Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

Abstract: The invention relates to methods for separating circulating cell free nucleosomes comprising linker DNA from a biological fluid sample, in particular nucleosomes of disease origin. Such methods allow for improved analysis of genetic and epigenetic markers associated with nucleosomes of disease origin.

Abstract: Provided for herein is a polynucleotide-modified bioconjugate comprising a substrate such as an antibody or bead linked to a conjugate component via a nucleic acid linker. Also provided are methods of making and using such bioconjugates. Conjugation methods for creating the bioconjugate are stable, not chemically harsh, and efficient enough that post-conjugation purification may not be required. Further this disclosure provides for reducing the logistic overheads related to product lines by eliminating the need for many unique linkers per conjugation pair.

Abstract: Disclosed is a gene panel which can evaluate lung adenocarcinoma molecular subtype and survival risk, and an application of a reagent, which detects the gene expression level of the gene panel, in preparing a product. The product is used for determining lung adenocarcinoma molecular subtype and evaluating lung adenocarcinoma patient survival risk. The product comprises a Next-Generation Sequencing (NGS) detection reagent kit, a fluorescence quantitative PCR detection reagent kit, a gene chip and a protein microarray. Also disclosed is a method which uses the detection reagent kits to evaluate lung adenocarcinoma molecular subtype and survival risk.

Abstract: A bait is provided, wherein the bait comprises a first portion capable of binding to a nucleic acid in a sequence-independent manner, and a second portion capable of binding to a non-silica capture substrate. Compositions comprising such a bait and methods for using such a bait are also disclosed.

Abstract: The present invention discloses a method for rapidly detecting the total mercury content of soil in urban relocation sites using archaea molecular marker OTU69. The present invention provides a DNA molecule (probe), as shown in SEQ ID NO. 1 of the sequence listing. The present invention also protects the application of the probe in detecting or assisting in detecting the total mercury content of the soil. The present invention also protects the application of the probe in comparing the total mercury content of the soil in different plots. Using the method provided by the present invention to detect the total mercury content of the soil or compare the total mercury content of the soil of different plots has the following advantages: small sample demand, no need for pre-treatment, short required time, low labor cost, and realizing the rapid automatic detection of large quantities of samples.

Abstract: The present invention relates to a novel method for an accurate quantification in intestinal samples of Faecalibacterium prausnitzii phylogroup I members (PHGI) and/or Faecalibacterium prausnitzii phylogroup II members (PHGII). It further relates to a method for detecting intestinal diseases, including the screening, diagnosis, differential diagnosis, and/or monitoring of disease activity or progression in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject. Moreover, it relates to a method for the prediction of the efficacy of a drug in the therapeutic treatment of an intestinal disease in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject.

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: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: Provided are methods, devices, and systems for a loop-mediated isothermal amplification (LAMP) reactions for detecting the presence of genetic material. A LAMP device includes an enclosure having outer walls configured to define an internal space. The LAMP device also includes a tray assembly configured to support a reaction vessel configured for holding a sample for amplification. The LAMP device also includes a plurality of light emitters configured to illuminate the reaction vessel for exciting a fluorescence of the sample in the reaction vessel. The LAMP device also includes an imaging device configured to obtain an image of the sample for determining a quantity of the fluorescence in the sample. The LAMP device also includes a controller configured to regulate a temperature of the tray assembly and instruct the imaging device to obtain the image for determining the quantity of the fluorescence in the sample.

Abstract: The present invention discloses a method for rapidly detecting the total nitrogen content of the soil in an urban green land by using archaea molecular marker OTU300. The present invention provides a DNA molecule (probe), as shown in SEQ ID NO.1 of the sequence listing. The present invention also protects the application of the probe in detecting or assisting in detecting the total nitrogen content of the soil. The present invention also protects the application of the probe in comparing the total nitrogen content of the soil in different plots. Using the method provided by the present invention to detect the total nitrogen content of the soil or compare the total nitrogen content of the soil of different plots has the following advantages: small sample demand, no need for pre-treatment, short required time, low labor cost, and realizing the rapid automatic detection of large quantities of samples. The present invention deserves to apply and promote in the evaluation of soil samples.

Abstract: The presently-disclosed subject matter includes methods for detecting methylation biomarkers in a biological sample from a subject in need of assessment for magnesium deficiency status, methods of diagnosing magnesium deficiency, methods of diagnosing magnesium insufficiency, methods of treating magnesium deficiency, methods of diagnosing magnesium insufficiency, and methods of preventing or reducing a risk of developing a condition linked to magnesium deficiency.

Abstract: Provided are synthetic strands for nucleic acid sequencing. In some embodiments, the strands include a plurality of rotatable molecular disks. The plurality of rotatable molecular disks comprises molecular disks each comprising a first moiety that binds to adenine (A), a second moiety that binds to cytosine (C), a third moiety that binds to guanine (G), and a fourth moiety that binds to thymine (T), uracil (U), or both (T/U). The first, second, third, and fourth moieties are spaced about the perimeter of the molecular disk. The molecular disks enable hybridization of the synthetic strand to a nucleic acid, where the rotational positions of the molecular disks indicate the sequence of the nucleic acid. Also provided are methods of using the synthetic strands, as well as related compositions, kits, and nucleic acid sequencing systems. Stem-loop structure-based sequencing methods and related compositions, kits, and nucleic acid sequencing systems are also provided.

Abstract: A method for determining if a tumor has a mutation in a microsatellite is provided. In some embodiments, the method may comprise: (a) isolating genomic DNA from a tumor sample and a non-tumor sample from the same patient to produce: i. a sample of tumor DNA and ii. a sample of non-tumor DNA, respectively, (b) without pre-amplifying the tumor or non-tumor DNA, sequencing a plurality of microsatellite loci from both the tumor and non-tumor DNA using OS-seq to provide sequence reads, wherein the sequenced microsatellite loci comprise mononucleotide, dinucleotide, trinucleotide and tetranucleotide microsatellites loci, and (c) comparing the results.