Abstract: Many studies have shown that CRISPR-Cas nucleases can tolerate up to five mismatches and still cleave; it is hard to predict the effects of any given single or combination of mismatches on activity. Taken together, these nucleases can show significant off-target effects but it can be challenging to predict these sites. Described herein are methods for increasing the specificity of genome editing using the CRISPR/Cas system, e.g., using RNA-guided FokI Nucleases (RFNs), e.g., FokI-Cas9 or FokI-dCas9-based fusion proteins.

Abstract: The invention relates to a process for the preparation of a sugar product from lignocellulosic material, comprising the following steps: a) optionally pre-treatment of the ligno-cellulosic material; b) optionally washing of the optionally pre-treated ligno-cellulosic material; c) enzymatic hydrolysis of the optionally washed and/or optionally pre-treated ligno-cellulosic material using an enzyme composition comprising at least two cellulase and whereby the enzyme composition at least comprises GH61; and d) optionally recovery of a sugar product; wherein during part of the time of the enzymatic hydrolysis, oxygen is added to the ligno-cellulosic material and during part of the time of the enzymatic hydrolysis less oxygen is added to the ligno-cellulosic material compared to the other part of the time of the enzymatic hydrolysis, preferably no oxygen is added to the ligno-cellulosic material.

Abstract: The present disclosure relates to methods for producing oxygenated terpenoids, and preparation of compositions and formulations thereof. Polynucleotides, derivative enzymes, and host cells for use in such methods are also provided.

Abstract: The present invention relates to the preparation of amines from aldehydes and ketones by reductive amination with enzymes having a reductive aminase activity on aldehydes and ketones devoid of any carboxyl group gamma of the carbonyl group. The invention also relates to the enzymes per se and their uses in biocatalysis. The enzymes are derived from Mycobacterium smegmatis and vaccae, Cystobacter fuscus, Microbacterium sp. and Aminomonas paucivorans.

Abstract: The invention provides microorganisms genetically modified to overexpress thermophilic lysine decarboxylase polypeptides in a mesophilic host to enhance the production of lysine and lysine derivatives by the microorganism, method of generating such microorganism, and methods of producing lysine and lysine derivatives using the genetically modified microorganisms

Abstract: The present disclosure relates to a putrescine-producing microorganism of the genus Corynebacterium, and a method of producing putrescine using the same.

Abstract: The present disclosure relates to an O-succinyl homoserine transferase mutant, a polynucleotide encoding the same, a microorganism including the mutant, and a method of producing O-succinyl homoserine using the microorganism.

Abstract: Metabolites produced by a microorganism using more particularly oxaloacetate as substrate or co-substrate upstream in the biosynthesis pathway. There is indeed a need in the art for transformed, in particular recombinant, microorganisms having at least an increased ability to produce oxaloacetate, thus allowing an increased capacity to produce oxaloacetate-derived amino acids and amino acid derivatives, the oxaloacetate-derived amino acids and amino acid derivatives being termed oxaloacetate derivatives. The solution is the use of a genetically modified yeast including many modifications as described in the present text.

Abstract: A method of the bio-production of methionine and/or of its derivatives thereof from a reduced source of sulfur, such as MeSH or MeSNa including genetically modified yeasts, having an increased ability to produce methionine and/or its derivatives thereof, as compared to the parent yeasts.

Abstract: Strains of yeasts are provided containing the genes for the production of cannabinoids from fatty acids. The enzymes that mediate cannabinoid production are localized to the cytosol, peroxisome or different compartments within the secretory pathway (e.g., endoplasmic reticulum, Golgi, vacuole) to ensure efficient production. The engineered microorganisms produce cannabinoids in a controlled fermentation process.

Abstract: Disclosed are methods for ergothioneine biosynthesis. More particularly, the present disclosure relates to methods for microbial ergothioneine biosynthesis.

Abstract: A method for producing ectoine by fermenting recombinant Corynebacterium glutamicum. The recombinant Corynebacterium glutamicum is obtained by overexpressing, in Corynebacterium glutamicum, an aspartokinase gene lysC of which feedback inhibition is relieved, then replacing the promoter of the dihydrodipicolinate synthase in the recombinant bacterium to attenuate the activity of the dihydropyrimidine dicarboxylic acid synthase, and then transforming the recombinant bacterium with the ectoine synthetic path related gene ectABC. The recombinant Corynebacterium glutamicum can be fermented using different cheap raw materials under a low salt condition to produce ectoine, and use cheap corn slurry instead of expensive yeast powder as a nutritional component, so as to further reduce the costs of the raw materials. In addition, the recombinant Corynebacterium glutamicum solves the biosafety problem, simplifies the post-extraction process, and has a good market application prospect.

Abstract: Disclosed herein are in vivo methods, compositions, and kits for producing nucleic acids which comprises at least one unnatural base. Disclosed herein are in vivo methods of producing a nucleic acid with an expanded genetic alphabet, the method comprising incorporatin at least one unnatural base in the nucleic acid. Disclosed herein are semi-synthetic organisms comprising an expanded genetic alphabet, wherein the genetic alphabet comprises at least one unnatural base. Disclosed herein are compositions that include a heterologous or recombinant polymerase and methods of use thereof. Further, disclosed herein are kits that are useful for stably incorporating an unnatural nucleic acid into a nucleic acid molecule, e.g., using the methods provided by the present invention in in vitro condition or under a cell free condition.

Abstract: The purpose of the present invention is to: determine the structure of a novel steviol glycoside which is detected from species containing a large amount of Reb. C (also referred to as dulcoside B), and a trace amount of which is capable of influencing the quality of taste; and understand the taste characteristics of said steviol glycoside. The present invention provides a compound represented by formula (1) or a salt thereof, or a hydrate thereof.

Abstract: Microorganisms and methods are provided for producing biomass that includes PHB and protein in weight ratios and polymer lengths that are beneficial in feed and nutritional supplement compositions. The compositions also may be used for improvement in feed compositions that improve survivability of livestock and aquaculture species.

Abstract: A soft sphere transfer device, includes: a water tank into which soft spheres are introduced; a transfer rotation member rotatably disposed in the water tank and including a plurality of accommodation grooves formed along a peripheral edge of the transfer rotation member; and an injection device configured to inject a predetermined substance into the soft spheres by piercing a needle into each of the soft spheres transferred to a needle piercing part by rotation of the transfer rotation member, wherein the water tank includes a pair of side walls facing each other in a width direction, and wherein a narrow width portion having a width equal to or smaller than a diameter of the soft spheres is provided on at least one portion in the width direction among portions of the side walls corresponding to the needle piercing part.

Abstract: The subject invention provides microbe-based products and efficient methods of producing them. In specific embodiments, methods are provided for symbiotic cultivation of Acinetobacter venetianus RAG1 and Bacillus subtilis B1, as well as growth by-products thereof. Methods are also provided for using the subject microbe-based products, for example, in microbially enhanced oil recovery (MEOR).

Abstract: The invention provides devices and methods for measuring how living cells function. The measurements can be made from tissue biopsy samples to measure functional properties of living cells from a solid tumor. After measuring a functional property of a cell, the cell remains alive and is available for other subsequent analyses. In certain aspects, the invention provides a method for measuring a cancer marker. The method includes obtaining a tissue sample comprising living cells, disaggregating the tissue sample and loading individual live cells into an input channel of a measurement instrument, and flowing the live cells through the measurement instrument to measure a functional property of the live cells.

Abstract: A system and method for monitoring or detecting a level of biofilm growth in a fluid system and controlling operating parameters of the fluid system based a measured level of growth. The monitoring system and method comprises a dye injection system for periodically injecting dye into a portion of fluid from the fluid system, passing the portion of fluid though a narrow lumen tube to achieve laminar flow and using a light source and optical sensor to detect a transmission or emission indicating a level of biofilm growth in the tube corresponding to a level of growth on components in the fluid system. Information based upon the measurements or calculations made by the monitoring system may be used to manually or automatically alter various operating parameters to control the fluid system and aid in maintaining stable operation of the fluid system within preferred specifications.

Abstract: Various methods, devices, and systems for determining the concentration of microorganisms in a sample and determining the susceptibility of such microorganisms to one or more antibiotics or other types of anti-infectives are disclosed herein. More specifically, methods for quantifying microorganisms based on redox reactions are disclosed along with systems and devices for quantifying such microorganisms using certain oxidation reduction potential (ORP) sensors. Moreover, methods for determining the susceptibility and the degree of susceptibility of microorganisms to one or more anti-infectives are disclosed along with multiplex systems for such assays.

Abstract: A rapid one-pass liquid filtration system efficiently concentrates biological particles that are suspended in liquid from a dilute feed suspension. A sample concentrate or retentate suspension is retained while eliminating the separated fluid in a separate flow stream. Suspended biological particles include such materials as proteins/toxins, viruses, DNA, and/or bacteria in the size range of approximately 0.001 micron to 20 microns diameter. Concentration of these particles is advantageous for detection of target particles in a dilute suspension, because concentrating them into a small volume makes them easier to detect. Additional concentration stages may be added in “cascade” fashion, in order to concentrate particles below the size cut of each preceding stage remaining in the separated fluid in a concentrated sample suspension. This process can also be used to create a “band-pass” concentration for concentration of a particular target size particle within a narrow range.

Abstract: Compositions and reagents for molecular profiling using proximity ligation-/>7 situ hybridization (PLISH) are disclosed. In particular, PLISH merges the specificity of proximity ligation, the sensitivity of tiling multiple probes for a target nucleic acid, and the high signal intensity of rolling circle amplification. The probe design capitalizes on the formation of Holliday-like junctions for optimal signal amplification. PLISH provides single molecule resolution and allows for quantitation of a virtually unlimited number of nucleic acids within individual cells. PLISH is also compatible with immunohistochemistry and archival formal-fixed, paraffin-embedded tissue samples.

Abstract: The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5? to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5? flap containing one or more nucleotides at its 3? end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribo

Abstract: The present disclosure relates to methods for providing a clinical assessment of a subject in need thereof using the gene expression level measurements from exosomes derived from the subject.

Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.

Abstract: Disclosed herein include systems, methods, compositions, and kits for PCR normalization. In some embodiments, after barcoding copies of a higher abundance target (e.g., a cDNA species), the barcoded copies are amplified using a pair of forward primers comprising one or more mismatches and a reverse primer. The amplified copies can be further linearly amplified using a forward primer comprising the sequence of one of the pair of forward primers, and a reverse primer.

Abstract: The present invention concerns the field of nucleic acid based methods suitable for the generation of tools for biomedical research and biotechnological applications, which allow to differentiate, identify and quantify microorganisms and viruses.

Abstract: Disclosed is a method for determining the quality, expressed in terms of a quality value, of an RNA sample based on a multiplex fluorescent ratiometric method, wherein the ratio of small RNA to large and/or structured RNA in a sample is determined, thereby obtaining the quality value. Also disclosed is a method for determining the quality value of an RNA sample wherein the relationship of the intensity of the fluorescent signal corresponding to small RNA is compared to the intensity of the fluorescent signal corresponding to large and/or structured RNA in a sample. The relationship of the intensity of the two fluorescent signals is used to determine the amount of intact RNA present in the sample.

Abstract: The invention provides a method for detecting a low-virulence infection in a patient, by distinguishing true infections from false positives. The method comprises testing for the presence or amount of commensal microorganism(s) in a patient sample, and in particular, the commensal microorganism is one that may be causative of a low-virulence infection. Since testing for commensal microorganisms will lead to a large number of false-positives due to frequent sample contamination, the sample is also tested to discriminate true chronic infection from these false positives. In accordance with the invention, false positives are discriminated by evaluating a nucleic acid profile from the sample.

Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Abstract: The present disclosure relates to improved methods for detecting nucleic acids using DNA fingerloop stem loop structures, wherein the DNA fingerloop stem loop structures diminish base pairing of a detection probe to a mismatched target nucleic acid. The present disclosure also relates to improved methods for amplifying nucleic acids. Further disclosed are chimeric fingerloop DNAs for use in methods for modulating protein expression levels and/or RNA stability.

Abstract: A method of detecting a nucleic acid including mixing a fluid including a target nucleic acid with a detection reagent including a first enzyme for cleaving a first nucleic acid having a first flap and a second enzyme for cleaving a second nucleic acid such that the target nucleic acid, the first nucleic acid and the second nucleic acid form a complex as a first invasive structure, conducting a first reaction which causes the first enzyme to cleave the first flap of the first invasive structure and produces a third nucleic acid that forms a complex, as a second invasive structure, with a fourth nucleic acid having a second flap, and conducting a second reaction which causes the second enzyme to cleave the second flap of the second invasive structure and produces a cleaved product.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: The present invention provides methods of detecting a nucleic acid analyte in a sample. The methods generally involve modifying immobilized nucleic acids from a sample onto an insoluble support in a substantially elongated configuration, where modification generates an identifying feature that identifies the analyte; and detecting the identifying feature(s) using scanning probe microscopy, to detect the analyte. The present invention further provides a method for assigning a profile of a feature to a nucleic acid. The present invention further provides a computer program product for use in a subject method. The present invention further provides a system for detecting a nucleic acid in a sample; and a system for assigning a profile of a feature to a nucleic acid. The present invention further provides a method for immobilizing a nucleic acid onto an insoluble support; and further provides insoluble support having nucleic acid(s) immobilized thereon.

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 present disclosure relates to a quencher having a quenching effect on a fluorescent material exhibiting luminescence characteristics at an excited energy level, and various uses thereof.

Abstract: Multi-biotinylated reactants are provided which can be used in divalent complexes for various applications such as colocalization, labeling, immobilization, and purification. Methods for constructing, purifying, and using the bis-biotinylated reactants are also provided. In certain embodiments, two bis-biotinylated reactants are bound to a single streptavidin tetramer to provide a complex having a 1:1 stoichiometry with respect to the bis-biotinylated reactants.

Abstract: A method for determining pregnancy in a ruminant includes measuring an expression level of molecules induced in response to IFN-? in mucosal epithelial cells using a sample containing the mucosal epithelial cells, and determining pregnancy in the test ruminant animal by comparing the expression level with an expression level of the molecules in corresponding mucosal epithelial cells of a non-pregnant ruminant animal of the same species.

Abstract: The use of Nucleic Acid Amplification Technologies (NAATs) to rapidly copy a specific fragment of DNA from a few starting molecules has been used to determine the presence of that DNA in a sample. It is of importance for various applications including the identification of a pathogen in a clinical sample. Non-specific DNA amplification occurring in the absence of any input DNA template is frequently observed after many amplification cycles or in the case of isothermal amplification, with time. The disclosed embodiments describe the surprising finding that the amplification of primer-only artefacts is suppressed in reactions where a fraction of the oligos involved in the reaction contain 3? blocked terminal bases that cannot support extension by DNA polymerases.

Abstract: An assay is provided for the rapid detection of nucleic acids via a modified LAMP reaction coupled with colorimetric reporter utilizing a gold nanoparticle-peptide nucleic acid (AuNP-PNA) probe system.

Abstract: The invention relates to improving the movement of a target polynucleotide with respect to a transmembrane pore when the movement is controlled by a polynucleotide binding protein.

Abstract: Nucleic acid sequencing methods and systems, the systems including nanochannel chip including: a nanochannel formed in an upper surface of the nanochannel chip and; a roof covering the nanochannel and comprising nanopores and a field enhancement structure; and a barrier disposed in the nanochannel. The method including: introducing a buffer solution including long-chain nucleic acids to the nanochannel chip; applying a voltage potential across the nanochannel chip to drive the nucleic acids through the nanochannel, towards the barrier, and to translocate the nucleic acids through nanopores adjacent to the barrier, such that bases of each of the nucleic acids pass through the field enhancement structure one base at a time and emerge onto an upper surface of the roof; detecting the Raman spectra of the bases of the nucleic acids as each base passes through the electromagnetic-field enhancement structure; and sequencing the nucleic acids based on the detected Raman spectra.

Abstract: The disclosure provides a novel system of storing information using a charged polymer, e.g., DNA, the monomers of which correspond to a machine-readable code, e.g., a binary code, and which can be synthesized and/or read using a novel nanochip device comprising nanopores; novel methods and devices for synthesizing oligonucleotides in a nanochip format; novel methods for synthesizing DNA in the 3? to 5? direction using topoisomerase; novel methods and devices for reading the sequence of a charged polymer, e.g., DNA, by measuring capacitive or impedance variance, e.g., via a change in a resonant frequency response, as the polymer passes through the nanopore; and further provides compounds, compositions, methods and devices useful therein.

Abstract: The invention provides a novel additive for improved analysis by mass spectrometry. More specifically, ascorbic acid has been found to reduce or eliminate the presence of adducts commonly present in mass spectra. The improved processes and compositions of the invention allow for increased accuracy, sensitivity and throughput for samples analyzed by mass spectrometry.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.

Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.

Abstract: The present invention is based on the use of the H3K9me2 methylation levels in plant genomes to predict transgene silencing, transgene stability, and/or transgene expression level. Provided are methods and/or systems for generating whole-genome H3K9me2 maps and its use with an assigned threshold value for predicting gene silencing. The methods and/or systems provided herein can be used in high-throughput setting for screening large number of transformed event in a relatively short period of time as compared to existing technologies.

Abstract: This disclosure describes detecting genetically distinct kinds of inherited myopathies in horses, variously referred to as Polysaccharide Storage Myopathy type 2 (PSSM2), Myofibrillar Myopathy (MFM), or idiopathic myopathy.

Abstract: In the field of transplant rejection, identified are SNPs wherein mismatches in variants present in a recipient and donor for such SNPs are predictive of transplant outcome, wherein the SNPs represent non-HLA loci newly implicated in rejection. By the invention, transplant outcomes such as elevated risk of antibody mediated rejection, elevated risk of T-cell mediated rejection, or low risk of rejection can be predicted by analyzing mismatches between donor and recipient for the enumerated SNPs. Certain SNPs enumerated are predictive of kidney transplant outcome. The compatibility of prospective donors can be assessed for a recipient, allowing for optimized donor-recipient pairing.