Patents by Inventor Robert C. James
Robert C. James has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11958765Abstract: Fluid purification systems employing a monolithic composite photocatalyst to remove volatile organic compounds (VOCs) and/or pathogenic organisms are disclosed. Pairing of systems tuned to abate each of these materials are discussed in different configurations such as series and parallel, as well as combining systems to target both materials simultaneously. System configurations that allow a portion of the fluid stream to be purified are also disclosed as are configurations that allow regeneration of the photocatalyst. These features may be augmented by sensors that allow closed loop control of bypass and regeneration cycles in the systems.Type: GrantFiled: January 19, 2022Date of Patent: April 16, 2024Assignee: Sonata Scientific LLCInventors: Jeffrey F. Roeder, Trevor E. James, Melissa A. Petruska, Peter C. Van Buskirk, Robert T. Henderson, III
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Publication number: 20240011009Abstract: Provided herein are modified dipeptide cleavases for removing amino acid(s) from peptides, polypeptides, and proteins. Also provided are methods of using the modified dipeptide cleavases for treating polypeptides, and kits comprising the modified dipeptide cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: ApplicationFiled: March 19, 2021Publication date: January 11, 2024Applicant: Encodia, Inc.Inventors: Kevin L. GUNDERSON, Robert C. JAMES, Lei SHI, Stephen VERESPY, III, Kevin DESAI
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Patent number: 11788080Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: GrantFiled: June 27, 2022Date of Patent: October 17, 2023Assignee: Encodia, Inc.Inventors: Kevin Desai, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
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Patent number: 11782062Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: GrantFiled: February 8, 2023Date of Patent: October 10, 2023Assignee: Encodia, Inc.Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
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Publication number: 20230295222Abstract: The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.Type: ApplicationFiled: March 10, 2023Publication date: September 21, 2023Applicant: Encodia, Inc.Inventors: Robert C. JAMES, Stephen VERESPY, III, Eric Cunyu ZHOU, Eric OKERBERG, Kelsey Rose SCHRAMMA, Fei HUANG
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Publication number: 20230257727Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: ApplicationFiled: January 18, 2023Publication date: August 17, 2023Applicant: Encodia, Inc.Inventors: Kevin DESAI, Kevin L. GUNDERSON, Robert C. JAMES, Lei SHI, Stephen VERESPY, III
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Publication number: 20230236198Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: February 8, 2023Publication date: July 27, 2023Applicant: Encodia, Inc.Inventors: Mark S. CHEE, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Publication number: 20230220589Abstract: The present disclosure relates to a binder that specifically binds to an N-terminally modified polypeptide through interaction with a modified N-terminal amino acid. Also provided herein is a method and related kits for treating a polypeptide using or comprising the binder and/or modified cleavase. In some embodiments, also provided herein is a method and related kits for transferring information using a plurality of enzymes, including for performing a ligation, extension, and cleavage reaction with nucleic acid molecules associated with the polypeptide for analysis.Type: ApplicationFiled: September 29, 2021Publication date: July 13, 2023Applicant: Encodia, Inc.Inventors: Kevin L. GUNDERSON, Soumya GANGULY, Robert C. JAMES, Kenneth KUHN, Zachary MILES, Lei SHI, Stephen VERESPY, III, Aaron WISE, Zongxiang ZHOU
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Publication number: 20230168254Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: August 11, 2022Publication date: June 1, 2023Applicant: Encodia, Inc.Inventors: Mark S. Chee, John M. BEIERLE, Norihito MURANAKA, Kevin L. GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Patent number: 11639366Abstract: The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.Type: GrantFiled: November 24, 2021Date of Patent: May 2, 2023Assignee: Encodia, Inc.Inventors: Robert C. James, Stephen Verespy, III, Eric Cunyu Zhou, Eric Okerberg, Kelsey Rose Schramma, Fei Huang
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Publication number: 20230021091Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: ApplicationFiled: June 27, 2022Publication date: January 19, 2023Applicant: Encodia, Inc.Inventors: Kevin DESAI, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
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Patent number: 11513126Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: GrantFiled: October 31, 2018Date of Patent: November 29, 2022Assignee: Encodia, Inc.Inventors: Mark S. Chee, John M. Beierle, Norihito Muranaka, Kevin L. Gunderson, Michael Phillip Weiner, Lei Shi, Robert C. James, Luca Monfregola
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Patent number: 11427814Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: GrantFiled: March 25, 2021Date of Patent: August 30, 2022Assignee: ENCODIA, INC.Inventors: Kevin Desai, Kevin L. Gunderson, Robert C. James, Lei Shi, Stephen Verespy, III
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Publication number: 20220227889Abstract: The present invention relates to methods of cleaving the N-terminal amino acid from a polypeptide, which may be in free form or conjugated to a carrier or surface, such as a bead. It provides methods to activate the N-terminal amine of a polypeptide to promote formation of a cyclic adduct of the N-terminal amino acid, resulting in cleavage of the N-terminal amino acid from the polypeptide. The method can be used to sequence and/or analyze a polypeptide. For example, the methods can be combined with methods described herein for sequencing and/or analysis that employ barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels. The invention also provides compounds and kits useful for practicing these methods.Type: ApplicationFiled: April 24, 2020Publication date: July 21, 2022Applicant: Encodia, Inc.Inventors: Kevin L. GUNDERSON, Fei HUANG, Robert C. JAMES, Luca MONFREGOLA, Stephen VERESPY, III, Eric Cunyu ZHOU
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Publication number: 20220144885Abstract: The present invention relates to methods to use cyclohexan-1,2-dione (CHD) groups to attach labels, linkers, and other molecules to a target compound comprising a CHD-reactive group such as a guanidine, amidine, urea, thiourea and the like. Methods of the invention include milder conditions than those previously known for promoting reaction of CHD with CHD-reactive groups, which makes the methods suitable for use with base-sensitive compounds and complex biomolecules. Methods of the invention are especially useful for attaching linking and labeling groups to a peptide that comprises at least one arginine residue, and can also be used to link such peptides to other target molecules such as nucleic acids. The invention also provides CHD-containing conjugation reagents and compositions comprising CHD-containing intermediates, and precursors useful for making CHD-containing compounds that can be used in the methods of the invention.Type: ApplicationFiled: November 24, 2021Publication date: May 12, 2022Applicant: Encodia, Inc.Inventors: Robert C. James, Stephen Verespy, III, Eric Cunyu Zhou, Eric Okerberg, Kelsey Rose Schramma, Fei HUANG
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Publication number: 20210214701Abstract: Provided herein are modified cleavases for removing amino acids from peptides, polypeptides, and proteins. Also provided are methods of using the modified cleavases for treating polypeptides, and kits comprising the modified cleavase. In some embodiments, the methods and the kits also include other components for macromolecule sequencing and/or analysis.Type: ApplicationFiled: March 25, 2021Publication date: July 15, 2021Applicant: Encodia, Inc.Inventors: Kevin DESAI, Kevin L. GUNDERSON, Robert C. JAMES, Lei SHI, Stephen VERESPY, III
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Publication number: 20200348307Abstract: The present disclosure relates to methods and kits for analysis of polypeptides. In some embodiments, the present methods and kits employ barcoding and nucleic acid encoding of molecular recognition events, and/or detectable labels.Type: ApplicationFiled: October 31, 2018Publication date: November 5, 2020Applicant: Encodia, Inc.Inventors: John M. BEIERLE, Robert C. JAMES, Luca MONFREGOLA, Kevin GUNDERSON, Michael LEBL, Lei SHI
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Publication number: 20200348308Abstract: Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information.Type: ApplicationFiled: October 31, 2018Publication date: November 5, 2020Applicant: Encodia, Inc.Inventors: Mark S. CHEE, John M BEIERLE, Norihito MURANAKA, Kevin GUNDERSON, Michael Phillip WEINER, Lei SHI, Robert C. JAMES, Luca MONFREGOLA
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Patent number: 6051263Abstract: A package is capable of enclosing a food product in two different gaseous atmospheres at different times. Initially, the food product may be packaged in a low oxygen atmosphere in order to prolong the shelf life of the product. When it is time to sell the product for example, it may be desirable to supply oxygen to the food product. In the case of red meats, the oxygenation process causes the meat to turn a bright red color. The package includes a tray covered by a film with a plurality of apertures formed in the tray. The package may be maintained at a pressure below atmospheric pressure. The apertures are covered by a bacterial barrier layer covered by resealable tape which can be removed to allow air ingress and then resealed to protect the integrity of the tray contents.Type: GrantFiled: March 31, 1999Date of Patent: April 18, 2000Assignee: World Class Packaging Systems, Inc.Inventors: Michael P. Gorlich, Robert F. McPherson, Jr., Robert C. James
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Patent number: 5866184Abstract: A package is capable of enclosing a food product in two different gaseous atmospheres at different times. Initially the food product may be packaged in a low oxygen atmosphere in order to prolong the shelf life of the product. When it is time to sell the product for example, it may be desirable to supply oxygen to the food product. In the case of red meats, the oxygenation process causes the meat to turn a bright red color. The package includes a tray covered by a film with a plurality of apertures formed in the tray. The apertures are covered by a resealable gas impermiable tape which can be removed to allow air ingress and then resealed to protect the integrity of the tray contents.Type: GrantFiled: March 12, 1997Date of Patent: February 2, 1999Assignee: World Class Packaging Systems, Inc.Inventors: Michael P. Gorlich, Robert F. McPherson, Jr., Robert C. James