Abstract: Provided herein are polynucleotides (e.g., plasmids), including transfer polynucleotides and landing pad polynucleotides, which are useful, e.g., in the generation of cell and virion libraries each expressing and encoding a protein of interest (e.g., viral entry proteins). The libraries described herein are further useful, e.g., in methods of assessing functional characteristics of the proteins of interest (e.g., neutralization of viral entry proteins by one or more antibodies).

Abstract: Disclosed is a system and method for the controlled clustering of gene regulatory proteins at the specific target genomic loci. The technology enables formation of liquid-like droplets closely interfaced with genome organization. This technology can be utilized for perturbing endogenous nuclear structures as well as nucleating synthetic membrane-less assemblies. The technology can also be utilized for inducing or detecting mechanical stresses within the genome.

Abstract: Described herein are reagents, products, methods, and uses thereof for modifying the genome of a cell at a MTOR locus, for example by nuclease-based (e.g. CRISPR/Cas9) modification. The modifications include a MTOR modification which confers resistance to an mTOR inhibitor. The modifications may further include a modification to introduce a nucleic acid or gene of interest. Introducing both modifications at the MTOR locus is an efficient and advantageous strategy which allows for targeted modification of both aspects (resistance and gene of interest) at the same locus, and further allows for the use of an mTOR inhibitor to select and enrich for such modified cells. Such modified cells may be used for a variety of applications, including therapeutic applications.

Abstract: A guide RNA comprising (17) to (24) nucleotides which are complementary to exon 1 of the human SH2D1A or the complement thereof. Ribonuclear proteins (RNP) complexes comprising the guide RNA and a Cas nuclease, and gene editing kits comprising the ribonuclear protein (RNP) complexes are also disclosed, including the use of these components in therapy, particularly for SAP-mediated diseases.

Abstract: Methods and compositions are provided for modifying one or more target loci in a cell. Such methods comprise providing a cell comprising a first polynucleotide encoding a first selection marker operably linked to a first promoter active in the cell, wherein the first polynucleotide further comprises a first recognition site for a first nuclease agent. A first nuclease agent is introduced into a cell, wherein the first nuclease agent induces a nick or double-strand break at the first recognition site. Further introduced into the cell is a first targeting vector comprising a first insert polynucleotide flanked by a first and a second homology arm that correspond to a first and a second target site located in sufficient proximity to the first recognition site. At least one cell is then identified comprising in its genome the first insert polynucleotide integrated at the target locus.

Abstract: The present invention relates to the use of alpha-ionylideneethane as an aroma compound, and to the use of an alpha-ionylideneethane synthase in the production of one or more aroma compounds. The inventive method for preparing one or more aroma compounds comprises a) providing farnesyl diphosphate and an alpha-ionylideneethane synthase as defined herein, under conditions suitable for the alpha-ionylideneethane synthase to produce alpha-ionylideneethane, b) converting farnesyl diphosphate to alpha-ionylideneethane, in vitro or in a host cell, c) optionally, converting alpha-ionylideneethane to one or more further aroma compounds, d) isolating alpha-ionylideneethane and the optionally one or more further aroma compounds and, e) optionally, purifying alpha-ionylideneethane and the optionally one or more further aroma compounds. The invention pertains also to method for scenting a product, particularly for imparting and/or enhancing an odor or flavor, in which at least one alpha-ionylideneethane synthase is used.

Abstract: Proposed is a method for CO2-free waste gas fermentation using microbial strains, and the method is capable of maximizing a consumption rate of gaseous substrates by additionally injecting methanol during a fermentation process of the microbial strains, and converting CO2, a greenhouse gas, generated during the fermentation process into hydrocarbon products therethrough. The method may comprise: 1) injecting microbial strains into a bioreactor; and 2) injecting gaseous substrates and methanol into the bioreactor, and converting the gaseous substrates and the methanol into hydrocarbon products through fermentation of the microbial strains, wherein all CO2 present inside the bioreactor is consumed and converted into hydrocarbon products.

Abstract: A method including reacting carboxylic acids obtained from fermentation and a carboxylic acid recovery step from said fermentation to produce short- or medium-chain triglycerides, wherein the reacting carboxylic acids comprises direct esterification with glycerol in the presence of a catalyst. Such method mentioned above wherein the produced short- or medium-chain triglycerides are further interesterified with an oil, butter, fat or other lipids in the presence of a catalyst to produce structured lipids. Yet another method comprising reacting carboxylic acids obtained from fermentation and a carboxylic acid recovery step from said fermentation to produce structured lipids, wherein reacting the carboxylic acids comprises transesterification with an oil, butter, fat or other lipids in the presence of a catalyst. The use of such short-chain triglycerides, medium-chain triglycerides and structured lipids as nutritional additives, dietary supplements, or both.

Abstract: The present application relates to: a novel acetohydroxy acid synthase subunit (ilvN) variant; a polynucleotide encoding the variant; an expression vector comprising the polynucleotide; microorganisms producing L-valine including the acetohydroxy acid synthase subunit (ilvN) variant; and a method for producing L-valine using the microorganisms.

Abstract: Metabolically-engineered yeast strains are provided. such as metabolically-engineered Saccharomyces cerevisiaestrains. producing high amounts of at least one. preferably all four natural cytokinins: trans-zeatin (tZ), trans-zeatin riboside (tZR). isopentenyladenine (iP) and isopenteny ladenine riboside (iPR).

Abstract: Provided is a method for producing circular DNA in which a region that is sandwiched by a region Ha and a region Hb in circular double-stranded DNA is substituted with the entirety or a portion of a linear-DNA fragment, wherein the region Hb is located downstream of the region Ha in the circular double-stranded DNA; the linear-DNA fragment is single-stranded or double-stranded linear DNA that has a homologous region that corresponds to the region Ha and a homologous region that corresponds to the region Hb, the latter homologous region being positioned downstream of the former homologous region; and the method comprising: preparing a reaction solution that contains the circular double-stranded DNA, the linear-DNA fragment, and a protein that has RecA-family-recombinase activity, and performing homologous recombination reaction by incubating the reaction solution for a predetermined period of time, thereby producing circular DNA in which the region that is from the region Ha to the region Hb in the circular do

Abstract: Improved methods for manufacturing a RNA by IVT and compositions for use therein are provided.

Abstract: The present invention relates to a method for producing cytidine 5?-monophospho-N-acetyl-neuraminic acid (CMP-Neu5Ac, 1) from low-cost substrates N-acetyl-D-glucosamine (GlcNAc), pyruvate, cytidine and polyphosphate in a single reaction mixture with a set of optionally immobilized or optionally co-immobilized enzymes comprising N-acylglucoamine 2-epimerase (AGE), an N-acetylneuraminate lyase (NAL), an N-acylneuraminate cytidylyltransferase (CSS), a uridine kinase (UDK), a uridine monophosphate kinase and a polyphosphate kinase 3 (PPK3). Further, said process may be adapted to produce Neu5Acylated i.e. sialylated biomolecules and biomolecules including a saccharide, a peptide, a protein, a glycopeptide, a glycoprotein, a glycolipid, a glycan, an antibody, and a glycoconjugate, in particular, an antibody drug conjugate, and a carbohydrate conjugate vaccine, or a flavonoid.

Abstract: The present invention relates inter alia to methods of biosynthetic production of QS-21, precursors and variants thereof, and to related aspects.

Abstract: The instant disclosure provides, among other things, novel nuclease proteins (enzymes), novel nuclease compositions and protein preparations thereof, recombinant polynucleotides (DNA) encoding such nuclease proteins, recombinant host cells expressing and producing one or more nuclease proteins (optionally co-expressing one or more proteins of interest) and the like. More particularly, the nuclease proteins (enzymes) of the instant disclosure are particularly useful in mitigating DNA contamination, such as contaminating DNA present in a fermentation broth in which microbial host cells have been fermented, contaminating DNA present in recovered proteins of interest, contaminating DNA present in protein preparations, and the like.

Abstract: The invention is related to a method for producing a secreted recombinant protein of interest in a cell, wherein the method comprises artificially co-expressing a protein different from the secreted recombinant protein of interest.

Abstract: Isolated mogroside and mogrol biosynthetic pathway enzyme polypeptides useful in mogroside biosynthesis are provided. Mogroside biosynthetic pathway enzymes of the invention include squalene epoxidase (SE), expoxy hydratase (EH), cytochrome p450 (Cyp), cucurbitadienol synthase (CDS) and udp-glucosyl-transferase (UGT), Also provided are methods of producing a mogroside using the isolated mogroside and mogrol biosynthetic enzyme polypeptides, the methods comprising contacting a mogrol and/or a glycosylated mogrol (mogroside) with at least one UDP glucose glucosyl transferase (UGT) enzyme polypeptide of the invention catalyzing glucosylation of the mogrol and/or the glucosylated mogrol to produce a mogroside with an additional glucosyl moietie(s), thereby producing the mogroside.

Abstract: A method for identifying a bacterium in a biological sample, and a method for testing antibiotic susceptibility of a bacterium in a biological sample, comprising: step (1), centrifugally separating the bacterium from the biological sample; step (2), staining the bacterium obtained in step (1); step (3), fixing the stained bacterium in step (2) by electrostatic adsorption; step (4), injecting an extraction solution into a capillary tip, and then extracting metabolites of the single living bacterium by in-situ extraction; step (5), inserting an electrode into the capillary obtained in step (4), applying a voltage, and performing mass spectrometry. The method does not depend on incubation, and the identification and the antibiotic susceptibility testing of a bacterium in a biological sample of an early bacterial infection can be realized, and the method has the advantages of being rapid, having high sensitivity, capable of performing a non-targeting analysis, etc., and has good application prospects.

Abstract: For providing a method for estimating a microbial growth rate in food that is capable of rapidly and non-destructively evaluating shelf life of food (e.g., best-by date) and the like while reducing cost and labor associated with the evaluation, the present disclosure includes: a step of placing a hydrophilic membrane filter on a surface of a food sample, and inoculating microorganisms on the hydrophilic membrane filter; a step of imaging the microorganisms growing on the hydrophilic membrane filter over time using a microscope; a step of digitizing area of the microorganisms from the image taken over time; and a step of estimating a growth rate of the microorganisms based on the digitized data.

Abstract: A sample analysis apparatus and a sample analysis method. The method includes preparing a specimen by means of a sample and a reagent, the sample being a blood sample or a body fluid sample. The specimen is tested to obtain one or more testing parameters of the sample with respect to particles; and for at least one testing parameter, control is performed according to the magnitude of the testing parameter to display the testing parameter with different precisions. By performing the control according to the magnitude of a testing parameter to display the testing parameter with different precisions, a result requirement of a low-value sample, such as a body fluid sample, can be satisfied.

Abstract: This invention relates to methods of selecting plant-associated bacterial isolates for promoting plant health.

Abstract: The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the determination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and/or predict the outcome of a transplantation procedure.

Abstract: The invention comprises a method and compositions for sequencing library preparation, which increases the throughput of single-molecule sequencing (SMS) platforms by generating long concatenated templates from pools of short DNA molecules.

Abstract: Methods, systems, compositions and kits for detection of multiple analytes are disclosed. The methods, systems, compositions and kits may comprise an oligonucleotide that may bind to more than one analyte. The oligonucleotide may allow for the generation of different signal depending on the analyte that the oligonucleotide is hybridized to. The signals generated from may be used to identify the presence of an analyte. The signals generated from may be used may be used to simultaneously identify the presence of multiple analytes in a sample.

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: In some examples, a structure is contacted with polynucleotides having a variety of lengths and each including first and second adapters. The structure includes a substrate including first and second regions spaced apart from one another by a gap of at least 100 nm, a first set of capture primers coupled to the first region of the substrate, and a second set of capture primers coupled to the second region of the substrate. The first adapter of the polynucleotide is hybridized to a capture primer of the first set of capture primers. Based on that polynucleotide being sufficiently long to bridge the gap, it is amplified using the first and second sets of capture primers. Based upon that polynucleotide being insufficiently long to bridge the gap, it is not amplified. Optionally, a wall may be disposed in the gap.

Abstract: A method of identifying and quantifying copy number variations in a gene of interest for a genomic DNA sample includes (i) fragmenting a genomic DNA sample to produce a plurality of polynucleotide fragments, (ii) isolating a plurality of target polynucleotide fragments, (iii) sequencing the plurality of target polynucleotide fragments, (iv) aligning fragment sequences to a reference sequence, (v) calculating read depths for base positions of the plurality of target polynucleotide fragments, (vi) calculating copy number likelihoods for each base position of the reference sequence, (vii) performing a breakpoint analysis on a set of fragment sequences to identify at least one sequence variation located between selected breakpoint regions of the target gene and calculate modified copy number likelihoods for base positions of the reference sequence based on the at least one sequence variation, and (viii) determining whether the target gene includes at least one copy number variation.

Abstract: The invention provides a method that includes performing a pre-amplification of nucleic acid in a sample to generate amplicons that include a copy of a variant, annealing and extending variant-specific primers to create copies of the amplicon, and copying the copies with tailed primers to form tailed amplicons. The tailed amplicons are amplified with universal primers and detection probes that anneal to the tailed amplicons. Extension of the universal primers along the tailed amplicons through annealed detection probes generates a signal that shows the presence of the variant in the sample.

Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.

Abstract: Aspects of the present invention relate at least in part to identification of regions within the genome that are sensitive to a condition. Particularly, although not exclusively, embodiments of the present invention relate to a method and system for identifying regions of the genome where DNA protection from digestion changes in response to a condition, e.g. the nucleosomal organisation is different as compared to a genomic region in a subject without the condition. The condition may be a pathological disorder e.g. cancer, or a variation of a healthy state e.g. depending on person's lifestyle or age. In certain embodiments, the method and systems may identify regions within the genome which differ in patients with sub-sets of the same condition. Aspects of the present invention comprise identification, stratification and monitoring of subjects suffering from a condition by sequencing predetermined regions of a genome.

Abstract: A method of base calling nucleobases of two or more polynucleotide sequence portions, wherein said polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase.

Abstract: The present invention belongs to the technical field of characterization of target analyte properties, and particularly provides a mutant of a porin monomer, a protein pore comprising same, and use thereof in the detection of a target analyte, wherein an amino acid of the mutant of the porin monomer comprises a sequence set forth in SEQ ID NO: 1 or a sequence having at least 99%, 98%, 97%, 96%, 95%, 90%, 80%, 70%, 60%, or 50% identity thereto, and the amino acid of the mutant of the porin monomer comprises mutations at one or more positions corresponding to T71, S75, or F76 of SEQ ID NO: 1.

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: Provided herein are methods for identifying a genetic characteristic, a fragment characteristic and an epigenetic characteristic of a double-stranded DNA molecule in a population of double-stranded DNA molecules by assaying both strands of the double-stranded DNA molecule.

Abstract: The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.

Abstract: Embodiments of the invention provide an improved biosensor for biological or chemical analysis. According to embodiments of the invention, backside illumination (BSI) complementary metal-oxide-semiconductor (CMOS) image sensors can be used to effectively analyze and measure fluorescence or chemiluminescence of a sample. This measured value can be used to help identify a sample. Embodiments of the invention also provide methods of manufacturing an improved biosensor for biological or chemical analysis and systems and methods of DNA sequencing.

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: This invention relates to methods for detecting the presence or absence of target nucleic acids in samples by excising and detecting specific target probes.

Abstract: This disclosure provides for devices, methods, and systems for performing a non-invasive prenatal testing (NIPT) digital assay upon generating at least a large number of counts per chromosome for a set of chromosomes present in a sample, where performing the NIPT digital assay can include: distributing nucleic acids of the sample and materials for an amplification reaction across a plurality of partitions; amplifying the nucleic acids with the materials, within the plurality of partitions; and generating counts per chromosome upon detecting signals from the plurality of partitions. The inventions enable processing of samples for NIPT digital analyses and/or other digital analyses involving other loci of interest, with unprecedented partitioning, reaction, readout, and analytical performance.

Abstract: An embodiment of the disclosure provides: a PCR kit for diagnosing asthma or asthma exacerbation, comprising an agent for measuring the mRNA level of a nectin-4 gene; and a method for providing information for diagnosing asthma or asthma exacerbation by using same. According to an embodiment of the disclosure, there is the effect of providing: a PCR kit for diagnosing asthma or asthma exacerbation, which enables the administration of an appropriate dose of a drug for asthma treatment by diagnosing not only asthma but also asthma exacerbation; and a method for providing information for diagnosing asthma or asthma exacerbation by using same.

Abstract: A method is provided for detecting the presence of mycobacterial infection or disease in a subject, comprising the steps of determining the level of expression of each of a plurality of miRNAs within a sample from a subject and using one or more Artificial Intelligence (AI) model to predict the disease condition of the subject.

Abstract: This document provides methods and materials related to treating a disease. For example, this document provides methods for treating a subject's disease based on identifying the risk of progressive multifocal leukoencephalopathy PML using a genetic test.

Abstract: The present disclosure provides methods and systems directed to cell-free identification and/or monitoring of pregnancy-related states. A method for identifying or monitoring a presence or elevated risk of a pregnancy-related state of a pregnant subject may comprise assaying a cell-free biological sample derived from said pregnant subject to detect a set of biomarkers, and analyzing the set of biomarkers with a trained algorithm to determine the presence or elevated risk of the pregnancy-related state.

Abstract: A microRNA biomarker is for early diagnosis of mild cognitive impairment or Alzheimer type dementia. The microRNA biomarker includes miRNAs of SEQ ID NOs: 1 to 5 obtained by molecule-based analysis are expressed in the blood plasma of patients with mild cognitive impairment or Alzheimer type dementia. The miRNAs have an effect of reducing the expression of proteins that are related to mild cognitive impairment or Alzheimer type dementia. As such, the early diagnosis of mild cognitive impairment or Alzheimer type dementia is enabled before symptoms appear by utilizing a novel miRNA present in relatively non-invasive blood plasma as a diagnostic indicator.

Abstract: The present invention relates to a colorectal cancer subtype identifier based on percent spliced-in (PSI) values from alternative splicing events. The invention further relates to a method for predicting the outcome for a subject suffering from colorectal cancer by using PSI values. The invention further relates to a kit for predicting the outcome for a subject suffering from colorectal cancer by PSI values. The invention further relates to a use of the PSI value as a marker of the outcome for a subject suffering from colorectal cancer. The invention further relates to method for treating a subject suffering from colorectal cancer using PSI values to obtain CMS likelihood on the outcome of the disease.

Abstract: Disclosed herein is a method for determining whether a subject is suffering from, or is at risk of developing breast cancer, wherein the method comprises detecting differential expression levels of at least two or more miRNA markers from a biological sample. Also disclosed herein is a method of determining whether a subject is suffering from, or is at risk of developing, breast cancer based on miRNA expression.

Abstract: The present invention belongs to the technical field of molecular biology, and specifically relates to the technical field of efficacy monitoring of a chimeric antigen receptor (CAR)-T cell therapy. The present invention provides use of a primer combination in the preparation of a product for detecting a prognostic effect of an anti-CD19 CAR-T cell therapy in a tumor, where the primer combination includes primers shown in Table 1. The present invention provides use of a primer combination in the preparation of a product for detecting an expression state of CD19 on a surface of a tumor cell in a tumor patient, where the primer combination includes primers shown in Table 1. The present invention provides a product for detecting a prognostic effect of an anti-CD19 CAR-T cell therapy in a tumor, where the product includes primers shown in Table 1 as effective components.

Abstract: Disclosed herein are methods for predicting the clinical or disease outcome of a subject with a disease. The methods for generating an index to predict the disease outcome are also provided. The methods comprise procedures for measuring miRNA levels in a cell-free sample of a subject. The compositions for practicing the same are further provided.

Abstract: Compositions and methods for treatment of tumor cells are presented in which tumor cells that overexpress monocarboxylate transporter 4 (Mct-4), HIF-1?, Hexokinase-2, and/or CD147 are targeted with one or more metabolic inhibitors.

Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as colorectal cancer.