Abstract: Disclosed herein are methods and compositions comprising a polymerase and a phosphorylated nucleoside, wherein the polymerase and the nucleoside are covalently linked by a cleavable linker at the terminal phosphate group. Further disclosed herein are enzymatic polynucleotide synthesis using polymerase and nucleotide conjugation strategies.

Abstract: Provided herein are methods and systems for sequencing proteins. One or more methods disclosed herein may use linkers comprising an amino acid-reactive group and an additional reactive moiety that may be used to couple a polymerizable molecule. The linker may couple to a polymerizable molecule and an amino acid of a peptide and a capture moiety via the polymerizable molecule, followed by cleavage of the amino acid from the peptide. Further processing and analysis may be conducted using, for example, nanopores or nanogaps.

Abstract: Provided herein are methods and systems for sequencing proteins. One or more methods disclosed herein may use linkers comprising an amino acid-reactive group and an additional reactive moiety that may be used to couple a polymerizable molecule. The linker may couple to a polymerizable molecule and an amino acid of a peptide and a capture moiety via the polymerizable molecule, followed by cleavage of the amino acid from the peptide. Further processing and analysis may be conducted using, for example, nanopores or nanogaps.

Abstract: An optical system is provided that includes a conduit fitting, a first connector, a first conduit, a first ferrule and a first nut. The conduit fitting includes a receptacle. The first connector is disposed within the receptacle. The first connector includes a first bore, a first counterbore and a first port radially outboard of the first bore. The first conduit includes a first optics line and a first fluid passage. The first conduit projects longitudinally into the first counterbore and is attached to the first connector. The first optics line projects longitudinally into the first bore. The first fluid passage is fluidly coupled with the first port. The first ferrule circumscribes the first connector. The first nut is threaded onto the conduit fitting and is configured to wedge the first ferrule radially between the first connector and the conduit fitting.

Abstract: A method of configuring a filter to perform pattern matching against input data is provided. The method includes receiving one or more rules, each rule including one or more field specifiers, each field specifier including a value specifier that specifies a value to be matched and a location specifier that specifies a location in the input data. For each rule of the one or more rules an empty buffer is initialized. For each field specifier the value specified by the field specifier is appended to the buffer, and the buffer contents are inserted into contents of a probabilistic data structure representing all of the field specifiers of the rule. The probabilistic data structure is configured to receive a query that includes query buffer contents determined from the input data and respond with a match status of probably present based on a predetermined probability, or definitely not present.

Abstract: Disclosed herein are methods and compositions comprising a polymerase and a phosphorylated nucleoside, wherein the polymerase and the nucleoside are covalently linked by a cleavable linker at the terminal phosphate group. Further disclosed herein are enzymatic polynucleotide synthesis using polymerase and nucleotide conjugation strategies.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: Provided herein are composition and process for using a device for the reduction of the oxidized state of phosphorylated or non-phosphorylated nicotinamide adenine dinucleotide to the reduced state, using a catalyst to enable the reduction of the oxidized form of the phosphorylated or non-phosphorylated nicotinamide adenine dinucleotide by hydrogen, and methods for providing the hydrogen.

Abstract: A method of configuring a filter to perform pattern matching against input data is provided. The method includes receiving one or more rules, each rule including one or more field specifiers, each field specifier including a value specifier that specifies a value to be matched and a location specifier that specifies a location in the input data. For each rule of the one or more rules an empty buffer is initialized. For each field specifier the value specified by the field specifier is appended to the buffer, and the buffer contents are inserted into contents of a probabilistic data structure representing all of the field specifiers of the rule. The probabilistic data structure is configured to receive a query that includes query buffer contents determined from the input data and respond with a match status of probably present based on a predetermined probability, or definitely not present.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction. In some aspects, the disclosure provides compositions comprising luminescently labeled nucleotides.

Abstract: The present disclosure relates generally to the use of a plastic and/or pliable, sterile container, such as a bag, bottle, or pouch as a sterile enclosure for the culturing of plant cells in a liquid medium.

Abstract: The present disclosure provides in vitro methods for producing cotton fiber, including methods using cotton varietals the were discovered to be particularly amendable for use in the presently disclosed in vitro methods of cotton fiber production.

Abstract: Provided herein are compositions, devices, systems and methods for single molecule sensing. Further provided are devices for nucleic acid sequencing. The compositions, devices, systems and methods described herein provide improved retrieval of biomolecule-based information.

Abstract: Provided herein are compositions, devices, systems and methods for DNA oligomer synthesis. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.). The compositions, devices, systems and methods described herein provide improved synthesis, storage, density, and retrieval of biomolecule-based information.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleotide connected to a nucleic acid comprising a FRET label comprising at least three luminescent molecules. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

Abstract: A logical expression engine and computer-implemented method for optimizing evaluation of a logical expression is provided. The method includes receiving an original logical expression to be applied by a computer program for processing input information, the original logical expression having at least one operator and a subexpression disposed on each side of a related operator of the at least one related operator. The method further includes receiving statistics accumulated about how the computer program applies the subexpressions of the original logical expression for processing the input information received by the computer program, using the accumulated statistics to optimize the order in which the subexpressions would be applied by the computer program, and outputting for application by the computer program an optimized logical expression having the subexpressions ordered in accordance with the optimized order.

Abstract: Disclosed herein are methods and compositions comprising a polymerase and a phosphorylated nucleoside, wherein the polymerase and the nucleoside are covalently linked by a cleavable linker at the terminal phosphate group. Further disclosed herein are enzymatic polynucleotide synthesis using polymerase and nucleotide conjugation strategies.

Abstract: A method of using an electrochemical cell, specifically a membrane bioreactor, to provide electrons to an electron transport chain capable of generating a proton gradient for performing ATP regeneration from ADP. Such an electron transport chain may be part of, or contained within, a synthetic membrane, or may be prepared by the suitable disruption of living cells. Electrons provided by the electrochemical cell are passed to the electron transport system via a suitable electron carrier, such as NADH2, FMNH2, FADH2, reduced ubiquinone(s), thiols, or other electron carriers or biological reducing equivalents that are compatible with the components of the electron transport chain performing ATP regeneration.