Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.

Abstract: Filtration head (1) for a filter system, comprising base (2) including filter support (3) for removable filter element (4) and a fluid path from one side of filter element (4) on filter support (3), through filter element (4), and to drainage outlet (5) of base (2), and holder device (6) for removably attaching funnel (7) to base (2) to form a sample fluid reservoir on one side of filter element (4), wherein holder device (6) comprises ring-shaped element (8) configured to extend about bottom peripheral flange (7a) surrounding a lower end of funnel (7) and to selectively apply a biasing force on a radially outward protruding portion (7b) of bottom peripheral flange (7a) of funnel (7) to press funnel (7) against base (2). The filtration head allows the use of cardboard funnels without risk of liquid leakage between the funnel and the base.

Abstract: The present invention provides a non-naturally occurring dendritic-like myeloid leukaemia cell according to ATCC Patent Deposit Designation PTA-123875, and methods and kits utilising such cells.

Abstract: Provided herein is technology related to the chemical modification and purification of DNA. Specifically, the technology provides methods for performing a bisulfite conversion reaction on small amounts of single-stranded, fragmented DNA and performing the subsequent desulfonation and purification steps on magnetic beads.

Abstract: Compositions and methods for improving cardiac structure and/or function in subjects in need thereof. The methods include administering to a subject a succinate dehydrogenase inhibitor in an amount and for a time effective to elicit an improvement in cardiac structure and/or function. The subjects include subjects suffering from cardiac damage, such as damage resulting from myocardial infarction or other cardiac events. Improvements in cardiac function include one or more of an increase in cardiomyocyte proliferation, an increase in ejection fraction, an increase in fractional shortening, a decrease in left ventricle internal diameter diastole, and a decrease in left ventricle internal diameter systole. Improvements in cardiac structure include one or more of decreased fibrosis, an increase in myocardial thickness, an increase in coronary artery formation, an increase in capillary density, an increase in revascularization, and a decrease in myocardial lesion size.

Abstract: Transgenic INIR20 soybean plants comprising modifications of the MON87701 soybean locus which provide for facile excision of the modified MON87701 transgenic locus or portions thereof, methods of making such plants, and use of such plants to facilitate breeding are disclosed.

Abstract: A microfluidic analysis system (1) performs polymerase chain reaction (PCR) analysis on a bio sample. In a centrifuge (6) the sample is separated into DNA and RNA constituents. The vortex is created by opposing flow of a silicon oil primary carrier fluid effecting circulation by viscous drag. The bio sample exits the centrifuge enveloped in the primary carrier fluid. This is pumped by a flow controller (7) to a thermal stage (9). The thermal stage (9) has a number of microfluidic devices (70) each having thermal zones (71, 72, 73) in which the bio sample is heated or cooled by heat conduction to/from a thermal carrier fluid and the primary carrier fluid. Thus, the carrier fluids envelope the sample, control its flowrate, and control its temperature without need for moving parts at the micro scale.

Abstract: The invention relates to processes for performing biochemical reactions, such as in an aqueous in vitro reaction system. The processes involve macromolecules, particularly polypeptides, comprising one or more functional intrinsically disordered regions (IDRs). The invention also relates to IDR-macromolecules, including IDR-polypeptides, including macromolecules or polypeptides comprising a tagged amino acid sequence which comprises or consists of one or more functional IDRs. Such functional IDRs are capable of increasing the efficiency of the biochemical reaction. The invention relates to kits comprising any such macromolecules and polypeptides. The invention further relates to processes for stimulating or enhancing liquid-liquid demixing in a solution using any such macromolecules and polypeptides, including in combination with multivalent metal ions, thereby providing reagents capable of increasing the efficiency of a biochemical reaction.

Abstract: This application provides for methods of treatment for IBD, especially in subjects who have R. gnavus species or R. gnavus group IBD strains as a component of their microbiome. The application also provides for methods of diagnosing IBD, as well as kits for use in the claimed methods.

Abstract: In accordance with the present invention, a method for increasing the yield of rLV vector particles comprising a trans gene encoding a therapeutic protein or fragment thereof is disclosed. In one approach, cells are transfected with plasmids encoding the necessary components for rLV production using a calcium chloride transfection mix at pH 7.1 wherein the calcium chloride and plasmids form a complex which is added to the cells at a constant speed. The cells are then incubated for a suitable time period wherein virus particle media is collected at least twice during the incubation period and stored in a cold storage unit, thereby reducing virus inactivation.

Abstract: A dispersant system comprises a plurality of taggant vessels, each having a taggant that corresponds to a position in a tag string and a computer controller convert the tag string into a selection of a taggant set while computer-controlled valves allow or block a flow of taggants to a manifold output tube. From the output tube, a mix of the taggants flow to form a dispersant formed according to the tag string. A nozzle disperses the dispersant onto an object to be tagged, possibly atomized with air. The taggant can comprise a DNA taggant comprising a static portion and a dynamic portion that is unique to each tag string position. Tag strings for adjacent lots might have a low Hamming distances to reduce cross-contamination and/or have redundancy for error detection and correction and selected so that consumption of taggants evens out over the plurality of taggant vessels.

Abstract: One embodiment provides methods to identify known and unknown gene fusions by creating a cDNA circle and analyzing the circle cDNA by amplification or sequencing. The circle cDNA is created in two approaches: 1) reverse transcribe a target RNA to cDNA, ligate the 3?end of the cDNA to its 5?end to form a circle cDNA, or 2). ligate the 3?end of target RNA to its 5? end to form a circle RNA, reverse transcribe the RNA to a cDNA, and ligate the cDNA to form a circle cDNA. The circle cDNA is amplified using a primer designed from a known sequence of a wild type target gene by rolling circle amplification or PCR methods. The known or unknown fusion gene sequences in the circle cDNA are amplified and identified by sequencing analysis.

Abstract: A method of tracking proximity relationships is disclosed, comprising: (a) introducing a body into a solution of bio-molecule(s), said body comprising at least two capture probes, wherein each capture probe comprises a barcode and a capture domain, and at least one capture probe is a releasable capture probe, connected to the body via at least one cleavable linker; (b) allowing at least two capture probes to bind to their respective target bio-molecule(s) via their respective capture domains; and (c) releasing the at least one releasable capture probe from the body by cleaving its at least one cleavable linker.

Abstract: Disclosed is a method for determining the presence of Mycobacterium avium complex nucleic acids in a biological sample. In particular, the mig gene of M. avium and the DT1 gene of M. intracellulare are detected, preferably following amplification. In addition, the method distinguishes between species of M. avium and M. intracellulare. Also described are oligonucleotides that can be used as primers to amplify target genes such as mig and DT1 genes and as probes as well as kits containing the oligonucleotide.

Abstract: An endoscopic imaging system for use in a light deficient environment includes an imaging device having a tube, one or more image sensors, and a lens assembly including at least one optical elements that corresponds to the one or more image sensors. The endoscopic system includes a display for a user to visualize a scene and an image signal processing controller. The endoscopic system includes a light engine having an illumination source generating one or more pulses of electromagnetic radiation and a lumen transmitting one or more pulses of electromagnetic radiation to a distal tip of an endoscope.

Abstract: Systems and methods for multiplexed cell sorting are provided herein. The disclosed cell sorting system is referred to as DNA gated sorting (DGS). An exemplary system provides a set of orthogonal sorting probes and release probes for sorting cells of one or more different cell types from a biological specimen.

Abstract: A machine learning (ML) architecture may be trained to determine an estimated epigenetic status at a target DNA locus based at least in part on epigenetic data associated with one or more other DNA loci. The ML architecture may additionally or alternatively be used to detect a failed epigenetic assay and/or determine a likelihood that a subject has falsified information provided about the subject.

Abstract: Personalized treatment plan generation from an inference engine of a system. The system may receive or retrieve data from a plurality of sources and parse the data to generate individual data fields defining characteristics of a patient. The inference engine may process the contents of the individual data fields in relation to rule blocks suggesting certain treatment actions and combinations thereof in response to satisfied conditions. The inference engine may implement machine learning to refine rule blocks and improve functioning of the system to optimize healthcare.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: A system and method for automatically calculating an accurate recommended dosage for hormone replacement therapy and automating the life cycle of a patient's treatment over time. The system and method can automatically acquire relevant patient parameters and apply a consistent formulaic approach to help reduce incorrect dosage determinations. A pellet insertion size may be determined and documented based on a calculated dosage, and an insertion side and lot numbers may be tracked and managed. In addition, corresponding revenues may be tracked and profitability may be reported for hormone replacement therapy practices.

Abstract: The present disclosure provides method and products for the selective enrichment of one population of DNA in a mixed sample comprising multiple populations of DNA. In some embodiments, the mixed sample comprises one or more populations of microbial DNA and the mammalian host DNA, particularly including pathogenic microbial DNA mixed with mammalian host DNA in a clinical sample from an infected individual.

Abstract: Methods, primers, sets of primers, probes, compositions, and kits for detecting presence or absence of SARS-CoV-2 in a sample are provided.

Abstract: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: Disclosed is a substance which down-regulates the activity of a MAST gene, or the activity of a transcription or translation product of a MAST gene, for use in the prevent and/or treatment of an inflammatory skin condition in a mammalian subject.

Abstract: To reduce an arithmetic processing load or an influence of noise at the time of virtual curve calculation processing, provided is a data processing device for a chromatograph, which is configured to execute data processing based on plot data measured by using a chromatograph, the data processing device including a virtual curve calculation data generator configured to obtain a smaller number of pieces of virtual curve calculation data than a number of pieces of the measured plot data; and an arithmetic processor (163) functioning as a virtual curve calculator configured to obtain a virtual curve based on the virtual curve calculation data.

Abstract: Described herein are biological devices and methods for using the same to produce oxidized zinc. The biological devices include microbial cells transformed with a DNA construct containing genes for producing a zinc-related protein, an alkaline phosphatase, and an alcohol dehydrogenase. In some instances, the biological devices also include a gene for lipase. The oxidized zinc compositions produced herein have numerous applications.

Abstract: The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.

Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Abstract: A contaminant detection system includes a light source configured to emit excitation light on an object to be inspected; a detector configured to detect fluorescence emitted from a contaminant adhering to the object to be inspected; and a processor. The fluorescence is caused by emission of the excitation light from the light source onto the object to be inspected. The processor is configured to perform a determination of a location of the contaminant and a type of the contaminant, based on the fluorescence emitted from the contaminant; and output a result of the determination.

Abstract: Methods and apparatuses for mechanically controlling microfluidic movement using a force applicator and an elastically deformable sheet are described herein. These apparatuses may include a mechanical microfluidics actuator devices and a cartridge. A microfluidic droplet may be moved or displaced within an air gap of the cartridge by applying a compressive force locally and selectively reduce the gap width of the air gap near the microfluidic droplet causing the microfluidic droplet to move toward the reduced gap. Compressive forces may also be used to divide, join, mix or perform other operations on the microfluidic droplets.

Abstract: The invention relates to a method for analyzing the diversity of the catalogue of T and/or B lymphocytes in an individual, based on the amplification, from a sample, of genomic DNA fragments by PCR multi-n-plexes, with n?2, carried out with a combination of at least 3 primers defining at least 2 primer couples, each of which includes a primer specifically hybridizing upstream and/or in a given V or D gene and a primer specifically hybridizing downstream and/or in a given J gene, in order to obtain the amplification of at least two fragments characteristic of two distinct V-J or D-J rearrangements from each primer couple. The invention also relates to the applications of this method, in particular in the treatment follow-up or in the diagnosis and/or prognosis of certain diseases.

Abstract: Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and/or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA/RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA/RNA modifications in parallel.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample analysis. Nucleic acid fragments comprising a capture sequence (or a complement thereof) can be generated from double-stranded genomic deoxyribonucleic acid (gDNA), barcoded to generate single-stranded DNA (ssDNA) fragments, and sequenced. Information relating to the gDNA (e.g., genome, chromatin accessibility, methylome) can be determined based on the sequences of the ssDNA fragments in the sequencing data obtained.

Abstract: Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Abstract: Some embodiments of the methods and compositions provided herein relate to the selective cleavage of a target nucleic acid. Some such embodiments include the selective cleavage of a target nucleic acid that is associated with a DNA-binding protein or comprises a methylated CpG island, with a recombinant nuclease. In some embodiments, the DNA-binding protein comprises a chromatin protein. Some embodiments also include the enrichment of non-target nucleic acids in a sample by selective cleavage of target nucleic acids in the sample, and removal of the cleaved target nucleic acids from the sample.

Abstract: Provided herein are synthetic size standards that allow one to detect size bias in a sample that includes a plurality of polynucleotides. The size standards can provide an internal control to detect and correct for size bias in data obtained after manipulating and/or processing of sample polynucleotide. Also provided herein are methods for detecting size bias in a sample or in a sequencing run.

Abstract: A quantum flow cytometer for detecting an analyte with photon-number statistics includes: a flow cytometer that: receives a pump light in a first direction; receives an analyte flow comprising the analyte in a second direction; and produces scattered light from scattering the pump light by the analyte; a single photon detector in optical communication with the flow cytometer and that: receives, in a third direction, the scattered light from the flow cytometer; provides a correlative time-of-arrival waveform comprising photon-number statistics as an amplitude and an integrated area, the integrated area being proportional to a number of photons received by the single photon detector, wherein the first direction, the second direction, and the third direction are arranged at oblique angles.

Abstract: A polypeptide probe for detecting G-quadruplexes (G4s), includes: from two to four G4-binding domains, and one or more linkers disposed between every two G4-binding domains. Each G4-binding domain includes a specific motif including a sequence of amino acids PGHLKGREIGMWY (SEQ ID NO: 1).

Abstract: Disclosed is a bioprocessing system comprising apparatus (200) including a centrifugal separation housing (210) having a temperature controllable compartment (215) for removably accepting a separation chamber (50), the apparatus further comprising at least one mixing station (250) for supporting one or more fluid storage vessels (10, 20, 30, 40), the station including a temperature controllable area (252) for increasing or decreasing the temperature of the contents of the or each supported vessel. The system further includes a disposable fluidic arrangement (100) including a centrifugal separation chamber (50) removably mountable within the compartment (215) and having one or more ports (52) allowing fluid ingress into, or egress out of the chamber, via the one or more ports in use, said ports being in fluid communication with one or more of said fluid storage vessels via fluid conduits (12, 22, 32, 42) and via one or more valve arrangement.

Abstract: Biomarkers and methods for identifying circulating serum-based cfDNA sequences. The cfDNA sequences (PDcRAs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.

Abstract: The present disclosure provides a novel loop-de-loop method of detecting a target nucleic acid using a biosensor-labeled oligonucleotide. Further provided herein is a looped primer and a kit for use in the method.

Abstract: The present disclosure provides systems and methods that can provide portable, real-time accessible DNA memories. An example DNA-based data storage system includes a loading region configured to receive a plurality of DNA-based data storage elements in a suspension fluid and a plurality of microtubes disposed in a capture/release region. The microtubes are configured to capture and release the DNA-based data storage elements. The DNA-based data storage system also includes a linearization region configured to linearize the DNA-based data storage elements and a readout region with a readout device configured to provide information indicative of the respective DNA-based data storage elements.

Abstract: Disclosed herein is the use of CER-001, a negatively charged lipoprotein complex which comprises recombinant human apolipoprotein A-I (ApoA-I), sphingomyelin (SM), and 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1?-rac-glycerol) (Dipalmitoylphosphatidyl-glycerol; DPPG) for treating kidney diseases, and methods for treating a subject having kidney diseases with CER-001. For example, the kidney disease can be associated with a lecithin cholesterol acyl transferase (LCAT) deficiency.

Abstract: An improved decision support tool is provided for detecting and treating human patients at risk for having (or developing) venous thromboembolism VTE. The tool determines a quantitative probability of VTE by utilizing a smart sensor based on a particular machine-learning model for detecting specific biomarkers determined to be related to VTE. In particular, a quantitative probability of VTE may be determined via a model based on interrelationships between multiple components of the human body's complement cascade and their coupling to coagulation processes. In one aspect, a quasi-Dirichlet distribution “mixture” relationship between total hemolytic complement (CH50) activity and complement protein C3 levels is employed as part of a smart sensor and decision support tool to provide predictive, diagnostic, and prognostic applications and for guiding prevention and treatment of acute VTE. Where the smart sensor determines a risk for VTE, then the decision support tool may initiate an intervening action.

Abstract: Non-human animal genomes, non-human animal cells, and non-human animals comprising a humanized coagulation factor XII (F12) locus and methods of making and using such non-human animal genomes, non-human animal cells, and non-human animals are provided. Non-human animal cells or non-human animals comprising a humanized F12 locus express a human coagulation factor XII protein or a chimeric coagulation factor XII protein, fragments of which are from human coagulation factor XII. Methods are provided for using such non-human animals comprising a humanized F12 locus to assess in vivo efficacy of human-coagulation-factor-XII-targeting reagents such as nuclease agents designed to target human F12. A short isoform of F12 that is produced locally in the brain, and methods of using the short isoform, are also provide.

Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PrognomiRs) can be used to differentiate patient's suffering from rapid progressing Parkinson's disease (PD) from slow progressing PD patients.

Abstract: The invention provides methods of digital amplification using primers of limited nucleotide composition. Limited nucleotide composition means that the primers are underrepresented in at least one nucleotide type. Such primers have much reduced capacity to prime from each other or to extend initiated by mispriming from other than at their intended primer binding sites in a target nucleic acid.

Abstract: A method for testing target nucleic acid includes the steps from (1) through (5) below: (1) mixing a specimen containing target nucleic acid with positive control nucleic acid to obtain a specimen mixture of the specimen and the positive control nucleic acid; (2) mixing the specimen mixture with a PCR buffer solution containing a surfactant to obtain a buffer solution mixture; (3) adding a portion of the buffer mixture to a solid composition for PCR control containing DNA polymerase, positive control nucleic acid, and PCR reaction control nucleic acid; (4) adding a portion of the buffer mixture to a solid composition for PCR reaction containing DNA polymerase and one or more kinds of PCR primer pair; and (5) detecting a PCR product generated as a result of the steps (3) and (4).

Abstract: Methods for measuring diffusion in a medium. One method includes dissolving a fluorescent sample in a medium, imaging the fluorescent sample with a patterned illumination Fluorescence Recovery After Photobleaching (FRAP) technique, and analyzing a set of microscope images of the photobleached dissolved fluorescent sample with the patterned illumination using a Fourier Transform (FT) FRAP technique.

Abstract: Methods for the rapid detection of the presence or absence of Hepatitis B Virus (HBV) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, competitive blocking oligonucleotides, and probes targeting HBV (in particular HBV RNA, in particular, HBV RNA transcribed from cccDNA, such as pgRNA) and kits are provided that are designed for the detection of HBV (in particular HBV RNA, in particular, HBV RNA transcribed from cccDNA, such as pgRNA).