. In some embodiments, the present invention is generally directed to systems, methods, or kits for amplifying a plurality of nucleic acids, e.g., without substantially selectively amplifying some nucleic acids over others. The nucleic acids may be contained within the droplets. In addition, in some embodiments, a plurality of microfluidic droplet containing a species of interest, such as a nucleic acid, may be mixed with microfluidic droplets free of the species, then pipetted or otherwise transferred such that, on average, a predetermined number of droplets containing species of interest is transferred.

Abstract: This disclosure relates generally to methods and kits useful for preparing samples, extracting nucleic acids from samples (e.g., biological samples), and/or detecting nucleic acids (e.g., pathogen nucleic acids) in samples (e.g., samples obtained from a subject). In particular, compositions, kits, and methods are provided comprising detergents and proteinases to treat biological samples prior to extraction of nucleic acids. Also described is use of cations for improved efficiency of nucleic acid hybridization. The prepared nucleic acid is suitable for PCR assays including those described for detection of Mycobacterium tuberculosis.

Abstract: Systems and methods for multiple analyte detection include a system for distribution of a biological sample that includes a substrate, wherein the substrate includes a plurality of sample chambers, a sample introduction channel for each sample chamber, and a venting channel for each sample chamber. The system may further include a preloaded reagent contained in each sample chamber and configured for nucleic acid analysis of a biological sample that enters the substrate and a sealing instrument configured to be placed in contact with the substrate to seal each sample chamber so as to substantially prevent sample contained in each sample chamber from flowing out of each sample chamber. The substrate can be constructed of detection-compatible and assay-compatible materials.

Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

Abstract: Methods for the high-throughput analysis of transgenic events are herein disclosed. The methods use libraries of sheared genomic DNA ligated to specialized adapters and pooled for sequence analysis and comparison to known genomic and insert sequence. The method finds use in detecting characterizing insertion site, transgene integrity, and transgene copy number.

Abstract: Provided is a method of authenticating an active pharmaceutical ingredient (API). The method includes providing an API or an API component and adding a nucleic acid marker having a nucleic acid marker sequence to produce a marked API or a marked API component. The presence of the nucleic acid marker is detected in the sample and the authenticity of the API is thereby determined according to whether the pharmaceutical product includes marked API or the marked API component.

Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

Abstract: A sensing device includes a stack of dielectric layers having conductive materials disposed between the dielectric layers. A nanopore is disposed through the stacks of dielectric layers and separates the conductive materials to provide electrodes on opposite sides of the nanopore. Contacts connect to each of the electrodes.

Abstract: Improved methods and compositions are provided herein for primer extension target enrichment of target polynucleotides.

Abstract: Disclosed is a method suitable for (long-range) mate pair sequencing wherein the mate pairs are located within a certain distance from each other on the same nucleotide sequence. By ligating a DNA fragment into an identifier section—containing backbone, a digestable circularized construct is provided to which adaptors can be ligated after digestion. Amplification yields amplicons that contain a combination of the identifier section with the terminal part of the fragments. The fragments are subsequently mated to each other to obtain a mated pair by identifying the corresponding identifier section in both amplicons. The mated pairs can be used in the construction of genome scaffolds or in the generation of draft genome sequences.

Abstract: The present invention provides a method for targeted enrichment of nucleic acids including contacting a nucleic acid including at least one region of interest with a plurality of transposase complexes. Each of the transposase complexes includes at least a transposase and a first polynucleotide having a transposon end sequence and a first label sequence. The method further includes incubating the nucleic acid and the transposase complexes under conditions whereby the nucleic acid is fragmented into a plurality of nucleic acid fragments including first polynucleotide attached to each 5? end of the nucleic acid fragments. The method further includes selectively amplifying the nucleic acid fragments, thereby enriching for a portion of the nucleic acid fragments including the at least one region of interest relative to a remaining portion of the nucleic acid fragments, and sequencing the enriched nucleic acid fragments.

Abstract: The invention generally provides a sieve valve including: a substrate defining a channel; a flexible membrane adapted and configured for deployment at an intersection with the channel; and one or more protrusions extending into the channel from the substrate or the flexible membrane. The one or more protrusions define a plurality of recesses extending beyond the intersection between the channel and the flexible membrane; A microfluidic circuit including one or more sieve valves. In particular embodiments, the circuit comprises one or more input/output valves. The one or one or more input/output valves can include one or more input valves and one or more output valves. The microfluidic circuit can further include a mixing circuit. At least one of the sieve valves can be positioned between the one or more input/output valves and the mixing circuit. The invention further provides methods of using the device for the analysis of samples comprising cells.

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 provides methods for predicting the risk of an individual developing antibodies to factor VIII by identifying a single nucleotide polymorphism of an immune response or immune modifier gene. The invention further provides oligonucleotides, diagnostic kits, microarrays, and isolated nucleic acids comprising single nucleotide polymorphisms of immune response or immune modifier genes.

Abstract: A method for assessing the predisposition of a subject to weight loss attainable by applying one or more dietary interventions to a subject and/or the predisposition of a subject to maintenance of weight loss following one or more dietary interventions which method comprises determining the nucleotide of the subject at one or more polymorphic positions selected from: (i) position 101 of SEQ ID NO:1 (rs953211) (ii) position 101 of SEQ ID NO:2 (rs1509290) (iii) position 101 of SEQ ID NO:3 (rs1509289) and/or detecting one or more biomarkers genetically linked to said polymorphic positions.

Abstract: The present invention relates to a novel procedure for evaluating the response of patients affected by Ataxia Talangiectasia (A-T) to glucocorticoids treatment. In particular, the procedure provides a step of qualitative and/or quantitative identification in the blood of said patients of the expression of a mRNA variant of the ATM (Ataxia-Talangiectasia-Mutated) gene produced by non-canonical splicing induced by glucocorticoid (GC). In fact, it was demonstrated that mRNA variant expression is present in the blood of patients who responded positively to treatment with GC.

Abstract: The present invention relates to the discovery that the expression levels of some RNA molecules, comprising messenger RNA (mRNA), non-coding RNA (ncRNA) and/or microRNA (miRNA), and protein can be used as a diagnostic signature to predict or monitor the bone healing ability in an acutely injured subject or in a chronic nonunion subject. In certain embodiments, the invention relates to methods and compositions useful for differentiating between a nonunion, slow healing, and/or normal healing of a fractured bone and treatment recommendations. The invention further includes a kit comprising biomarker probes for assessing the bone healing ability in an acutely injured subject or in a nonunion subject after receiving therapeutic treatment.

Abstract: The present invention provides a composition, a kit and the use thereof, as well as the method for detecting the cell proliferative abnormality in individuals or grading the disease degree in the individuals. The composition comprises nucleic acids for detecting the methylation level within at least one target region of a gene and the fragment thereof.

Abstract: Disclosed is a kit for detecting drug resistance of cetuximab in the treatment of metastatic colorectal cancer. The kit comprises a substance used for detecting gene mutations in Exon 19 of the PIK3CA gene, and may further comprise a specification recording the following contents: if Exon 19 in the PIK3CA gene of a patient with metastatic colorectal cancer as a subject to be tested, who is intended to receive cetuximab treatment or is receiving cetuximab treatment and does not have drug resistance, has at least one of K944N, F930S, V955G, V955I, and K966E mutations, the subject to be tested will develop drug resistance or will be a candidate to develop drug resistance when receiving or continuing to receive cetuximab for treating metastatic colorectal cancer.

Abstract: Provided herein is technology relating to enzymatic modification of nucleic acids and particularly, but not exclusively, to methods and compositions relating to using uracil-DNA-N-glycosylase for minimizing or eliminating errors in a DNA sequence due to deamination of cytosine residues.

Abstract: Provided herein are methods, systems and kits for stratification of risk of disease occurrence of a sample obtained from a subject by combining two or more feature spaces to improve individualization of subject management.

Abstract: The present invention relates to a kit and nucleic acid chip for diagnosing bladder cancer using a bladder cancer-specific marker gene. More particularly, the invention relates to a kit and nucleic acid chip for diagnosing bladder cancer, which can detect the promoter methylation of a bladder cancer-specific gene, the promoter or exon region of which is methylated specifically in transformed cells of bladder cancer. The use of the diagnostic kit or nucleic acid chip of the invention enables diagnosis of bladder cancer at an early stage of transformation, thus enabling early diagnosis of bladder cancer, and can diagnose bladder cancer in a more accurate and rapid manner compared to a conventional method.

Abstract: The present disclosure relates to a method for detecting methylation of the bowel-cancer-specific methylation marker GPM6A (NM_201591, glycoprotein M6A) gene in order to diagnose bowel cancer, and more specifically relates to a method for providing information for diagnosing bowel cancer by detecting the methylation of a bowel-cancer-specific marker gene that is specifically methylated in bowel cancer cells. The method for detecting methylation and a diagnostic composition, kit and nucleic-acid chip according to the present disclosure can be used to advantage in diagnosing bowel cancer more accurately and quickly than by normal methods as they permit bowel cancer to be diagnosed at the initial genetic transformation step and so allow early diagnosis.

Abstract: Methods and compositions to genotype microspores and/or pollen grains are provided. Methods provided include using meiotically-related products to non-destructively determine the genotype of one of the meiotically-related products such that it can be further used. For example, methods to obtain a genotype of a microspore are provided. The methods include: isolating tetrads, separating the tetrads to obtain four tetrad microspores; genotyping three of the four tetrad microspores, and inferring the genotype of the fourth tetrad microspore. Methods are also provided for generating doubled haploid plants from the microspores that are selected for further analysis based on inferred genotypes. Viable genotyped pollen produced by these methods, as well as seed, cells, plants, germplasm, progeny, and plant parts derived therefrom are also provided.

Abstract: The present invention provides methods and compositions for the identification and selection of loci modulating phenotypic expression of a chloride tolerant trait in plant breeding. In addition, methods are provided for screening germplasm entries for the performance and expression of this trait.

Abstract: The multiple embodiments described herein comprise the genome of a probiotic Bifidobacterium longum bifidobacteria strain and genes encoded by the genome. Various novel Bifidobacterium longum are described.

Abstract: The present invention relates to a lysosomal protein composition comprising a plurality of lysosomal proteins that are potentially diversely glycosylated according to a glycosylation pattern, wherein said glycosylation pattern has at least 45% paucimannosidic N-glycans; a method of manufacturing the lysosomal protein composition in a bryophyte plant or cell, and medical and non-medical uses of the lysosomal protein composition. E.g. the lysosomal protein can be a-Galactosidase for the treatment of Fabry Disease or ?-Glucoceramidase for the treatment of Gaucher's Disease. The unique glycosylation results in improved therapeutic efficacy—surprisingly even without mannose-6-phosphate that is common for CHO cell produced lysosomal proteins.