Patents by Inventor José L. Avalos

José L. Avalos 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: 20250059549
    Abstract: Disclosed herein are optogenetic circuits for the bacterium Escherichia coli that induce gene expression in darkness and repress it under blue light. Applying them to metabolic engineering improves chemical production compared to chemically induced controls in light-controlled fermentations. More particularly, these circuits can be used to control protein production with light. The system and method use light as a suitable alternative to chemical induction for microbial production of chemicals and proteins.
    Type: Application
    Filed: July 30, 2024
    Publication date: February 20, 2025
    Applicant: The Trustees of Princeton University
    Inventors: José L. Avalos, Makoto A. Lalwani, César Carrasco-López
  • Publication number: 20240368648
    Abstract: Microbial consortia exert great influence over the physiology of humans, animals, plants, and ecosystems. However, difficulty in controlling their composition and population dynamics have limited their application in medicine, agriculture, biotechnology, and the environment. The approach disclosed herein provides an effective method to dynamically control population compositions in microbial consortia, which we demonstrate in the context of co-culture fermentations for chemical production. Co-culture fermentations can improve chemical production from complex biosynthetic pathways over monocultures by distributing enzymes across multiple strains, thereby reducing metabolic burden, overcoming endogenous regulatory mechanisms, or exploiting natural traits of different microbial species. However, stabilizing and optimizing microbial sub-populations for maximal chemical production remains a major obstacle in the field.
    Type: Application
    Filed: July 16, 2024
    Publication date: November 7, 2024
    Applicant: The Trustees of Princeton University
    Inventors: Jose L. Avalos, Makoto A. Lalwani, Mark P. Brynildsen
  • Patent number: 11859223
    Abstract: A system and method for controlling metabolic enzymes or pathways in cells to produce a chemical above the levels of a wild-type strain is disclosed. The system utilizes cells, including yeasts, bacteria, and molds, having at least two genes capable of being controlled bi-directionally with light, where one gene is turned from off to on when exposed to light and another gene is turned from on to off when exposed to light, the two genes reversing when the light is turned off. Cells may utilize any number of sequences that benefit chemical production, including sequences that: encode for constitutive transcription of light-activated transcription factor fusions; encode for a metabolic enzyme; encode for a repressor; induce expression of metabolic enzymes; and an endogenous or exogenous activator expressed by a constitutive promoter, inducible promoter, or gene circuit.
    Type: Grant
    Filed: April 7, 2017
    Date of Patent: January 2, 2024
    Assignee: THE TRUSTEES OF PRINCETON UNIVERSITY
    Inventors: Jose L. Avalos, Jared E. Toettcher, Evan M. Zhao
  • Publication number: 20230212626
    Abstract: Disclosed is a technique for constructing optogenetic amplifier and inverter circuits utilizing transcriptional activator/repressor pairs, in which expression of the transcriptional activator or repressor, respectively, is controlled by light-controlled transcription factors. This system is demonstrated utilizing the quinic acid regulon system from Neurospora crassa, or Q System, a transcriptional activator/repressor system. This is also demonstrated utilizing the galactose regulon from Saccharomyces cerevisiae, or GAL System. Such optogenetic amplifier circuits enable multi-phase microbial fermentations, in which different light schedules are applied in each phase to dynamically control different metabolic pathways for the production of proteins, fuels or chemicals.
    Type: Application
    Filed: December 22, 2022
    Publication date: July 6, 2023
    Applicant: The Trustees of Princeton University
    Inventors: Jose L. Avalos, Jared E. Toettcher, Evan M. Zhao, Makoto A. Lalwani
  • Publication number: 20220403429
    Abstract: Microbial consortia exert great influence over the physiology of humans, animals, plants, and ecosystems. However, difficulty in controlling their composition and population dynamics have limited their application in medicine, agriculture, biotechnology, and the environment. The approach disclosed herein provides an effective method to dynamically control population compositions in microbial consortia, which we demonstrate in the context of co-culture fermentations for chemical production. Co-culture fermentations can improve chemical production from complex biosynthetic pathways over monocultures by distributing enzymes across multiple strains, thereby reducing metabolic burden, overcoming endogenous regulatory mechanisms, or exploiting natural traits of different microbial species. However, stabilizing and optimizing microbial sub-populations for maximal chemical production remains a major obstacle in the field.
    Type: Application
    Filed: June 21, 2022
    Publication date: December 22, 2022
    Applicant: The Trustees of Princeton University
    Inventors: Jose L. Avalos, Makoto A. Lalwani, Mark P. Brynildsen
  • Publication number: 20210147855
    Abstract: Disclosed herein are optogenetic circuits for the bacterium Escherichia coli that induce gene expression in darkness and repress it under blue light. Applying them to metabolic engineering improves chemical production compared to chemically induced controls in light-controlled fermentations. More particularly, these circuits can be used to control protein production with light. The system and method use light as a suitable alternative to chemical induction for microbial production of chemicals and proteins.
    Type: Application
    Filed: November 13, 2020
    Publication date: May 20, 2021
    Applicant: THE TRUSTEES OF PRINCETON UNIVERSITY
    Inventors: José L. Avalos, Makoto A. Lalwani, César Carrasco-López
  • Publication number: 20210062165
    Abstract: Provided herein is a system and method of optogenetically inducibly clustering metabolic enzymes for the production of chemicals using cell factories. More particularly, the described inducible protein clustering approach clusters metabolic enzymes by, e.g., a change in illumination conditions (either a switch from dark to light or from light to dark). Performing this clustering leads to an increase in the production of metabolites by the clustered enzymes. In some embodiments, a light-sensitive domain may be replaced with any inducible domain.
    Type: Application
    Filed: August 26, 2020
    Publication date: March 4, 2021
    Applicant: The Trustees of Princeton University
    Inventors: Jose L. Avalos, Jared E. Toettcher, Clifford P. Brangwynne, Evan M. Zhao, Maxwell Z. Wilson
  • Publication number: 20090012130
    Abstract: The instant invention describes methods of identifying compounds that modulate the activity of Sir2 enzymes. Sir2 enzymes form a unique class Of NAD+ dependent deacetylases required for diverse biological processes including transcriptional silencing, regulation of apoptosis, fat mobilization, and lifespan regulation. Sir2 activity is regulated by nicotinamide, a non-competitive inhibitor that promotes a base exchange reaction at the expense of deacetylation.
    Type: Application
    Filed: January 25, 2006
    Publication date: January 8, 2009
    Applicant: THE JOHNS HOPKINS UNIVERSITY
    Inventors: Cynthia Wolberger, Jose L. Avalos