Abstract: Polypeptides that fold into biologies are stabilized by diselenide bonds between selenocysteine amino acids. Methods to produce such polypeptides in genomically recoded organisms (GRO) can be scaled up for industrial production. Since diselenides have the same geometric bond angles and torsions as disulfides, as well as very similar bond lengths, they can be substituted into polypeptides without disrupting the three dimensional structure of the polypeptides. Diselenides render the polypeptides resistant to reduction when they are exposed to blood serum or to reducing components of blood serum or to reducing components components within cells.

Abstract: A reagent used for a glucose sensor for electrochemical, quantitative determination of glucose, includes a flavin adenine dinucleotide glucose dehydrogenase, single-walled carbon nanotubes, and a dispersant.

Abstract: A method of assessing neurotoxicity of nanoparticles, includes: preparing a tissue or cell sample of mammal exposed to the nanoparticles; analyzing at least one polyamine metabolite selected from the group consisting of putrescine, N1-acetylspermidine, N8-acetylspermidine, N1-acetylspermine and spermine in the sample; and comparing expression degree of the polyamine metabolite with that of a control.

Abstract: The present disclosure relates to a composition and its use for treating a sputum sample suspected to contain mycobacteria. The composition comprises thymol, a linear or branched alcohol, a chaotropic agent, a reducing agent, a detergent, and a buffer, and has a pH value between 8.5 and 10. Also disclosed is a method for treating a sputum sample suspected to contain mycobacteria.

Abstract: Provided is a method for detecting pathogenic microorganisms in a biological sample, which is a technique that can be used to perform high-sensitivity detection of pathogenic microorganisms, such as influenza virus, etc.

Abstract: The present invention is directed to novel methods, kits and uses to be employed for the generation of tagged DNA fragments of a target DNA and nucleic acid molecules associated therewith

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: Provided herein are systems and methods for whole genome amplification and sequencing. In particular, provided herein are systems and methods for detection of nucleic acid variants (e.g., rare variants) in limited samples.

Abstract: This specification generally relates to non-radioactive methods of detecting nucleic acid polymerase activity and methods of detecting compounds that modulate nucleic acid polymerase activity. The activity may be measured in real-time using a real-time PCR instrument.

Abstract: The invention relates to a method for modifying a template double stranded polynucleotide, especially for characterisation using nanopore sequencing. The method produces from the template a plurality of modified double stranded polynucleotides. These modified polynucleotides can then be characterised.

Abstract: In traditional plant breeding approaches, chemical mutagenesis may be utilized to introduce nucleotide substitutions at random in the genome of a plant, i.e. without possibilities to control the sites of nucleotide changes. Because of genome complexities, the statistical probability is extremely little when it comes to finding a predetermined nucleotide substitution. The present invention, however, demonstrates how a novel, alternative use of digital polymerase chain reaction (dPCR), preferably droplet dPCR (ddPCR), is developed to exploit finding of specific nucleotide substitutions in mutated genes. The entire platform comprises a screening method with a library of mutagenized organisms, digital PCR-based systems and a set-up to propagate and analyze identified, mutated organisms.

Abstract: Methods for incorporation of unique bowtie-barcodes into a nucleic acid origami nanostructure (FIG. 1). In particular, provided herein are methods that facilitate pairing and analysis of nucleic acids from individual cells using, for example, high-throughput next-generation sequencing.

Abstract: The present invention relates to a method of determining the presence or absence of active tuberculosis in a sample, in particular, comprising determining the levels of one or more biomarkers selected from basic leucine zipper transcription factor ATF-like 2 (BATF2), cluster of differentiation 177 (CD177), haptoglobin (HP), immunoglobulin J chain (IGJ) and galectin 10 (CLC), in said sample. Uses of biomarkers of the invention and kits for performing the method of the invention are also described.

Abstract: Provided herein is an antibiotic susceptibility test and related compositions, methods and systems based on detection of a nucleic acid from a target microorganism in a sample in the presence or absence of a lysis treatment of the sample.

Abstract: Embodiments of the invention herein described relate to multiplex polynucleotide sequence analysis without the use of size separation methods or blotting. In certain particulars the invention relates to multiplex sequencing using massively parallel sequencing methods, such as pyrosequencing methods and sequencing by synthesis. The invention provides increased throughput, increased accuracy of enumerating sample components, and the ability to analyze greater numbers of samples simultaneously or serially on presently available systems, as well as others yet to be developed. In certain of its embodiments the invention relates to the analysis of complex microbial communities, particularly to in-depth analysis thereof in large numbers of samples.

Abstract: Disclosed are compositions, methods and apparatus for diagnosing and/or monitoring an infection by a bacterium, virus or protozoan by measurement of pathogen-associated and non-infectious systemic inflammation and optionally in combination with detection of a pathogen specific molecule. The invention can be used for diagnosis, including early diagnosis, ruling-out, ruling-in, monitoring, making treatment decisions, or management of subjects suspected of, or having, systemic inflammation. More particularly, the present disclosure relates to host peripheral blood RNA and protein biomarkers, which are used in combination, and optionally with peripheral blood broad-range pathogen-specific detection assays, that are useful for distinguishing between bacterial, viral, protozoal and non-infectious causes of systemic inflammation.

Abstract: Methods of cleaving double-stranded DNA that can be recognized and cleaved by a rationally-designed, I-CreI-derived meganuclease are provided. Also provided are recombinant nucleic acids, cells, and organisms containing such recombinant nucleic acids, as well as cells and organisms produced using such meganucleases. Also provided are methods of conducting a custom-designed, I-CreI-derived meganuclease business.

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

Abstract: The present invention relates to methods and kits for identifying microsatellite instability (MSI) in a sample. In particular it relates to identifying microsatellite instability in a tumor sample, which may be from a subject suspected of having colorectal cancer or Lynch syndrome. The methods and kits can be used to identify mismatch repair defects. More particularly the invention relates to a panel of markers for a sequencing based MSI test, that can differentiate between MSI-H and MSS CRCs. The invention also allows for determination of biological significance, differentiating between PCR and sequencing errors and MSI induced indels/mutations.

Abstract: Devices and methods are provided for multiplex nucleic acid assembly. Specifically, the device includes a plurality of differentially labeled particles or beads, such that when in use, the labeled particles can barcode different oligonucleotides. The device can be used for nucleic acid singulation during and/or after assembly.

Abstract: The present invention features Nicotiana nucleic acid sequences such as sequences encoding constitutive, or ethylene or senescence induced polypeptides, in particular cytochrome p450 enzymes, in Nicotiana plants and methods for using these nucleic acid sequences and plants to alter desirable traits, for example by using breeding protocols.

Abstract: A method of screening for at least one biological entity of interest using a microfabricated device which has a top surface defining an array of microwells. A sample is loaded onto the microfabricated device such that at least one microwell of the array of microwells includes at least one cell and an amount of a nutrient. A membrane is applied to the microfabricated device to retain the at least one cell and the nutrient. A plurality of cells are cultured from the at least one cell in the at least one microwell of the array of microwells. The plurality of cells is then analyzed to determine a presence or absence of a biological entity of interest.

Abstract: A method of screening for at least one biological entity of interest using a microfabricated device which has a top surface defining an array of microwells. A sample is loaded onto the microfabricated device such that at least one microwell of the array of microwells includes at least one cell and an amount of a nutrient. A membrane is applied to the microfabricated device to retain the at least one cell and the nutrient. A plurality of cells is cultured from the at least one cell in the at least one microwell of the array of microwells. The plurality of cells in the at least one microwell of the array of microwells are split into a first portion of the plurality of cells and a second portion of the plurality of cells. The plurality of cells is analyzed to determine a presence or absence of a biological entity of interest.

Abstract: A kit includes a microfabricated device having a top surface defining an array of microwells for receiving a sample comprising at least one cell, and a membrane for applying on the top surface of the microfabricated device to retain the at least one cell in at least one microwell of the array of microwells after the sample is loaded on the microfabricated device.

Abstract: Described herein is an adapter comprising a population of first oligonucleotides, a second oligonucleotide and a third oligonucleotide, wherein the first oligonucleotides, the second oligonucleotide and the third oligonucleotide are hybridized together to produce a complex that comprises: (i) a first end comprising a transposase recognition sequence, (ii) a central single-stranded region of variable sequence and (iii) a second end comprising sequences that are non-complementary. A method, as well as a kit for practicing the method, are also provided.

Abstract: A digital store comprising of a method to store digital data in live micro-organisms, and a method to selectively retrieve subsets of stored data, is disclosed. Digital data is represented as a plurality of key-value pairs. The proposed system stores copies of key-value pairs in a plurality of live micro-organisms. Upon presentation of a retrieval key, the proposed digital store retrieves the value associated with the retrieval key.

Abstract: Nucleic acid memory strands encoding digital data using a sequence of homopolymer tracts of repeated nucleotides provides a cheaper and faster alternative to conventional digital DNA storage techniques. The use of homopolymer tracts allows for lower fidelity, high throughput sequencing techniques such as nanopore sequencing to read data encoded in the memory strands. Specialized synthesis techniques allow for synthesis of long memory strands capable of encoding large volumes of data despite the reduced data density afforded by homopolymer tracts as compared to conventional single nucleotide sequences.

Abstract: A method in which a microorganism operational taxonomic unit (OTU) in a sample is defined based on a DNA sequence of a system generation information gene of microorganism in the sample. In the method, qualified sequence segments are obtained by means of processing and reading of an original sequence; the segments are sorted according to a relative abundance value of each segment; and only the qualified sequences with the high abundance values are used to obtain the temporary OTU. The qualified sequences with the low abundance values are reallocated; and the qualified sequence can be distributed to the proper temporary OTU respectively when a sequence similarity degree between the qualified sequence and an OTU sequence reaches at least 97%. The present disclosure also provides a sequence-assisted microorganism separation method.

Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.

Abstract: An analytics system uses metagenomics to generate predictions indicating performance of biological or physical samples. In an embodiment, a method includes determining sequence data of a soil sample. The method further includes determining a plurality of features of the soil sample using the sequence data. The plurality of features is determined based at least in part on a measure of a first microbe detected in the soil sample and a different measure of a second microbe detected in the soil sample. The method further includes inputting the plurality of features to a model trained using measures of the first microbe and the second microbe detected in a plurality of soil samples. The method further includes generating, by the model using the plurality of features, a prediction of physical attribute of a plant grown in the soil sample.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

Abstract: The disclosure relates to novel particle compositions and methods of making said compositions having applications in nucleic acid analysis, as well as apparatuses and systems for the same.

Abstract: Disclosed herein are compositions, probes, devices, and processes useful for detecting specific reactions and binding interactions with biological molecules. In certain embodiments, methods of binding one or more biomolecules to a solid support are disclosed. Methods of generating site-specific sequences for one or more biomolecules from a solid support are also disclosed. Biological complexes generated by these methods are also disclosed.

Abstract: A nucleic acid oligomer for RNA hybrid formation, including a structure formed of from 3 to 50 continuous units of at least one unit of a nucleotide unit represented by the following General Formula (1) or a nucleotide unit represented by the following General Formula (2); and having a base length of from 8 bases to 50 bases: in which in the formulae, R1 represents a hydrogen atom, an alkoxy group, an alkenyloxy group, an acyloxy group, a trialkylsilyloxy group, or a halogenyl group, and, in the formulae, each Bs1 independently represents a pyrimidine base that may have a protecting group, a hydrogen atom bonded to a carbon atom at the 5-position of the pyrimidine base may be substituted with a group other than a hydrogen atom, in the formulae, each X independently represents S?Z+ or BH3—Z+, Z+ represents a counter cation, each R2 and R3 independently represents a hydrogen atom, or an alkyl group having from 1 to 10 carbon atoms, and R2 and R3 may be bonded to each other to form a ring.

Abstract: This invention relates to methods and compositions for detecting the presence or absence of a Respiratory Syncytial Virus target nucleic acid in a biological sample using isothermal nucleic acid amplification.

Abstract: Provided herein, among other things, is a method of processing a nucleic acid sample. In some embodiments, the method comprises a) hybridizing a sample comprising a target fragment to a nucleic acid probe comprising: i. a head sequence and a tail sequence, wherein the head and tail sequences are at the ends of a first oligonucleotide molecule; and ii.

Abstract: The invention relates to a method for the diagnosis of liver fibrosis, comprising detecting the level of expression of the gene GATA-4, or the quantity of the protein GATA-4, in the isolated biological sample of liver tissue. The invention also relates to a diagnosis kit.

Abstract: Disclosed herein are WNT and Hippo pathway markers associated with sensitivity to treatment with Aurora A kinase inhibitors. Claimed genes include LEF1, MAP3K7, APC, FZD2, PRKCA, RORA, CAMK2G, JUN, XP01, ROR2, CCND1 & CTNNB1 (WNT pathway) and AMOT, DVL2, LATS1, LATS2, MOB1 B, NPHP4, TJP1, TJP2, WCC1, WWTR1 & YAP1 (Hippo pathway). Sensitivity to treatment with an Aurora A kinase inhibitor is observed when the aforementioned markers have mutations in tumor cells. Compositions and methods are provided to assess marker genes to predict response to Aurora Kinase A inhibition treatment and for patient selection.

Abstract: Methods, systems, and devices are disclosed for enrichment and detection of molecules of a target biomarker. In one aspect, In one aspect, a biosensor device for enriching and detecting biomarker molecules include a substrate, and a microarray of hydrophilic islands disposed on the substrate. A sensing area on each of the microarray hydrophilic islands is structured to anchor bio-molecular probes of at least one type for detecting molecules of a target biomarker and to attract an array of nanodroplets of a biomarker solution that includes the target biomarker molecules. A hydrophobic surface is disposed to surround the microarray of hydrophilic islands.

Abstract: A method of treating a human patient with depressive and/or anxiety symptoms which includes administering an effective amount of a V1B receptor antagonist and/or CRHR1 antagonist to the patient in need thereof, wherein the patient's genome has certain polymorphoric variants.

Abstract: This document provides methods and materials related to genetic variations of developmental disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Autism Spectrum Disorder.

Abstract: The present invention describes a method of prognosing high or low probability of developing an inflammatory bowel disease (IBD) in a subject and a method of diagnosing an inflammatory bowel disease (IBD) in a subject. The invention further provides for a method of identifying genes/genetic loci associated with a disease condition, such as IBD, CD and/or UC.

Abstract: A method of diagnosing a disease associated with a DNA repeat sequence is disclosed. The method comprises: (a) determining the number of repeats of a DNA sequence in DNA molecules of a sample of the subject; and (b) determining the CpG methylation status of the DNA molecules, wherein the number of repeats of the DNA sequence and the CpG methylation status of the DNA molecules is indicative of the disease.

Abstract: The present invention relates to a gene panel of at least 14 genes or the combination of said at least 14 genes for use in a method of diagnosis of a genetic disposition to pulmonary arterial hypertension (PAH) and/or chronic thromboembolic pulmonary hypertension (CTEPH). The present invention relates to using said gene panel or combination of genes in the in vitro or ex vivo diagnosis of a genetic disposition to pulmonary arterial hypertension (PAH) and/or chronic thromboembolic pulmonary hypertension (CTEPH). The present invention relates to a method and a kit for the diagnosis of a genetic disposition to pulmonary arterial hypertension (PAH) and/or chronic thromboembolic pulmonary hypertension (CTEPH). The present invention further relates to said gene panel, method and kit with respect to a genetic disposition to pulmonary veno-occlusive disease (PVOD) and/or hereditary haemorrhagic telangiectasia (HHT).

Abstract: The present invention relates to the field of diagnostics, in particular, cancer diagnostics. More specifically, it relates to a method for identifying whether a subject suffering from a BRAF-positive cancer is a non-responder to a BRAF inhibitor, or not, and/or is a responder to an MAPK/ERK inhibitor, a method for diagnosing cancer, a method for assessing responsiveness to targeted therapy in a subject and a method for assessing cancer in a subject. Moreover, contemplated by the invention are a kit and a device for diagnosing cancer. Further, the invention relates to a MAPK/ERK inhibitor for use in treating a subject suffering from a BRAF-positive cancer.

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: 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: The present invention relates to methods of diagnosing, monitoring of a subject or determining the prognosis of a subject. In particular, the invention relates to a method of determining the prognosis of a cancer patient comprising the steps (a) determining the expression level of at least one marker gene selected from the group consisting of the marker genes as described herein in a sample of the cancer patient to obtain a gene expression profile; (b) determining the prognosis of the cancer patient based on the gene expression profile obtained in step (a). In addition, the present invention refers to kits, diagnostic compositions devices and microarrays for determining at least one marker gene and uses thereof.

Abstract: This document provides methods and materials for treating cancer (e.g., estrogen receptor positive breast cancer). For example, methods and materials for identifying a mammal (e.g., a human) with cancer (e.g., estrogen receptor positive breast cancer) as having A?G variant genotype of rs6990851 and/or as having an elevated level of CSMD1 nucleic acid expression and administering one or more aromatase inhibitors (e.g., anastrozole) to treat the mammal identified as having such genotype and/or elevated level are provided.

Abstract: A method of predicting variation of porcine intramuscular fat profile. The method includes detecting a BRCA1 gene and/or a JAML gene, or an expression product thereof. The disclosure also provides a method of selecting and breeding pigs. The method includes detecting a BRCA1 gene and/or a JAML gene, or an expression product thereof.