Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
Abstract: Image data analysis, particularly identifying cluster locations for performing base-calling in a digital flow cell image during DNA sequencing, is described. Each nucleic acid template molecule immobilized on a support may include an insert sequence and a sample index sequence. The sample index sequence may include a k-mer sequence. A sequencing system may conduct k cycles of sequencing reactions of the k-mer sequence before conducting one or more cycles of the insert sequence sequencing reactions and generate a first plurality of flow cell images. Pixel intensities may be determined for pixels of the first plurality of flow cell images. A base calling template may be determined and include base calling locations based on the pixel intensities and respective color purities of the pixel intensities. The base calling template may register a second plurality of flow cell images of the support in one or more cycles subsequent to the k cycles.
Type:
Application
Filed:
December 9, 2022
Publication date:
October 12, 2023
Applicant:
Element Biosciences, Inc.
Inventors:
Chunhong ZHOU, Semyon KRUGLYAK, Francisco GARCIA, Minghao GUO, Haosen WANG, Ryan KELLY
Abstract: Aspects of the invention relate to liquid transfer systems including a pipette tip having a body defining an inner volume and having first and second ends, the first end arranged to transfer a volume of liquid into and out of the pipette tip and the second end arranged for attachment to a pipette, and a bladder sealingly attached to the body. In some embodiments, the bladder is disposable in the inner volume. The bladder may be defined by a membranous sac and/or a planar membrane. The bladder may be moveable in response to an applied pressure to transfer liquid. The bladder also may be stretchable to accommodate a volume of fluid. In some embodiments, the pipette tip is used in a cell culture incubator, with a manipulator including a pipette that is in fluid communication with the pipette tip.
Abstract: Disclosed are synthetic nanocarrier compositions, and related methods, comprising therapeutic protein APC presentable antigens and immunosuppressants that provide tolerogenic immune responses specific to therapeutic proteins.
Type:
Application
Filed:
March 2, 2023
Publication date:
October 12, 2023
Applicant:
Selecta Biosciences, Inc.
Inventors:
Christopher Fraser, Takashi Kei Kishimoto, Roberto A. Maldonado
Abstract: Disclosed are synthetic nanocarrier compositions, and related methods, comprising MHC Class II-restricted epitopes and immunosuppressants that provide tolerogenic immune responses, such as a reduction in CD4+ T cell help specific to an antigen.
Type:
Application
Filed:
December 8, 2022
Publication date:
October 12, 2023
Applicant:
Selecta Biosciences, Inc.
Inventors:
Christopher Fraser, Takashi Kei Kishimoto, Roberto A. Maldonado
Abstract: Disclosed are synthetic nanocarrier compositions, and related methods, comprising immunosuppressants and MHC Class II-restricted epitopes of an allergen that provide tolerogenic immune responses specific to the allergen.
Type:
Grant
Filed:
March 4, 2016
Date of Patent:
October 10, 2023
Assignee:
Selecta Biosciences, Inc.
Inventors:
Takashi Kei Kishimoto, Christopher Fraser, Roberto A. Maldonado
Abstract: Provided are bispecific proteins that comprise a binding domain binding cell surface protein and a vascular endothelial growth factor (VEGF) inhibiting domain. Provided also is an antibody-drug conjugate that comprises a therapeutic agent and an antibody or an antigen-binding fragment binding PD-L1 and/or a VEGF inhibiting domain, wherein the therapeutic agent is covalently conjugated to the antibody or the antigen-binding fragment by a linker.
Abstract: Disclosed are synthetic nanocarrier compositions, and related methods, comprising immunosuppressants and MHC Class II-restricted epitopes of an allergen that provide tolerogenic immune responses specific to the allergen.
Type:
Application
Filed:
December 9, 2022
Publication date:
October 5, 2023
Applicant:
Selecta Biosciences, Inc.
Inventors:
Takashi Kei Kishimoto, Christopher Fraser, Roberto A. Maldonado
Abstract: Certain embodiments are directed to finite step emulsification device and/or methods that combine finite step emulsification with gradients of confinement for the formation of a 2D monolayer array of droplets with low size dispersion.
Abstract: The invention provides a method for determining whether a human immunodeficiency virus is resistant to a viral entry inhibitor. The methods are particularly useful for determining resistance to inhibitors that act by a non-competitive mechanism. In certain aspects, the methods comprise determining whether an HIV population is resistant to an HIV entry inhibitor, comprising determining a log-sigmoid inhibition curve comprising data points for entry of the HIV population in the presence of varying concentrations of the HIV entry inhibitor, wherein if the entry of the HIV population cannot be completely inhibited by the HIV entry inhibitor, the HIV population is resistant to the HIV entry inhibitor.
Abstract: Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and/or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA/RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA/RNA modifications in parallel.
Abstract: The disclosure provides methods and systems of analyzing single cells by simultaneously separating cells into monodisperse droplets and tagging each nucleic acid molecule from the cells with barcodes unique to each droplet. The methods and systems combine template particles with a plurality of single cells in a tube, generate in the tube monodispersed droplets encapsulating a single one of the template particles and a single one of the single cells, release nucleic acid molecules from the single cells and provide each nucleic acid molecule with a barcode unique to the respective droplet. The nucleic acid molecules can then be analyzed by any known method, for example by sequencing the nucleic acid molecules.
Type:
Grant
Filed:
August 20, 2021
Date of Patent:
October 3, 2023
Assignee:
Fluent Biosciences Inc.
Inventors:
Kristina Fontanez, Robert Meltzer, Yi Xue, Sepehr Kiani
Abstract: Disclosed herein are new compounds and compositions and their application as pharmaceuticals for the treatment of diseases. Methods of inhibition of KDM1A, methods of increasing gamma globin gene expression, and methods to induce differentiation of cancer cells in a human or animal subject are also provided for the treatment of diseases such as acute myelogenous leukemia.
Type:
Grant
Filed:
September 22, 2021
Date of Patent:
October 3, 2023
Assignee:
Imago Biosciences, Inc.
Inventors:
Hugh Y. Rienhoff, Jr., John M. McCall, Michael Clare, Cassandra Celatka, Amy E. Tapper
Abstract: Described herein are GPR35 modulators and methods of using these compounds in the treatment of diseases, disorders or conditions. Also described herein are pharmaceutical compositions containing such compounds.
Abstract: A method and apparatus for incubating sperm, eggs, and/or embryos for in vitro fertilization placing at least one of sperm, eggs, and embryos in at least one cell culture vessel in an incubator chamber having windows with filters to filter out ultraviolet light, wherein interior surfaces of the chamber comprises material that prevents the growth of fungus, and wherein the chamber includes sensors for regulating the levels of oxygen, carbon dioxide and nitrogen in the chamber, transporting the at least one cell culture vessel from a storage location in the chamber to an imager at an imaging location in the chamber using an elevator; and repeatedly imaging at least one of the sperm, eggs, and the embryos in the imager while maintaining the levels of oxygen, carbon dioxide and nitrogen throughout the chamber.
Abstract: Methods of loading extracellular vesicles with payload molecules via homogenization are disclosed herein.
Type:
Application
Filed:
October 11, 2022
Publication date:
September 28, 2023
Applicant:
Codiak BioSciences, Inc.
Inventors:
Aaron R. NOYES, Michael P. MERCALDI, Kathryn E. GOLDEN, Raymond W. BOURDEAU, Michael F. DOHERTY, Konstantin KONSTANTINOV, Douglas E. WILLIAMS
Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
Abstract: A system for dissociating cells from a cell culture vessel. The system comprises an imaging system configured to image a plurality of cells in a cell culture vessel being dissociated from at least one surface of the cell culture vessel by at least one cell dissociation agent; and at least one controller coupled to the imaging system and configured to: control the imaging system to capture a sequence of images of at least some cells in the plurality of cells during dissociation; and identify when to neutralize the at least one cell dissociation agent using the sequence of images.
Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.
Type:
Grant
Filed:
June 4, 2021
Date of Patent:
September 26, 2023
Assignee:
Molecular Loop Biosciences, Inc.
Inventors:
Gregory Porreca, Mark Umbarger, George Church