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).

  • 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
  • Publication number: 20220088092
    Abstract: The present disclosure relates to compositions, methods, and kits for increasing the viability of bacteria that have been subjected to freeze-drying/lyophilization. In particular, the disclosure relates to compositions and methods for increasing the viability of living medicines (e.g.
    Type: Application
    Filed: January 21, 2020
    Publication date: March 24, 2022
    Applicants: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Daniel S. Collins, Jonathan M. Stokes, Luis R. Soenksen, James J. Collins
  • Publication number: 20220081729
    Abstract: Disclosed herein are shelf-stable compositions based on synthetic gene networks and/or cell-free systems that are lyophilized on a solid support. The compositions can be easily transported and stored for a period of time, and activation can be done by simply adding water. Methods of use are also disclosed herein, including, but are not limited to, sensing and a variety of logic functions. The invention permits straightforward, sterile and abiotic distribution of synthetic biology-based technology to clinical settings, food processing and industry, the military and consumer products.
    Type: Application
    Filed: September 28, 2021
    Publication date: March 17, 2022
    Applicant: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: Keith PARDEE, James J. COLLINS
  • Patent number: 11124846
    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: July 14, 2015
    Date of Patent: September 21, 2021
    Assignees: President and Fellows of Harvard College, Trustees of Boston University
    Inventors: Alexander A. Green, Peng Yin, James J. Collins, Jongmin Kim
  • Patent number: 11071672
    Abstract: A method and wearable system and for enhancing human balance and gait and preventing foot injury through neurological stimulation of the foot and the ankle. Subthreshold stimulation for neurosensory enhancement is provided via electrodes or vibrational actuators, or combination thereof, disposed in or on a wearable a platform, such as an insole, sock shoe, removable shoe insert, or applied without the support of a platform, to the skin surface of an individual. Suprathreshold stimulation for therapeutic purposes, such as improving blood flow, is also provided by the vibrational actuators. The actuators and electrodes are driven by bias signals generated by a bias signal generator that is coupled to a controller. The signal generator under the control of the controller is adapted to generate a non-deterministic random signal, a repetitive pattern or series of patterns.
    Type: Grant
    Filed: August 21, 2018
    Date of Patent: July 27, 2021
    Assignee: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: Jason D. Harry, James J. Collins, James B. Niemi, Attila A. Priplata, Stephen J. Kleshinski
  • Publication number: 20210214713
    Abstract: Disclosed herein are a high-throughput continuous culture system and novel methodologies for the experimental evolution of natural and synthetic microbes using the continuous culture system. The microbial culture is exposed to a stress ramp function which is overlaid on top of a culture fitness function. The amount of stress applied to the culture is increased in response to increased fitness of the microbial culture.
    Type: Application
    Filed: February 17, 2018
    Publication date: July 15, 2021
    Applicants: Massachusetts Institute of Technology, Trustees of Boston University
    Inventors: Caleb J. Bashor, Jason Hung-Ying Yang, Arnaud Gutierrez, Wooseok Steven Ahn, James J. Collins, Brandon Gei-Chin Wong, Ahmad S. Khalil
  • Publication number: 20210164025
    Abstract: Described herein are compositions and methods for in vitro detection of nucleic acids. Nucleic acid sensors are activated for cell-free expression of an encoded reporter protein based on the presence of a target nucleic acid. The system is designed to function in low-cost cell extract without the need for instrumentation or stringent temperature control. These features are advantageous for point-of-use molecular diagnostics applications in consumer health, pet/animal health, food safety, and other areas where cost and portability are key factors.
    Type: Application
    Filed: August 14, 2019
    Publication date: June 3, 2021
    Applicants: PRESIDENT AND FELLOWS OF HARVARD COLLEGE, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: William Jeremy BLAKE, Carl W. BROWN, III, James J. COLLINS, Frederic VIGNEAULT
  • Patent number: 10842874
    Abstract: Provided herein are pharmaceutical compositions and kits useful for sensitizing a microorganism or a population of microorganisms to a quinolone antibiotic. In a particular aspect, a carbon source and an electron acceptor can sensitize an antibiotic persistent microorganism to treatment with a fluoroquinolone antibiotic. Methods for sensitizing a microorganism to a quinolone antibiotic, reducing the density-dependent persistence (DDP) of an antibiotic resistant microorganism, and reducing the number of persistent cells in a population are also provided. Theses compositions and methods are useful in treating infections resulting from high-density bacterial cultures, such as pneumonia, genitourinary infections, biofilms, prosthetic graft infections, sepsis, and endovascular infections.
    Type: Grant
    Filed: October 23, 2018
    Date of Patent: November 24, 2020
    Assignee: Massachusetts Institute of Technology
    Inventors: James J. Collins, Michael Andrew Lobritz, Arnaud Gutierrez
  • Publication number: 20200362345
    Abstract: The present disclosure is related to an engineered nucleic acid encoding a post-poly A signal RNA 3? to a terminator for expression of protein, and/or non-coding RNA. Also provided herein are methods for reducing epigenetic silencing, genetic modification, transcriptional regulation of the engineered nucleic acid described herein.
    Type: Application
    Filed: May 15, 2020
    Publication date: November 19, 2020
    Applicant: Massachusetts Institute of Technology
    Inventors: Ron Weiss, James J. Collins, Elvira Vitu, Casper Enghuus, Jeremy Jonathan Gam
  • Publication number: 20200308577
    Abstract: Disclosed herein are hydrogels comprising a polynucleotide-based structural component. Methods of altering a property of a hydrogel based on user-defined nucleic acid input sequences are also disclosed. In addition, various applications are described that utilize these hydrogels and methods.
    Type: Application
    Filed: January 31, 2020
    Publication date: October 1, 2020
    Applicant: Massachusetts Institute of Technology
    Inventors: James J. Collins, Helena de Puig Guixe, Luis Soenksen Martinez, Max English, Raphael Gayet, Nicolaas Angenent-Mari, Angelo S. Mao, Peter Q. Nguyen
  • Publication number: 20200199568
    Abstract: Disclosed herein are a high-throughput continuous culture system and novel methodologies for the experimental evolution of natural and synthetic microbes using the continuous culture system. The microbial culture is exposed to a stress ramp function which is overlaid on top of a culture fitness function. The amount of stress applied to the culture is increased in response to increased fitness of the microbial culture.
    Type: Application
    Filed: February 17, 2018
    Publication date: June 25, 2020
    Applicants: Massachusetts Institute of Technology, Trustees of Boston University
    Inventors: Caleb J. Bashor, Jason Hung-Ying Yang, Arnaud Gutierrez, Wooseok Steven Ahn, James J. Collins, Brandon Gei-Chin Wong, Ahmad S. Khalil
  • Patent number: 10676721
    Abstract: The present invention is generally related to engineered bacteriophages expressing antimicrobial peptides or lytic enzymes or fragments thereof for targeting a broad spectrum of bacterial hosts, and for the long-term suppression of bacterial phage resistance for reducing bacterial infections. In some embodiments, bacteriophages express antimicrobial peptides or antimicrobial polypeptides (e.g. phage lytic enzymes) which are secreted from the host bacteria, or alternatively released upon lysis of the bacterial host cell. Aspects of the present invention also relate to the use of the engineered bacteriophages for the reduction of bacterial infections, both in a subject or for bioremediation purposes, in clinical settings and wound healing.
    Type: Grant
    Filed: September 2, 2011
    Date of Patent: June 9, 2020
    Assignees: Trustees of Boston University, Massachusetts Institute of Technology
    Inventors: James J. Collins, Michael Koeris, Timothy Kuan-Ta Lu, Gregory Stephanopoulos, Christopher Jongsoo Yoon
  • Patent number: 10660911
    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 high, localized concentrations of one or more 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. These approaches and therapeutic methods are also useful with non-metabolic chemicals that induce proton-motive force in bacteria.
    Type: Grant
    Filed: August 27, 2018
    Date of Patent: May 26, 2020
    Assignee: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: James J. Collins, Kyle R. Allison, Mark P. Brynildsen
  • Patent number: 10617597
    Abstract: A wearable system is directed to neurological stimulation of a human foot, and includes a controller with at least one bias signal generator for outputting a driving signal. The system further includes a power source that provides electrical energy to the controller, including providing electrical energy to the bias signal generator. The system also includes a platform in the form of an insole insert of a shoe, the insole insert having a plurality of actuators positioned in a medial arch region of the foot. The plurality of actuators stimulate the medial arch region in response to receiving the driving signal from the controller. The stimulation of the plurality of actuators provides a subthreshold bias signal to target cells with a subthreshold bias signal magnitude that is below a threshold where the target cells are activated by a stimulus. The plurality of actuators is surrounded with a vibration dissipating material.
    Type: Grant
    Filed: October 21, 2016
    Date of Patent: April 14, 2020
    Assignee: President and Fellows of Harvard College
    Inventors: Arun Chawan, Hani Sallum, Robert Wood, James Niemi, James J. Collins
  • Patent number: 10614353
    Abstract: Described herein are novel biological converter switches that utilize modular components, such as genetic toggle switches and single invertase memory modules (SIMMs), for converting analog inputs to digital outputs, and digital inputs to analog outputs, in cells and cellular systems. Flexibility in these biological converter switches is provided by combining individual modular components, i.e., SIMMs and genetic toggle switches, together. These biological converter switches can be combined in a variety of network topologies to create circuits that act, for example, as switchboards, and regulate the production of an output product(s) based on the combination and nature of input signals received.
    Type: Grant
    Filed: April 27, 2017
    Date of Patent: April 7, 2020
    Assignees: TRUSTEES OF BOSTON UNIVERSITY, MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: James J. Collins, Timothy Kuan-Ta Lu
  • Publication number: 20200080137
    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: May 25, 2017
    Publication date: March 12, 2020
    Inventors: Alexander Green, Dana Braff, Melissa K. Takahashi, Keith Pardee, James J. Collins, Guillaume Lambert, Thomas Ferrante
  • Publication number: 20200002710
    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: June 28, 2019
    Publication date: January 2, 2020
    Applicant: TRUSTEES OF BOSTON UNIVERSITY
    Inventors: Ahmad S. Khalil, Caleb J. Bashor, Nikit Patel, James J. Collins
  • Publication number: 20190201532
    Abstract: Provided herein are pharmaceutical compositions and kits useful for sensitizing a microorganism or a population of microorganisms to a quinolone antibiotic. In a particular aspect, a carbon source and an electron acceptor can sensitize an antibiotic persistent microorganism to treatment with a fluoroquinolone antibiotic. Methods for sensitizing a microorganism to a quinolone antibiotic, reducing the density-dependent persistence (DDP) of an antibiotic resistant microorganism, and reducing the number of persistent cells in a population are also provided. Theses compositions and methods are useful in treating infections resulting from high-density bacterial cultures, such as pneumonia, genitourinary infections, biofilms, prosthetic graft infections, sepsis, and endovascular infections.
    Type: Application
    Filed: October 23, 2018
    Publication date: July 4, 2019
    Inventors: James J. Collins, Michael Andrew Lobritz, Arnaud Gutierrez