In alternative embodiments, the invention provides compositions such as devices, pills, beads, capsules, products of manufacture, particles, microparticles, nanoparticles, gels, liquid gels, liquid gel capsules, capsules, tablets, geltabs, liquids, sprays, emulsions, suspensions, pastes or yogurts, for the detection and isolation of biomarkers, nucleic acids, proteins or peptides, proteoglycans, lipids, fats, sugars or polysaccharides in the gastrointestinal tract for e.g., detecting the presence of particular exogenous or endogenous nucleic acids, e.g., DNA or RNA, or proteins, in the gastrointestinal tract, for example, to diagnose the presence of an infectious or exogenous agent such as a virus, a fungus, a parasite, a bacteria, intestinal helminths and protozoan parasites, and the like, or a biomarker such as a cancer-causing or cancer-predisposing allele, e.g., mutations of the KRAS2 oncogene in pancreatic cancer. In alternative embodiments, compositions of the invention comprise magnetic particles such as a magnetically-responsive microparticle or nanoparticle; a superparamagnetic bead or polystyrene bead; a superparamagnetic fine particle; a ferrimagnetic particle; or, a magnetic microsphere, nanosphere, microbead or nanobeads. In alternative embodiments, the invention provides methods for detecting, retrieving, capturing or isolating a sample of a nucleic acid, or an anionic, cationic or hydrophobic protein or peptide, a mucin, a phosphoprotein, a proteoglycan or a polysaccharide, in vivo.

In alternative embodiments, the invention provides compositions such as devices, pills, beads, capsules, products of manufacture, particles, microparticles, nanoparticles, gels, liquid gels, liquid gel capsules, capsules, tablets, geltabs, liquids, sprays, emulsions, suspensions, pastes or yogurts, for the detection and isolation of biomarkers, nucleic acids, proteins or peptides, proteoglycans, lipids, fats, sugars or polysaccharides in the gastrointestinal tract for e.g., detecting the presence of particular exogenous or endogenous nucleic acids, e.g., DNA or RNA, or proteins, in the gastrointestinal tract, for example, to diagnose the presence of an infectious or exogenous agent such as a virus, a fungus, a parasite, a bacteria, intestinal helminths and protozoan parasites, and the like, or a biomarker such as a cancer-causing or cancer-predisposing allele, e.g., mutations of the KRAS2 oncogene in pancreatic cancer. In alternative embodiments, compositions of the invention comprise magnetic particles such as a magnetically-responsive microparticle or nanoparticle; a superparamagnetic bead or polystyrene bead; a superparamagnetic fine particle; a ferrimagnetic particle; or, a magnetic microsphere, nanosphere, microbead or nanobeads. In alternative embodiments, the invention provides methods for detecting, retrieving, capturing or isolating a sample of a nucleic acid, or an anionic, cationic or hydrophobic protein or peptide, a mucin, a phosphoprotein, a proteoglycan or a polysaccharide, in vivo.

Disclosed probes comprise metal nanoparticle cores associated with magnetic particles that allow probes associated with targets to be concentrated by an applied magnetic field to increase detection sensitivity and provide sufficient spacing between concentrated probes to avoid signal quenching. The probe may comprise at least one recognition receptor, and may further comprise at least one reporter molecule, such as a fluorescent tag, a Raman reporter, or combinations thereof. Concentrating probe-target composites substantially enhances a sensing signal, such as from 5 to 10 times, compared to detection without concentrating the probes. The method may be used to detect, for example, interleukins at concentrations at least as low as 25 pg/ml in sputum or blood from a subject for early and precise profiling of viral infections, such as SARS-CoV-2 infections.

Disclosed probes comprise metal nanoparticle cores associated with magnetic particles that allow probes associated with targets to be concentrated by an applied magnetic field to increase detection sensitivity and provide sufficient spacing between concentrated probes to avoid signal quenching. The probe may comprise at least one recognition receptor, and may further comprise at least one reporter molecule, such as a fluorescent tag, a Raman reporter, or combinations thereof. Concentrating probe-target composites substantially enhances a sensing signal, such as from 5 to 10 times, compared to detection without concentrating the probes. The method may be used to detect, for example, interleukins at concentrations at least as low as 25 pg/ml in sputum or blood from a subject for early and precise profiling of viral infections, such as SARS-CoV-2 infections.

The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.

The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.

The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.

The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.

Provided herein are methods of proximity ligation and compositions for use in such methods. Also provided herein are embodiments related to single cell nucleic acid conformation assessment or single cell nucleic acid sequence or phase information determination or conformation-reconstructed nucleic acid samples can be fragmented and distributed in aliquots to which aliquot-distinguishing sequence segments are added so that, upon analysis of a paired end library generated from the samples, paired ends are assigned to a partition, or cell, of origin. Thus cell-specific variation in sequence and three-dimensional nucleic acid configuration can be determined.

Provided herein are methods of proximity ligation and compositions for use in such methods. Also provided herein are embodiments related to single cell nucleic acid conformation assessment or single cell nucleic acid sequence or phase information determination or conformation-reconstructed nucleic acid samples can be fragmented and distributed in aliquots to which aliquot-distinguishing sequence segments are added so that, upon analysis of a paired end library generated from the samples, paired ends are assigned to a partition, or cell, of origin. Thus cell-specific variation in sequence and three-dimensional nucleic acid configuration can be determined.