Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: Methods that stabilize allosteric cell attachment proteins in either an active or inactive conformation enable toggling a protein between conformational states by restricting the repacking of side chains that occurs during the conformational transition. This restriction traps the protein in the desired high affinity or low affinity state. An allosteric cell attachment protein stabilized in an ‘active’ (high-affinity) or ‘inactive’ (low-affinity) conformation is stabilized by the substitution of a hydrophobic amino acid residue with a charged amino acid, in some embodiments, the attachment protein is bacterial. In some embodiments, the attachment protein is viral, in some embodiments, the protein is a bacterial adhesin.

Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

Abstract: In some embodiments, techniques are provided for conducting similarity-based searches using DNA. In some embodiments, sets of features that represent stored data sets are encoded in DNA sequences such that a hybridization yield between a molecule having a given stored DNA sequence and a molecule having a reverse complement of a DNA sequence that encodes a set of features that represent a query data set reflects an amount of similarity between the set of features that represent the query data set and the set of features encoded in the given stored DNA sequence. In some embodiments, machine learning techniques are used to determine the DNA sequence encoding. In some embodiments, machine learning techniques are used to predict hybridization yields between DNA molecules.

Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.

Abstract: Example spatial transcriptomics techniques use “continuous” polony arrays on a customized gel surface for spatial barcoding. By screening polyacrylamide (PAA) gel fabrication conditions, polonies formed on a crosslinked PAA gel were shown to exhibit a continuous, homogenous DNA distribution, which is highly suited for tissue barcoding applications. Compared with widely used polonies formed in flow cells that utilize linear PAA gels, continuous polonies showed efficient DNA amplification and restriction digestion to generate capture oligo arrays, which have a significantly better spatial RNA capturing performance. In addition, the crosslinked PAA gel showed sufficient constraints on lateral RNA diffusion and provides better mechanical strength and stability for tissue mapping assays than a semifluidic linear PAA gel used by previous methods.

Abstract: Thin layer chromatography (TEC) devices for the analysis of pico-scale samples, methods for using the devices, and methods for fabricating the devices.

Abstract: Provided herein are methods for preparing a sequencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the methods include linear amplification of the nucleic acids. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the nucleic acids include three index sequences. Also provided herein are compositions, such as compositions that include the nucleic acids having three index sequences.

Abstract: Provided herein, among other aspects, are methods and apparatuses for ranking aliquots from a suspension containing bioparticles. In certain embodiments, the bioparticles may be cells, organelles, proteins, DNAs, debris of biological origin, microbeads coated with biological compounds, or viral particles. As such, the methods and apparatuses provided herein may be used to quantify rare cells such as circulating cancer cells, fetal cells and other rare cells present in bodily fluids for disease diagnosis, prognosis, or treatment.

Abstract: A method of measuring blood oxygenation including acquiring one or more images of a portion of a body with an RGB camera, converting RGB colors in the one or more images into a multispectral data imaging cube, wherein the multispectral date imaging cube comprises a red channel, a blue channel, and a green channel, decoupling an oxygenated blood information and a deoxygenated blood information from the multispectral data imaging cube based on a first reflectance of the green channel and a second reflectance of the red channel, and determining a blood measurement based on the oxygenated blood information and the deoxygenated blood information.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: Antibodies that bind the tumor (T) antigen of the Merkel cell polyomavirus are disclosed. The antibodies can be use used in cell-based immunotherapies, antibody-based therapies, diagnostics, and detection assays, among other uses.

Abstract: The present disclosure provides for the treatment of cardiac diseases and disorders using in vitro-differentiated cardiomyocytes. Such methods can take advantage of both autologous and allogeneic pluripotent stem cells.

Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.

Abstract: N-oxide and monomers, N-oxide polymers and copolymers, methods for making the N-oxide monomers, polymers, and copolymers, compositions and materials that include N-oxide polymers and copolymers, and methods for using the N-oxide monomers, N-oxide polymers, and N-oxide copolymers.

Abstract: The disclosure provides methods and related kits, reagents, and systems for selectively deaminating unmethylated cytosine residues in nucleic acid molecules. In some embodiments, the methods and related kits, reagents, and systems are applied for methods of detecting and/or mapping methylated cytosine residues in nucleic acids. The nucleic can be RNA or DNA. Some embodiments include contacting the polynucleic acid with a bacterial cytosine deaminase, for example DddA or SsdA, or functional fragments or derivatives thereof. Representative DddA and SsdA have sequences set forth in SEQ ID NOS:1 and 2, respectively. The bacterial cytosine deaminases of the disclosure are sensitive to methylation and, thus, deaminate only unmethylated cytosines to provide a cytosine to uracil conversion. The conversion can be detected as a C•G-to-T•A transitions in subsequent sequencing analysis.

Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.

Abstract: Examples of biomimetic codecs and biomimetic coding techniques are described herein. Morphologically-adaptive coding networks can be developed in accordance with energy dissipation driven “heat” generated by application of training data. The morphologically-adaptive coding networks may be representative of common features expected in an input signal or data stream. Decoding may proceed using the morphologically-adaptive coding network. Morphologically-adaptive coding networks may be used as a cortex that can be shared for boosting multimedia data compression rates and/or increasing the encode-decode fidelity of information content while the features remain queryable in encoded form. Examples of the biomimetic codecs and biomimetic coding techniques provide a broad-based technology platform that can be used in context-IDed multimedia storage, pattern recognition, and high-performance computing/big data management, the hallmarks of web- and cloud-based systems.

Abstract: Nucleotide sequences including a micro-dystrophin gene are provided. The micro-dystrophin genes may be operatively linked to a regulatory cassette. Methods of treating a subject having, or at risk of developing, muscular dystrophy, sarcopenia, heart disease, or cachexia are also provided. The methods may include administering a pharmaceutical composition including the micro-dystrophin gene and a delivery vehicle to a subject. Further, the methods may include administering the pharmaceutical composition a subject having Duchenne muscular dystrophy or Becker muscular dystrophy.

Abstract: A capacitive sensor system configured to measure capacitance, including a sample volume, a sample capacitive sensor configured to measure the capacitance of the sample volume without physical contact between the sample capacitive sensor and the sample volume, a control capacitive sensor, a differential sensing subsystem configured to measure a control sensor volume using the control capacitive sensor, and electrical circuitry connected to both the control capacitive sensor and the sample capacitive sensor.