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

Abstract: The present invention provides a method of producing a polymer, which comprises the step of performing a polymerization reaction using, as a starting material, an organic acid obtained by allowing a microorganism or a treated cell thereof to act on an organic raw material, wherein said microorganism has an ability to produce an organic acid and has been modified so as to produce less aromatic carboxylic acid as compared to an unmodified strain.

Abstract: The present disclosure relates to a novel strain capable of saccharifying and fermenting biomass-derived cellulose and a recombinant strain thereof with improved biomass saccharification capability. The present disclosure also relates to a method for producing a material useful as a bioenergy source material such as ethanol, acetic acid, formic acid, etc. using the strain or the recombinant strain. The strain or the recombinant strain may be usefully used in bioenergy industry.

Abstract: The present invention is to provide a preparation of variant recombinant whole cell biocatalysts, referred herein as “designer cells” having significantly enhanced carbonyl reductase activity for use in the efficient production of variant industrially important enantiomerically enriched alcohols. More specifically, the alcohol is optically pure ethyl (S)-4-chloro-3-hydroxybutyrate, which is useful as chiral building block and an intermediate for the production of hydroxymethylglutaryl-CoA (HMG-CoA) reductase inhibitors.

Abstract: The present disclosure relates to bioengineering approaches for producing biofuel and, in particular, to the use of a C1 metabolizing microorganism reactor system for converting C1 substrates, such as methane or methanol, into biomass and subsequently into biofuels, bioplastics, or the like.

Abstract: Disclosed are methods for producing optically active amino acids and amines. According to the methods, ?-keto acids are generated as reaction intermediates, and as a result, ?-transaminase-catalyzed kinetic resolution of racemic amino acids or amines as racemic amine compounds enables the production of optically active amine compounds without the need to use expensive ?-keto acids as starting materials. Therefore, the optically active amine compounds are produced at greatly reduced costs. In addition, the optically active amine compounds have high enantiomeric excess.

Abstract: The present invention describes a bacterium which has an ability to produce an amino acid and in which the rhtC gene encoding a protein having an enhanced activity of imparting L-threonine resistance to a bacterium expressing the protein. Preferably, the bacterium further includes an rhtB gene encoding for a protein having an enhanced activity of imparting to a bacterium L-homoserine resistance expressing the protein. The present invention also describes a method of cultivating the bacterium in a culture medium to produce and accumulate amino acids in the medium, and the amino acid is recovered from the medium.

Abstract: The present disclosure provides engineered ketoreductase enzymes having improved properties as compared to a naturally occurring wild-type ketoreductase enzyme. Also provided are polynucleotides encoding the engineered ketoreductase enzymes, host cells capable of expressing the engineered ketoreductase enzymes, and methods of using the engineered ketoreductase enzymes to synthesize chiral compounds.

Abstract: The invention relates to a novel process for the preparation of chiral 2-(4-aminophenyl) morpholines of the formula wherein R1 is hydrogen an amino protecting group. The chiral 2-(4-aminophenyl) morpholines of the formula I are key intermediates for the preparation of compounds that have a good affinity to the trace amine associated receptors (TAARs).

Abstract: The subject invention pertains to genetically modified microorganisms, e.g., genetically modified B. subtilis strain 168, that lack or which comprise an inactivated secreted endoxylanase of glycoside hydrolase family (GH) 10 or a homolog thereof, if present within the genome of the microorganism; that lack or comprise an inactivated secreted endoxylanase of GH11 or a homolog thereof, if present within the genome of the microorganism, and/or that lack or comprise an inactivated secreted endoxylanase belonging to GH 30 or a homolog thereof, if present within the genome of the microorganism.

Abstract: The present disclosure relates to methods of processing lignocellulosic feedstock that include grinding lignocellulosic feedstock to provide ground lignocellulosic feedstock; and compressing at least a portion of the ground lignocellulosic feedstock to form at least one discrete unit. In some embodiments, a plurality of discrete units have a bulk density in the range from 4 pounds per cubic foot to 25 pounds per cubic foot. The present disclosure also includes related systems.

Abstract: A method of diversification of human milk oligosaccharides (HMOs) or precursors thereof, compounds obtainable by the method, and uses and compositions involving such compounds. The method comprises a) providing at least one compound or a mixture of the compounds selected from the group consisting of: optionally sialylated and/or fucosylated lactose derivatives of general formula 2 and salts thereof; b) adding at least one enzyme comprising a transglycosidase activity to the at least one compound or a mixture of compounds provided according to step a); and c) incubating the mixture obtained according to step b).

Abstract: The present invention relates to methods for converting plant cell wall polysaccharides into one or more products, comprising: treating the plant cell wall polysaccharides with an effective amount of a spent whole fermentation broth of a recombinant microorganism, wherein the recombinant microorganism expresses one or more heterologous genes encoding enzymes which degrade or convert the plant cell wall polysaccharides into the one or more products.

Abstract: Provided herein are compositions for and methods of generating ligation-competent nucleic acids. In some aspects, the compositions comprise Exonuclease III, T4 DNA Polymerase, Klenow, and/or T4 polynucleotide kinase.

Abstract: This invention relates to a biogenic substance production process wherein a) at least one starting material has b) at least one enzyme added to it and the product resulting from b) has c) at least one liver cell added to it, and d) at least one biogenic substance is isolated.

Abstract: Methods for producing proteins, for example, recombinant meningococcal 2086 proteins, using fed-batch fermentation with continuous input of an inducer after achieving a threshold parameter, and optionally continuous input of a carbon source, for example, a constant rate input, to improve protein yields, as well as high density protein compositions and compositions for use in the methods of the present invention, are provided.

Abstract: Disclosed is a method of producing a glycoprotein, the method including the steps of: introducing a gene encoding a desired protein and a gene encoding an antibody that inhibits a decomposing enzyme preventing formation of a desired complex-type sugar chain in the desired protein into an insect organism or insect cells; and obtaining a desired protein having a desired complex-type sugar chain from the insect organism or insect cells obtained in the introduction step.

Abstract: Methods are provided to improve the expression of protein complexes by tuning the expression levels of each component required for the assembly of the complex. These methods are effective in limiting the expression of the dominant chain and, thus, equilibrating their relative abundance. The methods provided herein lead to a significant increase in productivity and final bispecific yields both in transient expression systems as well as in stably transfected mammalian cells.

Abstract: In a method for detecting fluorescence or absorbance of the present invention, a diaphorase causes reduction from resazurin to resorufin in the presence of an SH reagent and NADH or NADPH, and the resulting fluorescence intensity or absorbance is measured. A method for measuring ADP of the present invention includes a 2-1 process in which glucose is reacted with ADP and an ADP-dependent hexokinase, a 2-2 process in which the glucose-6-phosphate obtained in the 2-1 process is reacted with NAD or NADP and glucose-6-phosphate dehydrogenase, and a 2-3 process in which resazurin is reacted with the NADH or NADPH obtained in the 2-2 process and a diaphorase in the presence of an SH reagent, and the resulting fluorescence intensity or absorbance is measured.

Abstract: A system for automated microorganism identification and antibiotic susceptibility testing comprising a reagent cartridge, a reagent stage, a cassette, a cassette, stage, a pipettor assembly, an optical detection system, and a controller is disclosed. The system is designed to dynamically adjust motor idle torque to control heat load and employs a fast focus process for determining the true focus position of an individual microorganism. The system also may quantify the relative abundance of viable microorganisms in a sample using dynamic dilution, and facilitate growth of microorganisms in customized media for rapid, accurate antimicrobial susceptibility testing.

Abstract: A method of selectively identifying live microorganisms in a sample involves contacting a sample suspected of containing a live microorganism of interest with a biomolecular precursor labeled with a reactive chemical label. The live microorganism of interest is grown under conditions that promote selective growth of the microorganism to permit the microorganism to utilize the labeled biomolecular precursor to synthesize labeled biomolecules on a cell surface of the live microorganism. Labeled live microorganisms are contacted with a reporter and/or capture element bearing a functional group that reacts with the reactive chemical label. The labeled live microorganism is analyzed to identify it. The method can specifically isolate live microorganisms from dead ones thereby reducing the possibility of false identification of contaminating microorganisms and is able to detect specific strains using tailored metabolites that are specific for a given microorganism.

Abstract: The present invention is concerned with means and methods for determining neurotoxin activity. Specifically, it relates to a polynucleotide encoding a fusion polypeptide comprising (i) a transcription factor domain and (ii) a cytoplasmic retention domain, separated by a linker comprising a neurotoxin cleavage site and to a fusion polypeptide encoded by the polynucleotide of the invention. Also contemplated is a vector comprising the polynucleotide of the invention and a host cell comprising the polynucleotide, vector or fusion polypeptide of the invention. Moreover, envisaged is a method for determining neurotoxin activity in a sample. In addition, the invention pertains to the use of the polynucleotide, vector, fusion polypeptide or host cell of the invention for determining neurotoxin activity in a sample. Finally, the invention relates to a kit for determining neurotoxin activity comprising the polynucleotide, vector, fusion polypeptide or host cell of the invention.

Abstract: The present disclosure provides a monitoring device comprising a test composition, a test element comprising a test portion to which the test composition is releasably adhered, a detection reagent, and a container comprising a first end with an opening and a second end opposite the first end. The test composition comprises a predetermined quantity of tracer analyte. The container is configured to receive the test portion and configured to be operationally coupled to an analytical instrument. The tracer analyte and the detection reagent each are capable of participating in one or more chemical reaction that results in the formation of a detectable product. A method of using the monitoring device to assess the efficacy of a washing process is also provided.

Abstract: The present application discloses a biosensor that comprises a nucleic acid probe absorbed on reduced graphene oxide, the nucleic acid probe comprising an RCA primer sequence linked to a recognition moiety for an analyte to be detected by the biosensor.

Abstract: The invention relates to the use of Argonaute polypeptide:guide molecule complexes as fast and specific nucleic acid probes, as specific, nucleic acid-guided restriction enzymes for DNA and RNA substrates, and as a means to detect RNA-protein interactions, RNA detection, DNA detection, and RNA depletion. Using such Argonaute polypeptide:guide molecule complexes enables fast and specific detection, purification, and enzymatic activity.

Abstract: A method is provided herein, wherein the method of capturing a sperm deoxyribo nucleic acid (DNA) in a sample, comprises contacting a lysis solution to the sample comprising at least a sperm cell or a sperm cell lysate to lyse the sperm cell. The sperm cell or sperm cell lysate comprises a protamine-DNA complex. The method further comprises applying at least a protamine-specific antibody to the lysed sperm cell, wherein the protamine-specific antibody binds to the protamine-DNA complex of the lysed sperm cell to form an antibody-protamine-DNA complex. The antibody binding is followed by capturing the antibody-protamine-DNA complex; and isolating and detecting the sperm DNA from the captured antibody-protamine-DNA complex.

Abstract: Methods, devices, and kits are provided for performing PCR and other thermal cycling reactions in <20 seconds per cycle, using induction heating.

Abstract: The present invention relates to transposase adapters and uses thereof, including uses in preparing DNA molecules, in vitro amplification, sequencing of nucleic acids, and screening of DNA libraries for sequences of interest as well as nucleic acid delivery.

Abstract: The present invention provides a method for analysing the interaction of one or more nucleotide sequence(s) from one or more region(s) of interest with other nucleotides sequences in a three-dimensional DNA structure, comprising the steps of: (a) providing a sample of cross-linked DNA; (b) digesting the cross-linked DNA with a first restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross-linking; e) fragmenting the ligation and ligated molecules from (d); (f) hybridising the fragments from (e) to one or more oligonucleotides representing the sequences which are adjacent to the cleavage site of the first restriction enzyme in order to enrich for the ends of the nucleotide sequences that have been ligated to another nucleotide sequence in step (c); and (g) analysing the nucleotide sequence of the enriched fragments in order to identify the nucleotide sequences involved in interaction(s).

Abstract: A kit for optional use with a PCR method of amplification may include at least one reaction well, and an internal amplification control for a PCR amplification of an APS reductase gene having a sequence complementary to at least one sequence essentially identical to SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, and mixtures thereof. The kit may be used with a PCR method of amplifying at least one sulfur-reducing bacteria extracted from an oilfield fluid.

Abstract: The present disclosure provide compositions, methods and kits for generating a set of combinatorial barcodes, and uses thereof for barcoding samples such as single cells or genomic DNA fragments. Some embodiments disclosed herein provide compositions comprising a set of component barcodes for producing a set of combinatorial barcodes. The set of component barcodes can comprise, for example, n×m unique component barcodes, wherein n and m are integers, each of the component barcodes comprises: one of n unique barcode subunit sequences; and one or two linker sequences or the complements thereof, wherein the component barcodes are configured to connect to each other through the one or two linker sequences or the complements thereof to produce a set of combinatorial barcodes.

Abstract: The present application provides circular templates that are high in adenine and cytosine and methods and uses thereof for rolling circle amplification (RCA). These templates are particularly suitable for biosensing applications involving RCA.

Abstract: Methods for the selective enrichment of nucleic acids.

Abstract: The present invention is directed to methods of decalcification and tissue sample preparation that allows for the reproducible quantitative analysis of gene expression in hard tissue samples like bone, mineralizing cartilage and tendon, dentin, cementum and/or enamel that are too hard to section effectively using conventional means.

Abstract: Methods and apparatus for separating, concentrating and/or detecting molecules based on differences in binding affinity to a probe are provided. The molecules may be differentially modified. The molecules may be differentially methylated nucleic acids. The methods can be used in fields such as epigenetics or oncology to selectively concentrate or detect the presence of specific biomolecules or differentially modified biomolecules, to provide diagnostics for disorders such as fetal genetic disorders, to detect biomarkers in cancer, organ failure, disease states, infection or the like.

Abstract: Described herein is a method and assay of detecting the presence of a polynucleotide in a bodily fluid obtained from a subject treated with an anti-pathogenic agent comprising isolating the polynucleotide from a first and a second sample of a bodily fluid, amplifying the polynucleotide, and determining the polynucleotide, wherein the polynucleotide is a pathogen polynucleotide. Further provided is a method for diagnosing a pathogen infection in a subject, for detecting a pathogen infection in a subject treated with an anti-pathogenic agent, and for detecting the presence and/or genotype of a pathogen in a bodily fluid.

Abstract: The present invention provides novel methods of diagnosing and determining treatment strategies for Lyme disease and other tick-borne illnesses.

Abstract: A method for detecting a target nucleic acid sequence in a sample in the presence of at least protein capable of binding to single-stranded DNA is provided, comprising contacting said sample with at least one oligonucleotide probe comprising a fluorophore, a quencher and a region complementary to said target nucleic acid sequence. The sequence of the oligonucleotide probe comprises at least 20% RNA nucleotides, modified RNA nucleotides and/or PNA nucleotides.

Abstract: Methods for detecting Legionella (such as Legionella spp., Legionella pneumophila, Legionella pneumophila serogroup 1, Legionella bozemanii, Legionella dumoffii, Legionella feeleii, Legionella longbeachae, and/or Legionella micdadei) are disclosed. A sample suspected of containing one or more Legionella nucleic acids is screened for the presence or absence of that nucleic acid. Determining whether Legionella nucleic acid is present in the sample can be accomplished by contacting the sample with detectably labeled probes capable of hybridizing to a Legionella nucleic acid and detecting hybridization between the probes and nucleic acids in the sample. Detection of hybridization indicates that a Legionella nucleic acid is present in the sample. Also disclosed are probes and primers for the detection of Legionella, and kits that contain the disclosed probes and/or primers.

Abstract: A double-stranded nucleic acid hybridization probe and methods of using the same are described. The probe described is particularly suited for real-time RT-PCR reactions and has high tolerance to mismatches.

Abstract: The present invention provides a method for performing a localised RCA reaction comprising at least two rounds of RCA, wherein the product of a second RCA reaction is attached, and hence localised, to a product of a first RCA reaction, said method comprising: (a) providing a concatemeric first RCA product comprising repeated monomers; (b) directly or indirectly hybridising to monomers of said first RCA product a circularisable oligonucleotide comprising target-complementary 3? and 5? end regions such that the 3? and 5? ends of said oligonucleotide hybridise in juxtaposition for ligation directly or indirectly to each other, wherein the target is a sequence in a monomer of said first RCA product or an intermediate molecule hybridised thereto, and wherein the target-complementary end regions of said circularisable oligonucleotide are 6 to 16 nucleotides in length; (c) directly or indirectly ligating the ends of said circularisable oligonucleotide to circularise the oligonucleotide, thereby to provide a template

Abstract: The invention relates to the field of multiplex amplification. In particular, the invention relates to methods for assaying a sample for one or more nucleic acid targets in a single reaction based on the distinct melting temperatures or melting profiles of primers and/or probes. The invention also provides probes and kits for use in such methods.

Abstract: The invention relates to a novel buffer formulation that is able to reduce reaction time compared to conventional LAMP buffer and may be universally applied to other LAMP reactions with little optimization required. The invention also relates to a modified LAMP method making use of the novel buffer and may incorporate SNP-discriminating forward loop primers to enhance the LAMP reaction while also reducing the likelihood of false-positives.

Abstract: A method of evaluating a sequence variation in a sample is provided. In some embodiments, the method may involve: amplifying a nucleic acid product from an initial sample; fragmenting an amount of the nucleic acid product to produce fragments; attaching an adaptor to each end of the fragments to produce adaptor-tagged fragments; sampling no more than 10% of the tagged fragments and amplifying them; sequencing at least some of the copies of the fragments to produce a plurality of sequence reads; grouping sequence reads for copies of fragments that have the same fragmentation breakpoints; deriving a consensus sequence for each of the read groups; and aligning the consensus sequences with a reference sequence.

Abstract: The invention discloses diagnostic techniques based on single cell genomics, consisting of obtaining a blood sample, enriching a sub-population of cells present in the blood sample, sequestering individual cells or group of cells from the blood sample, obtaining sequencing data from the sequestered cells or group of cells, using genetic variant information to determine the provenance of the cells, and genetically analyzing the cells of the correct provenance to provide a diagnostic readout. Using the cell-based testing techniques of the invention, the number of false positives is greatly reduced when compared to cell-free DNA (cfDNA) based traditional testing techniques. The invention may be effectively employed for non-invasive prenatal (NIPT) diagnostics, oncological testing and other diagnostic procedures.

Abstract: The invention relates to DNA-adapter-molecules for the preparation of DNA-libraries and methods for producing them and their use. The invention is useful for the application in molecular biology, in particular for Next Generation Sequencing and/or Library Multiplexing. The present invention discloses DNA-adapter-molecules, comprising a double-stranded polynucleotide molecule, whereat the 5? end of the first strand is modified in a way, that no binding site for kinases is available, the 3? end of the first strand is modified in a way that no ligation can occur, the 5? end of the reverse strand is modified in a way, that no binding site for a kinase is available, and the 3? end of the reverse strand features a free hydroxyl group (at the 3? position of the last nucleotide).

Abstract: Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed.

Abstract: The invention relates to a method for detecting RNA sequences. The invention also relates to nucleotide sequences, primers, probes and microarrays.

Abstract: Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of Pyrroline-5-carboxylate reductase 1 (PYCR1), in particular, by targeting natural antisense polynucleotides of Pyrroline-5-carboxylate reductase 1 (PYCR1). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of PYCR1.