Abstract: This invention relates to metabolically engineered microorganism strains, such as bacterial strains, in which there is an increased utilization of malonyl-CoA for production of a fatty acid or fatty acid derived product, wherein the modified microorganism produces fatty acyl-CoA intermediates via a malonyl-CoA dependent but malonyl-ACP independent mechanism.

Abstract: The present disclosure describes biocatalytic processes for producing a product, comprising providing an aqueous stream (AS) comprising at least one fermentable substrate and a gaseous stream (GS) comprising at least one of CO2/H2, H2, methane, and/or CO to a fermentation zone, wherein the GS and AS stream, are optionally contacted and/or mixed; the fermentation zone comprising at least one organism capable of metabolizing an AS substrate and a GS substrate, wherein the fermentation operates at conditions to mixotrophically metabolize at least one gaseous substrate in the GS and at least one substrate in the AS, producing the product.

Abstract: Methods of using ?-lactone biosynthetic enzyme genes and host cells expressing one or more of those genes, e.g., heterologous expression, are provided.

Abstract: The invention relates to a process for the preparation of a fermentation product from lignocellulosic material, comprising the following steps: a) optionally, pre-treatment of the lignocellulosic material, b) optionally, washing of the optionally pretreated lignocellulosic material, c) enzymatic hydrolysis of the optionally washed and/or optionally pretreated lignocellulosic material using an enzyme composition comprising at least two cellulases and whereby the enzyme composition at least comprises LPMO, and optionally purifying the hydrolysed lignocellulosic material, d) fermentation of the hydrolysed lignocellulosic material to produce a fermentation product, and e) optionally, recovery of a fermentation product, wherein oxygen is consumed in amounts corresponding to between 20 and 5000 mmol molecular oxygen per kg glucan present in the lignocellulosic material, the oxygen is added after the pretreatment and before and/or during the enzymatic hydrolysis of the lignocellulosic material, preferably in an

Abstract: The present disclosure relates to a method for improving the yield and production intensity of Gluconobacter oxydans (G. oxydans) sorbose, and belongs to the technical field of fermentation engineering. By knocking out genes related to formation of D-sorbitol or L-sorbose metabolic by-products in G. oxydans, the formation of the by-products is reduced, and the efficiency of transforming D-sorbitol into L-sorbose is improved, thereby improving the yield and production intensity of L-sorbose. A recombinant strain G. oxydan-11 constructed by the present disclosure, compared with a control strain, has an L-sorbose transformation rate of 96.12%, which is 4.47% higher than that of a wild strain, has a production intensity of 14 g/L·h, which is 14.7% higher than that of the wild strain, and has a fructose by-product content of only 5.6 g/L, which is 45.6% lower than that of the wild strain.

Abstract: A method of treating a patient who has melanoma includes administering to said patient a composition containing a population of activated T cells that selectively recognize cells in the patient that aberrantly express a peptide. A pharmaceutical composition contains activated T cells that selectively recognize cells in a patient that aberrantly express a peptide, and a pharmaceutically acceptable carrier, in which the T cells bind to the peptide in a complex with an MHC class I molecule, and the composition is for treating the patient who has melanoma. A method of treating a patient who has melanoma includes administering to said patient a composition comprising a peptide in the form of a pharmaceutically acceptable salt, thereby inducing a T-cell response to the melanoma.

Abstract: The present invention provides a process for production of a solid material containing isomaltulose crystals and trehalulose comprising the process steps A) bringing an enzyme complex which is able to catalyse the reaction of sucrose to isomaltulose and trehalulose into contact with a sucrose-containing solution; B) isomerizing at least some of the sucrose to isomaltulose and trehalulose; C) separating off the enzyme complex to give a solution containing isomaltulose, trehalulose and water; D) partial removal of the water by evaporation, while obtaining a concentrated solution with, based on the total solution, a solid content of 75 wt % to 95 wt %, preferably 80 wt % to 93 wt %, particularly preferably 86 wt % to 92 wt %; E) bringing the concentrated solution to a temperature of 30° C. to 63° C., preferably 45° C. to 62° C., even more preferably 55° C. to 60° C.

Abstract: In various aspects, the present invention is directed to a scalable method of producing rhamnolipids by bacterial fermentation with higher product concentrations, yields and productivities and preventing excessive foaming during the cell growth phase when the cell respiration rate is higher. It has been found that by slowing the growth rate of the bacteria by altering the ratio of the nitrogen source to the non-nitrogen source in the initial fermentation medium and supplementing the nitrogen source, excessive foaming in the growth phase can be prevented. Further, by using the non-nitrogen source as the limiting nutrient that initiates the stationary phase and then supplementing fermentation broth with the nitrogen and carbon sources, the length of the standing phase, and with it the time during which rhamnolipid production occurs can be greatly extended.

Abstract: Recombinant enzymes BesA, BesB, BesC, BesD and/or BesE are used generate non-canonical amino acids comprising a useful functional group, such as an alkynlyl, alkenyl or halogen.

Abstract: A method of producing a substance includes synthesizing a molecule at least by mixing substrates, a synthase, adenosine triphosphate (ATP), a polyphosphate kinase 2, and a polyphosphoric acid mixture. The polyphosphoric acid mixture includes 50% or more of polyphosphoric acid with a degree of polymerization of not less than 15. Adenosine diphosphate (ADP) is generated from the ATP during the synthesis. The synthesis is coupled with an ATP regeneration reaction in which the ATP is regenerated by the polyphosphate kinase 2 from the ADP and the polyphosphoric acid.

Abstract: The subject of the present invention is a process for preparing a genetically modified yeast by multicopy integration of at least four expression cassettes, allowing the production of a molecule of interest at high titre. The subject of the present invention is also yeasts transformed according to said process, and the use thereof for producing hydrocortisone.

Abstract: The present disclosure discloses to a method for determining optimum preservation temperature of a sulfur autotrophic denitrifying bacteria biofilm, and belongs to the technical field of environment engineering. The method of the present disclosure comprises: determining the cell activity state of a sulfur autotrophic denitrifying bacteria biofilm preserved at different temperatures by flow cytometry, and determining the preservation temperature of the cell activity state closest to the cell activity state of the sulfur autotrophic denitrifying bacteria in pilot operation as the optimum preservation temperature. The cell activity state and performance effect are verified to be reliable after activity recovery by the test data.

Abstract: The present invention relates to a novel process for biological detection of mycobacteria via electrochemical analysis methods of the catalytic activity of antigen 85.

Abstract: A device for differentially enumerating colonies of coliform and Escherichia coli microorganisms is provided. The device comprises a water-impermeable first sheet; a water-impermeable second sheet attached to the first sheet; a dry, rehydratable culture medium comprising a lactose-fermentation indicator system, a ?-D-glucuronidase indicator system, and a first cold-water soluble gelling agent adhered to the first sheet, the culture medium disposed in a microbial growth zone; and a second cold-water-soluble gelling agent adhered to the second sheet. The microbial growth zone is disposed between the first sheet and the second sheet. The first sheet and second sheet are configured to retard passage of carbon dioxide therethrough. Methods of using the device are also provided.

Abstract: A fluidic device has a culture chamber configured to house a 3D culture matrix comprising a culture of microorganisms. A concentration gradient of a test substance is established over the 3D culture matrix by providing respective fluid flows at different end portions of the culture chamber and comprising different concentrations of the test substance. The response of the microorganisms to the test substance is determined based on the position of a border zone in the 3D culture matrix.

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: The present invention describes methods for performing higher multiplexed real-time PCR for detection and quantitation of target nucleic acids using tagged hydrolysis probes.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: Provided are compositions, kits, and methods for the identification of Listeria. In certain aspects and embodiments, the compositions, kits, and methods may provide improvements in relation to specificity, sensitivity, and speed of detection.

Abstract: Interaction with a protein is detected by using an RNA probe containing the following sequences; (i) a complementary strand sequence to a DNA barcode sequence, (ii) a sequence of a first stem portion, (iii) a sequence of a second stem portion complementary to the first stem portion for hybridizing with the first stem portion to form a double-stranded stem, and (iv) a sequence of a loop portion contained in RNA for linking the first and second stem portions.

Abstract: The present disclosure relates to development and performance of screening methods capable of efficiently identifying candidate lead compounds that bind regulatory RNA oligonucleotides in a sequence-specific manner and exert a biological effect upon such regulatory molecules. Candidate lead compounds possessing RNA binding sequence specificity and targeted biological activity are described, as are approaches for merging structural, NMR-derived data with biological reporter assay results. Compound validation approaches capable of identifying the site(s) of action of such compounds within targeted RNA oligonucleotides are also provided.

Abstract: Kits for detecting analyte polynucleotides and an internal control in a sample. Included in the kit are an internal control polynucleotide and amplification reagents to co-amplify a first analyte polynucleotide and the internal control. Also included are first and second hybridization probes, each having a label indistinguishable from the other. The probes are respectively capable of hybridizing with a first analyte amplicon and an internal control amplicon. The first and second labels are indistinguishable homogeneous labels.

Abstract: A method of detecting the length of an individual telomere is provided. In one embodiment, the method includes contacting genomic DNA with a guide RNA having a portion complementary to a telomere repeat sequence in the genomic DNA and with Cas9 nickase to produce a single-strand break in the genomic DNA at the telomere repeat sequence. The nicked DNA is contacted with a polymerase and fluorescently labeled nucleotide, wherein the fluorescently labeled nucleotide is incorporated into the nicked DNA at the telomere repeat sequence. The genomic DNA is contacted with a second nicking endonuclease which is specific for a sequence motif in the genomic DNA thereby producing a second nick in the genomic DNA at the motif sequence. The nicked DNA is contacted with a polymerase and second fluorescently labeled nucleotide of different color, wherein the second fluorescently labeled nucleotide is incorporated into the nicked DNA at the motif sequence location.

Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: The presently-disclosed subject matter generally relates to methods, systems, compositions, and kits for the rapid, isothermal amplification of nucleic acids. The chemistry of the presently-disclosed amplification technique is isothermal, can be adapted to respond to a broad range of input target molecules, and results in a novel, biphasic reporter oligonucleotide amplification scheme with a high-gain second phase “burst” demonstrating a non-linear amplification rate (i.e., cooperative Hill kinetics). The switch-like amplification technique acts decisively to a true signal while filtering out noise, thus eliminating high levels of non-specific background amplification and false-positives.

Abstract: Embodiments of the disclosure encompass methods of enriching one or more target nucleic acid sequences utilizing initial linear amplification steps followed by adaptor ligation to the amplified products. In specific embodiments, the linear amplification employs primer extension that spans the target nucleic acid sequences and occurs at least in two or more cycles following which adaptors with unique identifier sequences are attached to the extension products.

Abstract: A kit for amplifying a nucleic acid, using RNA as a template, which can realize elimination of the risk of non-specific amplification caused by DNA mixed from reagents and/or working environment, an increase in the detection sensitivity of trace RNA, and a reduction in amplification bias. The kit includes a degrading enzyme specific to DNA in an RNA-DNA hybrid that is a double strand-specific DNA degrading enzyme or a non-specific DNA degrading enzyme, and an RNase H minus reverse transcriptase. If the degrading enzyme specific to DNA in an RNA-DNA hybrid is a non-specific DNA degrading enzyme, then the kit further comprises a single-stranded DNA-binding protein.

Abstract: The present invention is a method and compositions for primer extension target enrichment of nucleic acids and improvements thereto including simultaneously enriching for RNA and DNA and optionally sequencing the enriched products.

Abstract: This application relates to methods for ligating oligonucleotides having complementarity to a target nucleic acid, and amplifying the ligated oligonucleotides, where ligation and amplification occur in the same reaction mixture.

Abstract: Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.

Abstract: In one aspect, provided herein is an integrated method for simultaneous detection of both a genomic variance and quantification of a DNA methylation state/status on one or more (e.g., hundreds of thousands of) targets, without splitting the limited materials for two different workflows. The present disclosure relates to compositions, kus, devices, and methods for conducting genetic arid genomic analysis, for example, by polynucleotide sequencing in particular aspects, provided herein are compositions, kits, and methods for constructing libraries for simultaneous detection of genomic variants and DNA methylation status on limited DNA inputs, such as circulating polynucleotide fragments in the body of a subject, including circulating tumor DNA.

Abstract: A gene sequencing substrate and a method for manufacturing the same, and a gene sequencing device are provided. It belongs to the technical field of gene sequencing, and can solve the problem of high cost of the high-throughput sequencing chip in the prior art. The gene sequencing substrate of the present disclosure comprises a plastic material with concave structures as base substrate, and the concave structures serve as reaction cells. Since the base substrate has plasticity, the concave structures can be formed by a simple process to reduce the cost of the gene sequencing substrate. Meanwhile, a first protective layer may be provided on the inner wall of the concave structures for preventing the inner wall of the concave structures from being corroded by the reaction liquid.

Abstract: Provided are methods of adding adapters to nucleic acids. The methods include combining in a reaction mixture a template nucleic acid, a template switch oligonucleotide, a polymerase, and dNTPs. The reaction mixture components are combined under conditions sufficient to produce a product nucleic acid that includes the template nucleic acid and the template switch oligonucleotide each hybridized to adjacent regions of a single product nucleic acid including a region polymerized from the dNTPs by the polymerase. The methods further include attaching sequencing platform adapter constructs to ends of the product nucleic acid or a derivative thereof. Aspects of the invention further include compositions and kits.

Abstract: Provided are compositions and methods for the conversion of thiolated nucleotides, and subsequent detection of the converted nucleotides in RNA or DNA. Also provided herein are compositions and methods for the metabolic labeling of RNA and DNA by incorporation of thiolated nucleotides, and their subsequent conversion and detection.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.

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 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: Under one aspect, a device is provided for use in luminescent imaging. The device can include a photonic superlattice including a first material, the first material having a first refractive index. The first material can include first and second major surfaces and first and second pluralities of features defined through at least one of the first and second major surfaces, the features of the first plurality differing in at least one characteristic from the features of the second plurality. The photonic superlattice can support propagation of a first wavelength and a second wavelength approximately at a first angle out of the photonic superlattice, the first and second wavelengths being separated from one another by a first non-propagating wavelength that does not selectively propagate at the first angle out of the photonic superlattice.

Abstract: The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

Abstract: The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

Abstract: Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.

Abstract: Methods and systems for differential expression analysis of ribonucleic acid sequencing (RNA-Seq) data, and in particular to an automated workflow for differential expression analysis of RNA-Seq data. More particularly, an automated workflow for differential expression analysis of RNA-Seq data permitting analysis of pairs of any number of RNA-Seq reads subjected to multiple experimental conditions and tested in replicate.

Abstract: Disclosed herein is a simple, sensitive, and fully-recyclable fluorescence resonance energy transfer (FRET)-based multiplex detection platform that overcomes current requirements of complex labeling schemes and complicated data analysis algorithms for employing single-molecule FRET (smFRET) microscopy in multiplexing. While conventional smFRET detection techniques allow for the analysis of one target at a time, the disclosed approach utilizes the gaps between high- and low-FRET signals to provide simultaneous detection and quantification of multiple nucleic acid targets.

Abstract: Provided herein are compounds, methods, and compositions for use in determining the cellular origin of circulating cell-free DNA.

Abstract: The invention provides computer assisted methods for selecting an antidepressant medication for a patient. The methods utilize a combination genotype comprising at least three genes to guide medication selection.

Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.

Abstract: Disclosed are a method and a device for acquiring the fetal fraction of cfDNA, a storage medium and an electronic device. The method comprises: acquiring sequencing data of a sample taken from a mother pregnant with a fetus; establishing a joint probability distribution model of the maternal and fetal genotypes, the joint probability distribution model containing one or more factors affecting the read heterozygosity, the percentage of the read heterozygosity being the ratio of the number of SNPs covered by different bases to the total number of SNPs covered by more than one reads in the sequencing data; substituting the values of the one or more factors and of the acquired read heterozygosity into the established joint probability distribution model; and obtaining the fetal fraction of cfDNA by maximum likelihood estimation of the joint probability distribution model.

Abstract: The present teachings concern a method for determining the presence or absence of a fetal chromosomal aneuploidy and/or loss of heterozygosity (LOH) in a biological sample obtained from a pregnant female, the method comprising: obtaining sequence information indicative of targeted-capture massively parallel sequencing of the biological sample comprising both maternal and fetal nucleic acids; determining the amount of off-target reads obtained from said targeted capture massively parallel sequencing; and deriving from said off-target read counts information for determining the absence or presence of said aneuploidy or LOH.