Abstract: The present disclosure relates in some aspects to recombinant Bacillus phage AP50 polymerases, modified AP50 polymerases, and compositions thereof. Also provided are methods of using the recombinant and/or modified AP50 polymerases for nucleic acid amplification (e.g., rolling circle amplification). In some aspects, the compositions and methods disclosed herein provide more robust amplification (e.g., RCA) reactions for improved in vitro and in situ analysis.

Abstract: The disclosure provides recombinant reverse transcriptases comprising one or more DNA binding domains conjugated to an engineered reversed transcriptase that have been modified to exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both. The disclosure further provides compositions and kits comprising the recombinant reverse transcriptase enzymes and methods of producing, amplifying or sequencing nucleic acid molecules using these fusion reverse transcriptase enzymes.

Abstract: The present disclosure relates in some aspects to recombinant Bacillus phage AP50 polymerases, modified AP50 polymerases, and compositions thereof. Also provided are methods of using the recombinant and/or modified AP50 polymerases for nucleic acid amplification (e.g., rolling circle amplification). In some aspects, the compositions and methods disclosed herein provide more robust amplification (e.g., RCA) reactions for improved in vitro and in situ analysis.

Abstract: The present disclosure provides methods of processing or analyzing a sample. A method for processing a sample can comprise barcoding a nucleic acid molecule, circularizing the resultant product, and performing an extension reaction, without the need of a template switching molecule. One or more processes of the methods described herein can be performed within a partition, such as a droplet or well.

Abstract: The present disclosure relates in some aspects to compositions and methods of using Phi29 polymerase fusion proteins. In some aspects, the compositions and methods provided herein address certain limitations associated with the Phi29 polymerase. In some aspects, the composition and methods disclosed herein provide more robust nucleic acid amplification for improved in vitro and in situ analysis.

Abstract: The application provides compositions including engineered fusion reverse transcriptases with at least one altered reverse-transcriptase related activity. The engineered fusion reverse transcriptases or reverse transcription enzymes unexpectedly exhibit one or more altered reverse transcriptase related activities such as but not limited to altered template switching efficiency, altered transcription efficiency or both.

Abstract: A recombinant ligase composition including a recombinantly-produced ligase isolated from Acanthocystis turfacea chlorella virus 1 (ATCV-1) fused to at least one polynucleotide-binding polypeptide is provided. Compositions containing the recombinant ligase composition, vectors encoding the recombinant ligase composition, and methods of making and using the recombinant ligase composition are also provided.

Abstract: The present disclosure relates in some aspects to recombinant Bacillus phage AP50 polymerases, modified AP50 polymerases, and compositions thereof. Also provided are methods of using the recombinant and/or modified AP50 polymerases for nucleic acid amplification (e.g., rolling circle amplification). In some aspects, the compositions and methods disclosed herein provide more robust amplification (e.g., RCA) reactions for improved in vitro and in situ analysis.

Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing a target nucleic acid in a biological sample. In some aspects, the methods disclosed herein promote hybridization of polynucleotides to target nucleic acids and/or splints for enhanced ligation efficiency and/or enhanced hybridization efficiency in situ in a biological sample. In some aspects, the presence, amount, and/or identity of a target nucleic acid is analyzed in situ. Also provided are compositions and kits for use in accordance with the methods.

Abstract: The present disclosure relates generally to engineered nucleic acid processing enzymes and derivatives thereof, compositions and kits comprising the same; and methods of generating and using the same.

Abstract: The present disclosure relates in some aspects to methods for analyzing a target RNA in a biological sample, such as detection of a sequence of interest in an RNA. In some aspects, provided herein are methods of using an RNase such as RNase H to provide in situ RNA detection methods having high sensitivity, efficiency, and/or specificity.

Abstract: A testing and verification system for an equivalent physical configuration of an in-flight entertainment and communications system with one or more hardware components includes a virtual machine manager. One or more virtual machines each including a hardware abstraction layer is instantiated by the virtual machine manager according to simulated hardware component definitions corresponding to the equivalent physical configuration of the hardware components. The virtual machines are in communication with each other over virtual network connections. A test interface to the one or more virtual machines generate test inputs to target software applications installed on the virtual machines. A display interface is connected to the virtual machines, with results from the execution of the target software applications responsive to the test inputs are output thereto.

Abstract: The present disclosure relates in some aspects to methods for analyzing a target nucleic acid in a biological sample. In some aspects, provided herein are methods and compositions for improving the specificity of ligation in situ in biological samples, as well as in single cell analysis and spatial applications of RNA templated ligation reactions.

Abstract: Disclosed herein are compositions and methods for determining a presence or abundance of an analyte in a biological sample. The methods disclosed herein include: (a) providing a biological sample on a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises a capture domain; (b) releasing the analyte from the biological sample; (c) affixing a stretching moiety to the analyte; (d) hybridizing the analyte to the capture domain of the capture probe; (e) applying a stretching force to the stretching moiety, thereby elongating the analyte hybridized to the capture domain; and (f) generating an extended capture probe using the analyte as a template.

Abstract: A testing and verification system for an equivalent physical configuration of an in-flight entertainment and communications system with one or more hardware components includes a virtual machine manager. One or more virtual machines each including a hardware abstraction layer is instantiated by the virtual machine manager according to simulated hardware component definitions corresponding to the equivalent physical configuration of the hardware components. The virtual machines are in communication with each other over virtual network connections. A test interface to the one or more virtual machines generate test inputs to target software applications installed on the virtual machines. A display interface is connected to the virtual machines, with results from the execution of the target software applications responsive to the test inputs are output thereto.

Abstract: Methods and systems are provided for a transportation vehicle. One method includes parsing by a processor on an aircraft, metadata of media content received by the aircraft, while the aircraft is in flight, the media content includes a media file and the metadata. The metadata indicates a start date when the media content can be presented to a device on the aircraft and an end date when media content is to become inaccessible. The method further includes dynamically generating a unique identifier for the media content by the processor, the unique identifier based on an aircraft identifier; updating the metadata by the processor by associating the unique identifier with the media content; storing the media content with the updated metadata and an indicator when the media content is to be deleted; and using the unique identifier by the processor for tracking usage of the media content on the aircraft.

Abstract: Methods and systems are provided for a transportation vehicle. One method includes parsing by a processor on an aircraft, metadata of media content received by the aircraft, while the aircraft is in flight, the media content includes a media file and the metadata. The metadata indicates a start date when the media content can be presented to a device on the aircraft and an end date when media content is to become inaccessible. The method further includes dynamically generating a unique identifier for the media content by the processor, the unique identifier based on an aircraft identifier; updating the metadata by the processor by associating the unique identifier with the media content; storing the media content with the updated metadata and an indicator when the media content is to be deleted; and using the unique identifier by the processor for tracking usage of the media content on the aircraft.

Abstract: A testing and verification system for an equivalent physical configuration of an in-flight entertainment and communications system with one or more hardware components includes a virtual machine manager. One or more virtual machines each including a hardware abstraction layer is instantiated by the virtual machine manager according to simulated hardware component definitions corresponding to the equivalent physical configuration of the hardware components. The virtual machines are in communication with each other over virtual network connections. A test interface to the one or more virtual machines generate test inputs to target software applications installed on the virtual machines. A display interface is connected to the virtual machines, with results from the execution of the target software applications responsive to the test inputs are output thereto.

Abstract: A system for providing entertainment on a vehicle for passengers in which the system includes a network and a content data source onboard the vehicle. The content data source stores media files and is connected in communication with the network. Seat displays disposed in the vehicle are connected in communication with the network and configured to present media selections to passengers corresponding to media files available from the content data source. Each seat display is configured to receive an input from a passenger for playing a selection and includes a data processor executing program logic. The program logic performs tasks including accepting authentication information from a passenger, verifying the authentication information received by comparison with information available from the network, and if the authentication information is verified, presenting a media selection corresponding to a media file associated with the authentication information.

Abstract: Methods and systems for boarding a transportation vehicle are provided. One method includes configuring a passenger assist device (PAD) for use at a location for arriving and departing transportation vehicles by storing location data with maps and amenities information for the location; initializing a location tracking module to prevent unauthorized removal of the PAD from the location by a passenger; selecting a language by the passenger for communication with the PAD, when the passenger does not want to use a default language; retrieving connection and passenger transportation vehicle boarding location from where the passenger boards the vehicle; and presenting directions to the boarding location and information regarding amenities along a route to the boarding location.