Abstract: A genetically engineered bacterial strain that produces N-acetylglucosamine, as well as a method of construction and use thereof. The genetically engineered bacterial strain can ferment N-acetylglucosamine under a condition of 40-50° C. Through knocking out genes for glucosamine 6-phosphate deaminase, N-acetylglucosamine-6-phosphate deacetylase and the N-acetylglucosamine transporter protein from a parental bacterium, an N-acetylglucosamine catabolism pathway is blocked. Moreover, overexpression genes for glucosamine 6-phosphate synthase and glucosamine 6-phosphate acetylase are introduced, enabling extra cellular accumulation of N-acetylglucosamine and high-temperature fermentation of N-acetylglucosamine at a temperature higher than 40° C.

Abstract: The present disclosure discloses a method for efficient catalytic synthesis of PAPS based on constructing an ATP regeneration system, and belongs to the technical field of bioengineering. Efficient production of PAPS is realized through microbial recombination expression and artificial construction of PAPS bifunctional synthetase. On the basis, an ATP regeneration system coupling with polyphosphate kinase from Corynebacterium glutamicum and Mycobacterium tuberculosis can be used for recovering two byproducts: pyrophosphoric acid and ADP at the same time, the equivalent conversion of a substrate and a product is realized, the PAPS generated in a catalysis system has high purity, and the sulfonic acid group donation in most sulfonic acid transfer reactions can be realized.

Abstract: The present invention relates to the finding of methods to shift the glycosylation profile of recombinant produced serum glycoproteins to the predominant bi-antennary form found in human plasma. This is accomplished by providing a mammalian cell line according to the invention with a series of gene disruptions and/or gene insertions that facilitate this shift.

Abstract: Methods and systems for designing proteins are disclosed, as well as proteins and protein assemblies designed. A computing device can determine a protein repeating unit that includes one or more protein helices and one or more protein loops. The computing device can generate a protein backbone structure with a copy of the protein repeating unit. The computing device can determine whether a distance between a pair of helices of the protein backbone structure is between lower and upper distance thresholds. After determining that the distance between the pair of helices is between the lower and upper distance thresholds, the computing device can: generate a plurality of protein sequences based on the protein backbone structure, select a particular protein sequence of the plurality of protein sequences based on an energy landscape that has information about energy and distance from a target fold of the particular protein sequence, and generate an output based on the particular protein sequence.

Abstract: The invention features devices and kits for capturing and culturing microorganisms (e.g., bacteria, fungi, or protists) and methods of using the devices and kits to detect microorganisms in environmental and other samples. The device includes a nutrient media having a flat growth area on which microorganisms can grow. Samples are collected by contacting the device with any environmental sample, e.g., rolling device on a work surface or exposing device to air, or by filtering a sample through a membrane. Microorganisms deposited on the membrane derive nutrients from the underlying media and grow into colonies that can then be detected using methods known in the art. The detected colonies can be imaged digitally or with film.

Abstract: The present invention relates to obtaining single incubation condition for cocktail of probe substrates of 8 major Cytochrome P450 (CYP) isoforms to assess in vitro drug-drug interactions (DDIs) of novel drug candidates using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) method. The present invention provides an improved and reduced substrate concentration and is developed in lower microsomal protein to avoid any non-specific binding of substrates with the microsomal proteins.

Abstract: The present invention provides compounds useful as inhibitors of TIR NADase activity, compositions thereof, and methods of using the same. The present invention is useful for inhibition of TIR-domain NADase activity and/or treating microbial infection and/or modulating microbial physiology.

Abstract: The present invention relates to a method for detecting a pathogen in cellular lysate by measuring pathogen-specific enzyme activity. The method comprises contacting the cellular lysate with a substrate the pathogen of interest recognizes and modifies, and obtaining a measurable, recordable, signal. The method may comprise detection of SARS-CoV viruses using the activity of SARS PLpro enzyme in tongue scrape lysate as a readout.

Abstract: A method of determining activity of a target enzyme of a grain material is described. The method comprises providing a fluid extract sample of the grain material using a preselected extraction procedure, providing a dyed and/or chromogenic substrate for the target enzyme, subjecting the fluid extract sample to the substrate for a preselected incubating time, and determining the target enzyme activity of the grain material. The extraction time is relatively short while still obtaining high accuracy.

Abstract: The present invention provides for single-molecule profiling of combinatorial protein modifications and single-molecule profiling of combinatorial protein modifications combined with single-molecule sequencing of protein/nucleic acids complexes. High-throughput single-molecule imaging was applied to decode combinatorial modifications on millions of individual nucleosomes from pluripotent stem cells and lineage-committed cells. Applicants identified bivalent nucleosomes with concomitant repressive and activating marks, as well as other combinatorial modification states whose prevalence varies with developmental potency. Applying genetic and chemical perturbations of chromatin enzymes show a preferential affect on nucleosomes harboring specific modification states. The present invention also combines this proteomic platform with single-molecule DNA sequencing technology to simultaneously determine the modification states and genomic positions of individual nucleosomes.

Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.

Abstract: Disclosed herein include systems, methods, compositions, and kits for immune repertoire profiling. There are provided, in some embodiments, primer panels enabling the determination of the nucleotide sequence of the complete variable region of nucleic acids encoding mouse B cell receptor (BCR) and T cell receptor (TCR) polypeptides. In some embodiments, the method comprises single cell transcriptomic analysis.

Abstract: Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

Abstract: The invention relates generally to systems and methods for assaying a biological sample suspected of comprising a target biomolecule using cascading amplification.

Abstract: Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Abstract: The present disclosure provides improved detection (e.g., diagnostic) assays that utilize a Cas protein collateral cleavage activity.

Abstract: An affinity reagent, having: (a) a retaining component such as a structured nucleic acid particle; and (b) one or both of (i) one or more label components attached to the retaining component, and (ii) one or more binding components attached to the retaining component.

Abstract: The present invention provides methods for the non-enzymatic cleavage of target nucleic acids, for example for use in epigenomic and epitranscriptomic mapping and therapy. The method comprises contacting a target nucleic acid molecule with a bifunctional probe comprising a cleavage group and a covalent binding group such that the bifunctional probe covalently binds to the target nucleic acid molecule and cleaves the 5 target nucleic acid molecule bound thereto. Also provided is a method of selectively cleaving a target nucleic acid in a cell, a method for determining the modification of nucleic acid molecules by a nucleic acid modification enzyme in a cell, and a bifunctional probe for use in the methods.

Abstract: The present invention relates to improved processes for production of closed linear deoxyribonucleic acid (DNA), in particular cell-free enzymatic production of closed linear DNA molecules, preferable using a closed linear DNA as a template for DNA synthesis. The invention further relates to a novel closed linear DNA species, suitable for use as a template in the improved processes for production of closed linear DNA. Further, the invention pertains to the intermediate products of the processes, since this enables the production of larger quantities of closed linear DNA from the template than with methods known in the art.

Abstract: Kits, methods, polypeptides, systems, and non-transitory, machine-readable storage media for detecting a nucleic acid in a sample are described. In an embodiment, the kit comprises a loop primer nucleic acid molecule configured for loop-mediated isothermal amplification (LAMP), the loop primer nucleic acid molecule comprising: a targeting sequence complementary to a target portion of a target nucleic acid sequence; and an adapter sequence; a displacement nucleic acid probe comprising: a fluorophore adapter sequence; and the adapter sequence; and a fluorophore adapter complement nucleic acid molecule complementary to the fluorophore adapter sequence, wherein the fluorophore adapter sequence or the fluorophore adapter complement nucleic acid molecule is coupled to a fluorophore. In an embodiment, the system comprises a thermal subsystem for heating a sample disposed therein, and an optical subsystem for optically excited the sample and detecting light emitted from the sample.

Abstract: Provided herein are methods for enrichment from a library of nucleic acid sequences of interest using primers against identification sequences. The nucleic acid sequences of interest can be subsequently cloned, and the protein products can be analyzed.

Abstract: Modified nucleotides, such as ?-phosphoseleno-nucleotides (dNTP?Se and NTP?Se), can be incorporated into nucleic acids by enzymatic processes in a similar manner as naturally occurring nucleotides. Altering the properties of modified nucleotides can alter the interaction between the nucleotide and the enzyme. Enzymatic incorporation of modified nucleotides may occur at a lower rate than for native nucleotides, and can significantly inhibit misincorporation of nucleotides into nucleic acids during enzymatic extension and/or polymerization processes.

Abstract: Turning now to the drawings, systems and methods to enhance RNA transcription in a cost-effective manner and uses thereof are provided. One of the most common enzymes for RNA transcription is T7 RNA polymerase. Many embodiments increase RNA yield in transcription reactions by adding ribonucleoside vanadyl complex (VRC) to the transcription reaction. Various embodiments use VRC at low concentrations in an RNA transcription reaction. Reactions in accordance with many embodiments are capable of increasing RNA yield by approximately 2-fold or more.

Abstract: Provided herein are methods and systems for absolute quantification of a target 16S rRNA and/or of a target prokaryotic taxon, based on amplifying and sequencing a same 16S rRNA recognition segment in which target 16S rRNA conserved regions flank 16S rRNA variable regions, conserved and variable among a plurality of sample 16S rRNAs and/or of a sample prokaryotic taxon of higher taxonomic rank with respect to the target taxon. In the methods and systems, absolute abundance of the a plurality of sample 16S rRNAs and/or of the sample prokaryotic taxon detected by the amplifying, is multiplied by the relative abundance of the target 16S rRNA and/or of a target prokaryotic taxon detected by the sequencing to provide the absolute quantification in accordance with method and systems of the disclosure.

Abstract: The present invention provides a method for sequencing a nucleic acid using an immersion reaction protocol. The immersion reaction protocol comprises sequentially immersing a solid support having nucleic acid molecules immobilized thereon in different reaction containers to realize nucleic acid sequencing.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: An example of a method includes providing a substrate with an exposed surface comprising a first chemical group, wherein the providing optionally comprises modifying the exposed surface of the substrate to incorporate the first chemical group; reacting the first chemical group with a first reactive group of a functionalized polymer molecule to form a functionalized polymer coating layer covalently bound to the exposed surface of the substrate; grafting a primer to the functionalized polymer coating layer by reacting the primer with a second reactive group of the functionalized polymer coating layer; and forming a water-soluble protective coating on the primer and the functionalized polymer coating layer. Examples of flow cells incorporating examples of the water-soluble protective coating are also disclosed herein.

Abstract: Aspects of this disclosure relate to luminescently labeled nucleic acid nanostructures and methods and compositions for the detection and/or sequencing of one or more target molecules derived from a sample.

Abstract: Gene expression is measured in a sample of peripheral blood mononuclear cells (PBMCs) obtained from a subject and used to predict organ function recovery. A Function Recovery Potential (FRP) score is assigned to a sample that reflects the measured expression level of the genes identified herein in a direction associated with recovery from organ failure. Treatment of the subject with optimal medical management (OMM) and/or palliative care (PC) is advised when the FRP score is lower than the reference value, and referring the subject for treatment with therapies including—but not limited to—mechanical circulatory support (MCS) surgery, heart transplant (HTx) surgery, or other intervention for advanced heart failure is advised when the FRP score is greater than the reference value. A method for developing an FRP scoring algorithm that predicts a subject's ability to recover from medical intervention for organ failure is also described.

Abstract: The present invention is drawn to a method for in vitro for differential diagnosing bipolar disorder and unipolar depression in a human patient from a biological sample of said patient, using at least one or a combination of particular A to I editing RNA biomarkers associated to a specific depression score and algorithm. The present invention is also directed to a method for diagnosing bipolar disorder implemented the particular combination of A to I editing RNA biomarkers associated to a specific depression score and algorithm of the present invention. The present invention is also directed to a method for monitoring treatment for bipolar or unipolar disorder, said method implementing the method for differential diagnosing bipolar disorder and unipolar depression of the present invention. Kit for determining whether a patient presents a bipolar disorder versus unipolar depression disorder or healthy control patient is also comprised in the present invention.

Abstract: The present disclosure provides a detection method, kit and system for non-invasive prenatal screening of fetal chromosome copy number variation, fetal chromosome microdeletion/microduplication, and/or dominant monogenic variation. The present disclosure further provides a method of designing a targeted capture probe. The detection method is used for non-invasive prenatal screening of fetuses, and compared with the existing detection method for non-invasive prenatal screening, its application scope in clinical genetic detection can be expanded, and the detection accuracy can be improved.

Abstract: This disclosure is directed to a method for detecting melanoma in a tissue sample by measuring a level of methylation of one or more regulatory elements differentially methylated in melanoma and benign nevi. The invention provides methods for detecting melanoma, related kits, and methods of screening for compounds to prevent or treat melanoma.

Abstract: The present invention discloses a method for detecting the mutation and methylation of tumor-specific genes in ctDNA, and this method can simultaneously detect the mutation (including point mutation, insertion-deletion mutation, HBV integration and other mutation forms) and/or methylation of tumor-specific genes in ctDNA in one sample. Not only the sample size requirement is low, but the MC library prepared by this method can support 10-20 subsequent detections. The results of each test can represent the mutation status of all the original ctDNA specimens and the methylation modification status of the region covered by the restriction sites, without reducing the sensitivity and specificity. The present invention has important clinical significance for early tumor screening, disease tracking, efficacy evaluation, prognosis prediction and the like, and has great application value.

Abstract: The present invention provides methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. Further provided are compositions and methods for predicting outcome or response to therapy of a subject diagnosed with or suspected of having breast cancer. These methods are useful for guiding or determining treatment options for a subject afflicted with breast cancer. Methods of the invention further include means for evaluating gene expression profiles, including microarrays and quantitative polymerase chain reaction assays, as well as kits comprising reagents for practicing the methods of the invention.

Abstract: Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies multiple SNP site contamination markers and indel site contamination markers. The multiple SNP site contamination markers include at least two SNP sites within a threshold distance, having population haplotype frequency within a range of threshold frequencies, excluding guanine-adenine polymorphisms and/or cytosine-thymine polymorphisms, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The indel site contamination markers include indel sequences that are within a threshold length, having high complexity, having population haplotype frequency within a range of threshold frequencies, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The system identifies contamination markers for which the sample is homozygous.

Abstract: The present invention relates to a use of using, as biomarkers for the detection and diagnosis of hepatocellular carcinoma, genes of which the expression changes specifically to hepatocellular carcinoma, and treating liver cancer by using same as targets. In the present invention, it has been discovered that the expression of SMARCA4 is increased in HCC and SMARCA4 directly increases the expression of IRAK1, and it has been ascertained that oncogenic proteins Gankyrin and AKR1B10 are induced through the transcriptional activation of IRAK1, and thus SMARCA4-IRAK1-Gankyrin and AKR1B10 can be used as markers specific for liver cancer and can be effectively used as targets for liver cancer treatment.

Abstract: Disclosed are any of the methods or compositions herein. Disclosed are methods of treating a subject having cancer comprising administering a proteasome inhibitor to the subject having cancer, wherein the subject having cancer has a non-functional ATAD1 gene. Disclosed are methods of diagnosing and treating cancer, the method comprising: diagnosing a subject as being susceptible to treatment by a proteasome inhibitor; and administering a proteasome inhibitor to the subject.

Abstract: Methods for classifying neuroendocrine neoplasms (NENs) are based on comprehensive microRNA (miRNA) expression profiling and data mining of multiple pathological types. Reference miRNA expression profiles are generated for multiple NEN pathological types and site-matched non-NEN controls, and candidate category and type specific miRNAs are identified and used for 5 classification. A multilayer hierarchical classifier for discriminating NEN pathological types is based on the candidate category and type specific miRNAs. Methods and software products include products that enable construction of discriminator functions including hierarchical classifiers for discriminating among multiple conditions of interest in a dataset, the methods and software products being applicable to a wide range of data modalities, including, for example, omits data 0 such as miRNA expression data wherein multiple conditions of interest include different cancer pathologies.

Abstract: Use of at least one microRNA comprising a nucleotide sequence set forth in any of SEQ ID NOS: 1 to 15 in a biological sample derived from a subject as a pancreatic cancer biomarker, wherein the pancreatic cancer biomarker is for determining whether the subject suffers from pancreatic cancer, for determining a pathological condition of the subject suffering or suffered from pancreatic cancer, or for identifying a test substance capable of treating pancreatic cancer.

Abstract: This document relates to methods and materials for detecting premalignant and malignant neoplasms. For example, methods and materials for determining whether or not a stool sample from a mammal contains nucleic acid markers or polypeptide markers of a neoplasm are provided.

Abstract: The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient’s tumor mutation burden.

Abstract: A method of prognosing a subject diagnosed with multiple myeloma (MM) is provided. Also provided a method of treating a subject diagnosed with MM selected expressing intracellular PPIA and/or RRM2 above a predetermined threshold, the method comprising administering to the subject a therapeutically effective amount of at least one agent which specifically down-regulates activity or expression of PPIA and/or RRM2, thereby treating the subject.

Abstract: Provided herein are methods of treating cancer in a subject, wherein the cancer is extrachromosomal DNA-positive (ecDNA-positive) or therapeutically resistant, the method comprising administering to the subject a therapeutically effective amount of a replication stress (RS) pathway agent alone or in combination with a targeted therapeutic.

Abstract: A computer-implemented method for generating a tumor fraction estimate from a DNA sample of a subject is disclosed. The method may include receiving a dataset of methylation sequence reads from the sample of the subject. The method may also include dividing the dataset into a plurality of variants. The method may further include determining methylation states of the plurality of variants. The method may further include filtering the plurality of variants based on a bank of reference sequence reads to generate a filtered subset of variants. The bank may include reads generated from non-cancer samples and biopsy samples of a plurality of tissues of reference individuals. The counts of the methylation states of variants in the filtered subset are determined and input to a model that is trained based on recurrence rates of the variants in the reference sequence reads. The tumor fraction estimate may be generated by the model.

Abstract: A method of processing a fecal sample from a human subject comprising combining a first portion of a collected fecal sample with a stabilizing buffer that maintains DNA integrity in a fecal sample, and combining a second portion of the sample with a solution that prevents denaturation or degradation of blood proteins found in a fecal sample. Embodiments comprise testing DNA extracted from the first portion of the fecal sample for the presence of a human DNA, and testing the second portion of the fecal sample for the presence of human blood.

Abstract: Provided herein are novel organoid culture media, organoid culture systems, and methods of culturing tumor organoids using the subject organoid culture media. Also provided herein are tumor organoids developed using such organoid culture systems, methods for assessing the clonal diversity of the tumor organoids, and methods for using such tumor organoids, for example, for tumor modelling and drug development applications. In particular embodiments, the tumor organoid culture media provided herein is substantially free of R-spondins (e.g., R-spondin1).

Abstract: Sets of bacterial features were identified in the nostrils, nasopharynx, and lungs of cows that can be used to predict the likelihood that a cow will develop bovine respiratory disease (BRD) or to diagnose BRD. The present invention provides methods and kits for selecting cows to treat for BRD based on the levels of these biomarkers in the respiratory microbiome. Using these methods and kits, producers may selectively treat cows deemed to be at risk for BRD, saving money and decreasing antibiotic use.

Abstract: The present invention relates to compositions comprising and methods of producing genetically engineered bacteriophages, bacteriophage-like particles and non-replicating transduction particles (NRTPs) that contain non-native tail fibers that display altered host specificity and/or reactivity. The present invention also relates to methods of using these bacteriophages and NRTPs for the development of novel diagnostics, therapeutics and/or research reagents for bacteria-related diseases.

Abstract: Provided is a bead complex for detecting a nucleic acid molecule in a biological sample, and a method of detecting nucleic acid using the same. According to an aspect, the bead complex may effectively isolate, extract, and detect a target nucleic acid molecule in a biological sample, and by analyzing whether a target nucleic acid molecule is present in a biological sample, there is an effect of improving sensitivity of the assay.

Abstract: Methods of detecting, including early detection, of cancer mediated by SARS-CoV-2 and HPV, may include detection of such viral infections alone or together with one or more biomarkers selected from gene specific DNA methylation levels, whole genome DNA methylation levels, host RNA expression levels, T-Cell receptor amount or clonality, B-Cell receptor amount or clonality, microbiome. One method includes analysis of SARS-CoV-2 nucleic acid and the one or more biomarkers from samples of the same tissue, biofluid, or both. These methods are useful for, among other things, assessing the effectiveness of treatment, monitoring relapse, and clinical staging of cancer. These methods are also useful for among other things to monitor the effectiveness of strategies and therapies used to modify lifestyle and contextual effects to prevent disease, foster wellness and enable health promotion.