Patents by Inventor James J. Collins

James J. Collins 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).

  • Publication number: 20240123132
    Abstract: A drain cassette for a dialysis unit has a fluid channel between venous and arterial connection ports, and a valve may controllably open and close fluid communication between a drain outlet port and the venous connection port or the arterial connection port. A blood circuit assembly and drain cassette may be removable from the dialysis unit, e.g., by hand and without the use of tools. A blood circuit assembly may include a single, unitary member that defines portions of a pair of blood pumps, control valves, channels to accurately position flexible tubing for an occluder, an air trap support, and/or other portions of the assembly. A blood circuit assembly engagement device may assist with retaining a blood circuit assembly on the dialysis unit, and/or with removal of the assembly. An actuator may operate a retainer element and an ejector element that interact with the assembly.
    Type: Application
    Filed: December 22, 2023
    Publication date: April 18, 2024
    Applicant: DEKA Products Limited Partnership
    Inventors: Kevin L. Grant, Michael J. Wilt, Brian D. Tracey, Brett A. Rudolf, David E. Collins, Lisa A. Gustin, James D. Dale, Jesse T. Bodwell
  • Publication number: 20240067957
    Abstract: Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. The present disclosure relates to engineered programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert trigger hybridization into a translational output. This system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. The circuits and systems disclosed herein leverage an ability to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.
    Type: Application
    Filed: June 22, 2023
    Publication date: February 29, 2024
    Applicants: Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: James J. Collins, Raphael Gayet, Katherine IIia, Shiva Razavi, Nathaniel Tippens, Kehan Zhang, Jack Chen, Jonathan Chen, Makoto Lalwani
  • Publication number: 20240024383
    Abstract: Provided herein are compositions and methods comprising engineered microorganisms and their use for locally degrading an antibiotic in the gastrointestinal tract to prevent or limit death of beneficial flora.
    Type: Application
    Filed: December 1, 2021
    Publication date: January 25, 2024
    Applicants: PRESIDENT AND FELLOWS OF HARVARD COLLEGE, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Andres Fernando CUBILLOS, James J COLLINS
  • Patent number: 11788156
    Abstract: The invention provides novel and versatile classes of riboregulators, including inter alia activating and repressing riboregulators, switches, and trigger and sink RNA, and methods of their use for detecting RNAs in a sample such as a well and in modulating protein synthesis and expression.
    Type: Grant
    Filed: September 16, 2021
    Date of Patent: October 17, 2023
    Assignees: President and Fellows of Harvard College, Trustees of Boston University
    Inventors: Alexander A. Green, Peng Yin, James J. Collins, Jongmin Kim
  • Patent number: 11781149
    Abstract: Embodiments disclosed herein provide artificial expression systems comprising multivalent transcription factor complexes for cooperative transcription factor assembly and modulating gene expression. More specifically, engineered synthetic transcription factors are recruited and structurally organized on synthetic gene circuits using molecular clamps, where the strength of intra-complex interactions can be modulated for fine tuning of gene expression as desired.
    Type: Grant
    Filed: June 28, 2019
    Date of Patent: October 10, 2023
    Assignee: Trustees of Boston University
    Inventors: Ahmad S. Khalil, Caleb J. Bashor, Nikit Patel, James J. Collins
  • Publication number: 20230313215
    Abstract: Embodiments disclosed herein provide artificial expression systems comprising multivalent transcription factor complexes for cooperative transcription factor assembly and modulating gene expression. More specifically, engineered synthetic transcription factors are recruited and structurally organized on synthetic gene circuits using molecular clamps, where the strength of intra-complex interactions can be modulated for fine tuning of gene expression as desired.
    Type: Application
    Filed: May 31, 2023
    Publication date: October 5, 2023
    Applicant: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: Ahmad S. Khalil, Caleb J. Bashor, Nikit Patel, James J. Collins
  • Publication number: 20230277489
    Abstract: Provided herein are compositions and methods to improve treatment of chronic infections, and reduce, delay, or inhibit formation of biofilms, using specific combinations of aminoglycoside antibiotics and treatment with one or more proton motive force (PMF) stimulating compounds. These novel methods are easily adapted to clinical settings as toxicity and efficacy of the antibiotics and metabolites used have already been studied in vivo, and as dosing for both the antibiotics and metabolites are known.
    Type: Application
    Filed: May 25, 2022
    Publication date: September 7, 2023
    Applicants: TRUSTEES OF BOSTON UNIVERSITY, THE GENERAL HOSPITAL CORPORATION
    Inventors: James J. Collins, Sylvain Meylan, Samuel Moskowitz
  • Publication number: 20230212592
    Abstract: The present disclosure provides genetic constructs comprising a recombinant internal ribosome entry site (IRES), which may be used as riboswitches to modulate translation of an operably-mRNA sequence encoding a protein of interest. In other aspects, the disclosure provides recombinant cells, methods, kits and systems that utilize the same, e.g., to provide a platform for modulating the expression of essentially any protein of interest in a eukaryotic cell.
    Type: Application
    Filed: June 11, 2021
    Publication date: July 6, 2023
    Applicant: PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: James J. COLLINS, Evan M. ZHAO, Xiao TAN, Fei RAN, Angelo S. MAO, Helena DE PUIG GUIXE, Emma J. CHORY
  • Publication number: 20230022775
    Abstract: This disclosure provides riboregulators specific for particular viruses or for particular human transcription factors. The viral-specific riboregulators may be used to detect the presence of the particular virus, and this may enable diagnosis of an infection. The transcription factor specific riboregulators may be used to detect the presence and/or measure the level of the particular transcription factor, and this may enable diagnosis or prognosis of a particular condition such as cancer.
    Type: Application
    Filed: December 11, 2020
    Publication date: January 26, 2023
    Applicants: President and Fellows of Harvard College, Massachusetts Institute of Technology
    Inventors: Luis Ruben Soenksen Martinez, Nicolaas Angenent-Mari, Alexander S. Garruss, James J. Collins, George M. Church, Katherine Collins, Diogo M. Camacho
  • Publication number: 20220411855
    Abstract: Methods for detecting the presence of a pathogen infection are described. In particular, this document provides a method of detecting target nucleic acids, such as pathogen-specific RNA, in a biological sample obtained from a subject, where the method comprises using one or more toehold switch sensors and an isothermal amplification step to detect the target nucleic acid. Methods specific for detecting and identify the presence of a virus such as Zika virus are also provided.
    Type: Application
    Filed: June 24, 2022
    Publication date: December 29, 2022
    Inventors: Alexander Green, Dana Braff, Melissa Takahashi, Keith Pardee, James J. Collins, Guillaume Lambert, Thomas Ferrante
  • Publication number: 20220412961
    Abstract: Embodiments of various aspects described herein are directed to assays and devices for detecting a target molecule in a sample. In particular, there is described a lateral assay comprising a plurality of serially oriented capture zones, where each capture zone independently comprises an immobilized competitive molecule on a lateral flow matrix. The immobilized competitive molecule and the analyte competitively bind with a capture agent capable of binding the analyte.
    Type: Application
    Filed: November 13, 2020
    Publication date: December 29, 2022
    Applicants: PRESIDENT AND FELLOWS OF HARVARD COLLEGE, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Pawan JOLLY, Helena DE PUIG GUIXE, Olivier Yves Frederic HENRY, Donald E. INGBER, James J. COLLINS, Nur MUSTAFAOGLU, Nooralhuda ARKAN
  • Publication number: 20220403451
    Abstract: This disclosure is generally directed to electrochemical readout of rapid diagnostics related to use of CRISPR effector systems. In one aspect, the disclosure provides a nucleic acid detection system. Generally, the system comprises: (1) a detection CRISPR system comprising an effector protein and one or more guide nucleic acid (gNA) strands designed to bind to corresponding target nucleic acid molecules; (2) an effector strand and (3) an electrode.
    Type: Application
    Filed: October 30, 2020
    Publication date: December 22, 2022
    Applicants: PRESIDENT AND FELLOWS OF HARVARD COLLEGE, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Helena DE PUIG GUIXE, Pawan JOLLY, James J. COLLINS, Donald E. INGBER
  • Patent number: 11473104
    Abstract: Provided herein, in some embodiments, are engineered phagemids that comprise at least one synthetic genetic circuit, wherein the at least one synthetic genetic circuit comprises gene sequences encoding at least one non-lytic antimicrobial peptides (AMPs) and/or antibacterial toxin proteins, a stable origin of replication, and a bacteriophage-packaging signal, wherein the engineered phagemid does not comprise some or all gene sequences encoding bacteriophage proteins required for assembly of a bacteriophage particle.
    Type: Grant
    Filed: December 4, 2015
    Date of Patent: October 18, 2022
    Assignees: Massachusetts Institute of Technology, Trustees of Boston University, President and Fellows of Harvard College
    Inventors: Russell-John Krom, James J. Collins, Prerna Saluja Bhargava, Michael Andrew Lobritz
  • Patent number: 11459573
    Abstract: Provided herein are systems, methods and compositions for rendering cells or the expression of an effector protein sensitive to a predetermined condition. In one aspect, cells can be rendered dependent upon the presence of an environmental agent, e.g., an exogenous agent, without which the cell will default to expression of a death protein and be killed. In another aspect, cells can be rendered sensitive to the presence of a set of predetermined conditions such that cells will only grow when two or more necessary exogenous agents are supplied, and without either of which, the cells are killed. In this aspect, hybrid transcription factors provide a vast array of possible predetermined conditions.
    Type: Grant
    Filed: September 30, 2016
    Date of Patent: October 4, 2022
    Assignee: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: Tsz Yan Clement Chan, James J. Collins, Jeong Wook Lee, Douglas Ewen Cameron
  • Publication number: 20220296594
    Abstract: The present disclosure provides compositions (e.g., pyrimidines) and methods capable of potentiating the effects of antimicrobial agents and/or antiviral agents against bacterial infections and/or viral infections, respectively. Methods of sensitizing bacteria to antimicrobial agents and/or antiviral agents, as well as pharmaceutical compositions and therapeutic/prophylactic methods directed at microbial infections and/or viral infections are also provided.
    Type: Application
    Filed: May 7, 2020
    Publication date: September 22, 2022
    Applicants: MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION
    Inventors: Jason H. Yang, James J. Collins, Miguel A. Alcantar, Roby Bhattacharyya
  • Publication number: 20220282341
    Abstract: Described herein are nucleic acid detection systems, devices, and kits having a CRISPR component comprising an effector protein and a guide RNA, and/or a polynucleotide encoding a guide RNA, that binds or hybridizes to a corresponding target molecule. Also described herein are methods that utilize these nucleic acid systems, devices, and kits.
    Type: Application
    Filed: August 5, 2020
    Publication date: September 8, 2022
    Applicants: Massachusetts Institute of Technology, The Brigham and Women's Hospital, Inc.
    Inventors: Leonardo V. Riella, James J. Collins, Michael M. Kaminski
  • Patent number: 11382883
    Abstract: Provided herein are compositions and methods to improve treatment of chronic infections, and reduce, delay, or inhibit formation of biofilms, using specific combinations of aminoglycoside antibiotics and treatment with one or more proton motive force (PMF) stimulating compounds. These novel methods are easily adapted to clinical settings as toxicity and efficacy of the antibiotics and metabolites used have already been studied in vivo, and as dosing for both the antibiotics and metabolites are known.
    Type: Grant
    Filed: August 29, 2014
    Date of Patent: July 12, 2022
    Assignees: TRUSTEES OF BOSTON UNIVERSITY, THE GENERAL HOSPITAL CORPORATION
    Inventors: James J. Collins, Sylvain Meylan, Samuel Moskowitz
  • Patent number: 11371081
    Abstract: Methods for detecting the presence of a pathogen infection are described. In particular, this document provides a method of detecting target nucleic acids, such as pathogen-specific RNA, in a biological sample obtained from a subject, where the method comprises using one or more toehold switch sensors and an isothermal amplification step to detect the target nucleic acid. Methods specific for detecting and identify the presence of a virus such as Zika virus are also provided.
    Type: Grant
    Filed: May 25, 2017
    Date of Patent: June 28, 2022
    Assignees: ARIZONA BOARD OF REGENTS ON BEHALF OF ARIZONA STATE UNIVERSITY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Alexander Green, Dana Braff, Melissa K. Takahashi, Keith Pardee, James J. Collins, Guillaume Lambert, Thomas Ferrante
  • Publication number: 20220195494
    Abstract: The disclosed subject matter relates to compositions, systems, kits, and methods that typically comprise and/or utilize a lyophilized composition comprising components for performing in vitro transcription prepared by lyophilizing an aqueous composition that includes: (i) the one or more components for performing in vitro transcription; and (ii) a non-reducing polysaccharide at a concentration of at least about 40 mM and/or a sugar alcohol at a concentration of at least about 40 mM. In some embodiments, the lyophilized composition is prepared by lyophilizing an aqueous composition that comprises no more than 5% (v/v) glycerol.
    Type: Application
    Filed: April 27, 2020
    Publication date: June 23, 2022
    Inventors: Khalid K. Alam, Matthew S. Verosloff, Jaeyoung K. Jung, Julius B. Lucks, James J. Collins, Phillip R. Clauer, Jeong Wook Lee, Peter Q. Nguyen
  • Publication number: 20220170116
    Abstract: The invention provides novel and versatile classes of riboregulators, including inter alia activating and repressing riboregulators, switches, and trigger and sink RNA, and methods of their use for detecting RNAs in a sample such as a well and in modulating protein synthesis and expression.
    Type: Application
    Filed: September 16, 2021
    Publication date: June 2, 2022
    Applicants: President and Fellows of Harvard College, Trustees of Boston University
    Inventors: Alexander A. Green, Peng Yin, James J. Collins, Jongmin Kim