Abstract: Provided herein are methods for isolating nucleic acids from intact cells in a sample of intact cells, contamination dead cells, cell debris, and biofilm using two separation steps, either by centrifugation or filtration, performed in sequentially. Also provided is a method for isolating nucleic acids from intact cells using a first separation step followed by treatment with a nuclease and then a second separating step. Provided herein is a related method for isolating DNA from intact cells using a nuclease that produces DNA cuts on double stranded DNA, followed by a second separating step.

Abstract: The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Abstract: Methods and systems for storing digital data into peptide sequences and retrieving digital data from peptide sequences are disclosed. The method for storing digital data into peptide sequences may include: encoding the digital data into a digital code; translating the digital code into the peptide sequences; and synthesizing the translated peptide sequences. The method for retrieving digital data from peptide sequences may include: sequencing and determining an order of the peptide sequences; converting the peptide sequences with the determined order into a digital code; and decoding the digital data from the digital code. Codes with error-correction capability are developed for encoding digital data into peptide sequences, and a computational method implemented in a software is developed for sequencing the digital data bearing peptides.

Abstract: The invention relates generally to the field of nanopores and the use thereof in various applications, such as analysis of biopolymers and macromolecules, typically by making electrical measurements during translocation through a nanopores. Provided is a system comprising a funnel-shaped proteinaceous nanopore comprising an a-helical pore-forming toxin that is a member from the actinoporin protein family, more in particular Fragaceatoxin C (FraC), a mutant FraC, a FraC paralog, or a FraC homolog.

Abstract: Disclosed are methods utilizing specific amplification of Candida sp. target nucleic acid for detecting the presence or absence of Candida sp. in a sample. Also disclosed are corresponding oligomers, including amplification oligomers, capture probes and detection probes, and combinations thereof, as well as corresponding reaction mixtures and kits.

Abstract: Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PTOCE (PTO Cleavage and Extension) assay. The present invention detects a target nucleic acid sequence in which the PTO (Probing and Tagging Oligonucleotide) hybridized with the target nucleic acid sequence is cleaved to release a fragment and the fragment is hybridized with the CTO (Capturing and Templating Oligonucleotide) to form an extended duplex, followed by detecting the presence of the extended duplex. The extended duplex provides signals (generation, increase, extinguishment or decrease of signals) from labels indicating the presence of the extended duplex and has adjustable Tm value, which are well adoptable for detection of the presence of the target nucleic acid sequence.

Abstract: Methods and devices are provided for sample collection. In one example, a device is provided comprising at least one capillary tube or collection channel directed to a sample vessel, wherein in a one-step removal step of detaching the sample vessel from the collection channel, a vacuum force is created within the sample vessel, due in part of the pulling of the sealed vessel away from the device, wherein this vacuum force draw out residual sample that may still be resident in the collection channel.

Abstract: Specific, accurate, and cost effective primers for performing digital PCR, compositions and kits containing the primer and methods for using and making the same are useful for detecting nucleic acid mutations. A primer useful as a first forward primer in performing digital PCR to detect a target nucleic acid in a sample, includes: a detection portion located upstream to a target sequence binding portion, and including a second forward primer binding portion having a sequence substantially complementary to a second forward primer, and a probe binding portion downstream to the second forward primer binding portion having a sequence substantially complementary to a probe; the target sequence binding portion includes a mismatch portion having a sequence not complementary to the target nucleic acid, and an amplification determinant portion downstream to the mismatch portion having a sequence complementary to a gene allele or a variant thereof encoded by the target nucleic acid.

Abstract: Techniques are described for determining the strain on a cell wall using two models: 1) a short timescale model, describing the relationship between physical properties assumed to be fixed and 2) a long timescale model, describing the dynamic chemical composition of a cell wall. Short term modeling of the physical properties in a cell wall is used to properly understand how physical factors such as osmotic pressure affects the strain on the cell wall, which is in turn used to identify conditions under which a cell wall will cease to function properly or lyse entirely. Although temporally the physical properties which cause cell walls to underperform/lyse can be evaluated under a short time frame, the chemical properties that lead to the physical properties which cause that behavior themselves change over much longer timescales, in a relative sense.

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.

Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.

Abstract: Methods and reagents are provided for the rapid extraction of nucleic acids from a fixed paraffin embedded sample (e.g., a FFPET sample). In some embodiments, the methods comprise incubating one or more sections of said tissue sample in a lysis solution comprising a buffer sufficient to maintain the pH of said solution at a pH ranging from about pH 4 to about pH 9; a chaotropic agent; a chelating agent; and a detergent; where the incubating is at a temperature ranging from about 50° C. to about 100° C.; and recovering the nucleic acid from said lysis solution.

Abstract: A screening method for the identification of a characteristic of a target nucleic acid in a whole blood sample, including positioning a composition comprising whole blood and at least one preservative agent within a centrifuge, centrifugating the composition to isolate a plasma that includes at least one target nucleic acid for further analysis and analyzing the at least one target nucleic acid to identify a characteristic about the at least one target nucleic acid, and a composition including the plasma, the preservative agent, and any other ingredient, which is produced by the method.

Abstract: A method of identifying a polynucleic acid (PNA) is presented, including the steps of providing a PNA; modifying one or more nucleobases of the PNA by addition or removal of a hydrogen bonding partner, thereby altering the base pairing capacity of the one or more nucleobases; base pairing a complementary nucleic acid to the PNA, including base pairing to at least one modified nucleobase; identifying the sequence of the complementary nucleic acid at least at the position that is complementary to at least one modified nucleobase.

Abstract: The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.

Abstract: The present disclosure provides methods, compositions and kits as well as systems for manipulating nucleic acids, including implementing isothermal amplification, such as recombinase-polymerase amplification (RPA), of a nucleic acid template using a pre-seeded solid support. Provided are rapid and efficient methods for generating template nucleic acid molecules comprising specific nucleotide sequence bound to solid support. Such methods can be used, for example, in manipulating nucleic acids in preparation for analysis methods that utilize monoclonal populations of nucleic acids.

Abstract: The invention discloses a quasi-volumetric sensing system and method. Plural short-range order (SRO) units are configured on the carrier of a quasi-volumetric device, and arranged as an array, i.e. a long-range order (LRO) unit. Protrusions, configured on the SRO units, can modify the wettability of the carrier to control the liquid volume retained thereon so that the precise volume of the liquid sample or droplets are calculated. Based on the applied force on the LRO unit and the gradient of hydrophilicity-hydrophobicity on the surface, the redundant volume of the liquid sample is removed. Macromolecules, e.g. antibodies, complements, receptor proteins, aptamers, oligosaccharides or oligonucleotides, configured on the protrusions are coupled to specific molecules in the liquid sample or droplets so as to determine characteristics of the specific molecules. Therefore, the open chip device of the invention can be used to achieve the quasi-volumetric measurement and the analysis of specific molecules.

Abstract: The present disclosure relates to the use of recombinant proteins for inducing epigenetic modifications at specific loci, as well as to methods of using these recombinant proteins for reducing the expression of genes in plants.

Abstract: The invention provides a mass spectrometry analysis method and a mass spectrometry system. During implementation of the mass spectrometry analysis method, intensity data of the daughter ions, a first parameter of the daughter ions associated with the first physicochemical property, and a second parameter of the daughter ions associated with the second physicochemical property are all recorded to form a spectrogram data set. In a deconvolution step, the spectrogram data set is deconvoluted to categorize the daughter ions from the same parent ion according to two-dimensional features including the first parameter and the second parameter. In the above manner, the mass spectrometry analysis method and the mass spectrometry system provided by the invention can detect ions that partially overlap spectral peaks of other ions significantly, thereby improving the qualitative and quantitative ability of data analysis for data independent acquisition.

Abstract: A microscope stage is movably mounted to a base and is movable relative to the base by two separate drive units on separate rail systems situated at an angle relative to one another. The drive units are mechanically isolated from one another and one of the drive units uses a belt drive.

Abstract: The present disclosure relates to systems and methods for high efficiency electronic sequencing of nucleic acids and molecular detection.

Abstract: The invention provides compositions and methods for regulating intracellular osmolarity in cells, e.g., in cultured cells, including in cultured cells in bioreactors. The invention provides nucleic acids comprising at least one osmo-responsive transcriptional regulatory element (OR-TRE), and cells, vectors, products of manufacture, artificial organs or implants and the like containing an osmo-responsive transcriptional regulatory element (OR-TRE).

Abstract: Methods, compositions and kits for capturing, detecting and quantifying mature small RNAs are provided herein. Embodiments of the methods comprise tailing both the 5? and 3? ends of mature small RNA by ligating a 5? ligation adaptor to the 5? end and polyadenylating the 3? end. Other embodiments comprise reverse transcribing the adaptor ligated, polyadenylated mature small RNA with a universal reverse transcription primer and amplifying the cDNA with universal primers.

Abstract: Methods and kits for excising HIV-1 DNA in vivo are provided, which employ Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Associated (cas) proteins. Vectors harboring nucleic acids encoding one or more guide RNA, wherein said guide RNA hybridizes with a target HIV-1 DNA are also provided.

Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: A micro-fluidic device 100 for performing digital PCR is presented. The device comprises: a semiconductor substrate; a first micro-fluidic channel 104, comprising an inlet 102 and an outlet 103, embedded in the semiconductor substrate; a heating element 101 thermally coupled to the first micro-fluidic channel 104; a droplet generator 107 connected to the inlet 102 of the first micro-fluidic channel 104 for generating droplets and pumping generated droplets at a flow rate into the first micro-fluidic channel 104; characterized in that: the heating element 101 is a single heating element connected to a temperature control unit 111 configured to cycle the temperature of the complete first micro-fluidic channel 104 through at least two temperature values; and wherein the flow rate of the droplet generator 107 is adaptable. Further, a method to perform digital PCR is presented using the micro-fluidic device 100.

Abstract: The present disclosure relates to, inter alia, an easy-to-operate, fully closed component, which can be part of an instrument, for purification of biomolecules from biological samples, and subsequent transfer, and testing of the biomolecules, as well as an instrument comprising the component, and a method for using the component.

Abstract: A device for synthesis of macromolecules is disclosed. In one aspect, the device comprises an ion-releaser having a synthesis surface comprising an array of synthesis locations arranged for synthesis of the macromolecules. The ion-releaser also includes an ion-source electrode, which is arranged to contain releasable ions and is arranged to be in contact with each of the synthesis locations of the synthesis surface, thereby release ions to the synthesis locations. The ion-releaser further comprises activating electrodes, which are arranged to be in contact with the ion-source electrode, wherein each one of the activating electrodes is arranged in association with one of the synthesis locations via the ion-source electrode. The ion-releaser is arranged to release at least a portion of the releasable ions from the ion-source electrode to one of the synthesis locations, by activation of the activating electrode associated with the synthesis location.

Abstract: The present disclosure relates to compositions and methods for investigating Zika virus (ZIKV) biology and pathogenicity. The present disclosure provides genetically stable viral vectors to produce functional RNA transcripts of ZIKV cDNAs. In particular, the present disclosure provides full-length infectious cDNAs as bacterial artificial chromosomes for spatiotemporally distinct and genetically divergent ZIKVs. The present disclosure also provides methods of generating a genetically engineered attenuated ZIKV using the genetically stable viral vectors described herein.

Abstract: The present disclosure provides methods and compositions of modified oligonucleotide primer and probe combinations, structurally modified with locked nucleic acids, quenchers, and dyes, effective to detect tumor-derived Human Papilloma Virus (HPV) and tumor-derived Epstein-Barr virus (EBV) and, especially, to distinguish viral DNA derived from tumors from viral DNA derived from infectious viral particles.

Abstract: Disclosed herein are methods for detecting presence of a target nucleic acid (such as an influenza virus nucleic acid) in a sample. In some embodiments, the methods include contacting the sample with a first probe capable of hybridizing to the target nucleic acid and a second probe capable of hybridizing to the target nucleic acid, contacting the resulting complex with one or more gap filling reagents, thereby producing a gap-filled target nucleic acid, isolating and amplifying the gap-filled target nucleic acid. The amplified gap-filled target nucleic acid covalently linked to the substrate is then detected, for example with a detectably labeled probe. Also disclosed herein are probes capable of hybridizing to influenza virus nucleic acids. The disclosure also includes kits for detecting and/or discriminating influenza virus nucleic acids in a sample. In some examples, the kits include two or more of the disclosed probes.

Abstract: The present invention relates to a buffer system comprising a dicarboxylic acid or tricarboxylic acid or a salt thereof for synthesizing RNA molecules as well as a method of RNA in vitro transcription using this buffer system. The present invention also provides the use of this buffer system in RNA in vitro transcription and in the reduction or prevention of precipitates during RNA in vitro transcription.

Abstract: The present teachings relate to methods, systems, and kits for the preparation, purification and/or analysis of a glycan or glycoconjugate, and specifically to a magnetic bead based sample preparation protocol. In some aspects, the sample preparation protocol can provide for glycoconjugate capture, glycan release, fluorescent derivatization, and glycan purification for subsequent capillary electrophoresis, liquid chromatography, or other glycoanalytical method using magnetic beads containing negatively charged carboxyl groups extending from the surface of the magnetic beads.

Abstract: Provided is a method for isolating exosomal DNA, the method comprising: (i) providing a sample, wherein the sample comprises a blood sample from peripheral blood of a pregnant woman; and (ii) subjecting the sample to isolating, thus obtaining the exosomal DNA. Also provided are a method for detecting a blood sample, a method for constructing a sequencing library on a blood sample, a method for high-throughput sequencing an exosomal DNA sequencing library, a method for non-invasive prenatal gene detection, a device for non-invasive prenatal gene detection, and a kit for detecting a blood sample and use thereof.

Abstract: Solutions, reagents, and methods for nucleic acid purification. In certain aspects, cationic surfactant and, optionally, an anionic surfactant solutions are provided which can be used for phase separation and capture of nucleic acids, such as plasmid or genomic DNA, to a solid phase carrier, such as a mineral matrix.

Abstract: Some embodiments of the present application relate to novel modified nucleotide linkers for increasing the efficiency of nucleotide incorporation in Sequencing by Synthesis applications. Methods of preparing these modified nucleotide linkers are also provided herewith.

Abstract: The present invention is directed to a method for the synthesis of a bi-functional complex comprising a molecule part and an identifier oligonucleotide part identifying the molecule part. A part of the synthesis method according to the present invention is preferably conducted in one or more organic solvents when a nascent bi-functional complex comprising an optionally protected tag or oligonucleotide identifier is linked to a solid support, and another part of the synthesis method is preferably conducted under conditions suitable for enzymatic addition of an oligonucleotide tag to a nascent bi-functional complex in solution.

Abstract: A single-grain seeder for introducing seeds into soil, including a singulating member which is suitable for singulating seeds supplied from a storage container and for dispensing the seeds individually, wherein the single-grain seeder has an application unit for applying a dressing agent to a singulated seed, wherein the application unit is arranged with respect to the singulating member in such a manner that the dressing agent is applied to a seed after the seed has been singulated and prior to the seed being dispensed from the singulating member.

Abstract: The present invention relates to a method of diagnosing cancer in a subject comprising detecting in the DNA of said subject at least one hypermethylated CpG island associated with said cancer, wherein an elevation in the level of methylation in said CpG island of said subject, relative to the level of methylation in said CpG island of a control subject, is indicative of said CpG island being hypermethylated.

Abstract: The present invention is directed to a method for immobilizing nucleic molecule on solid support and to a use of a nucleic acid non-immobilized primer in combination with a nucleic acid primer linked to a solid support in said a method.

Abstract: Described herein are methods, compositions, kits, and uses thereof for analysis of nucleic acid segments comprising a repeating A/T-rich segment, wherein the repeating A/T-rich segment is: (i) a homopolymeric segment comprising at least 10 A residues, at least 10 T residues, or at least 10 U residues, wherein the at least 10 A, T, or U residues are consecutive or interrupted once by one to three other nucleotides; or (ii) a segment comprising (TnA)m, (ATn)m, (TAn)m, or (AnT)m, wherein n is 2 or greater and m is such that the length of the repeating A/T-rich segment is 10 or more residues.

Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.

Abstract: Systems and methods for storing large data sets, such as genetic sequence information. Within a “targeted subset” of positions with information, the system stores, both variant states and missing states at each position. Reference states are not stored, but are inferred within the targeted subset when neither a variant nor a missing state is stored at a given position. The absence of a variant state at a given position is assumed to be a reference state. The criteria for missing data are defined in pre-processing and are customizable based on the use case. For example, each data point may represent the genetic information of a sample at a position in the genome. The targeted subset may represent those positions that were included in a sequencing test.

Abstract: The present disclosure provides for methods and compositions useful for imaging inflammation and inflammatory disease markers with an affinity for TREM-1 antibodies. The methods and compositions can include a labeled probe having a TREM-1 antibody and a radiolabel.

Abstract: Methods, compositions and kits for capturing, detecting and quantifying mature small RNAs are provided herein. Embodiments of the methods comprise ligating 5? and 3? ligation adaptors to the 5? and 3? ends of the mature small RNAs, respectively, in the presence of 5? and 3? semi-degenerate ligation splints to generate a ligation product. Other embodiments comprise reverse transcribing polyadenylated mature small RNA with a universal reverse transcription primer and ligating an adaptor to the 3? end of the cDNA in the presence of a semi-degenerate ligation splint to generate a cDNA ligation product.

Abstract: A kit for use with a nucleic acid sequencing instrument can include a plurality of combinatorial barcodes sequences meeting the following criteria: each of the combinatorial barcode sequences comprise a plurality of iterations of a sequence motif, where the sequence motif comprises a first nucleotide base from a first group of nucleotide bases followed by a second nucleotide base from a second group of nucleotide bases, the first group and the second group differing from each other; and the plurality of combinatorial barcode sequences is at least 1,000,000 different barcode sequences.

Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a ligation and/or polymerase reaction. In some embodiments, the ligation products formed in the ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

Abstract: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.