[
    {
        "id": "authors:fpyjb-qw793",
        "collection": "authors",
        "collection_id": "fpyjb-qw793",
        "cite_using_url": "https://authors.library.caltech.edu/records/fpyjb-qw793",
        "type": "article",
        "title": "Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness",
        "author": [
            {
                "family_name": "Li",
                "given_name": "Jinyang",
                "orcid": "0000-0003-3190-4021",
                "clpid": "Li-Jinyang"
            },
            {
                "family_name": "Squyres",
                "given_name": "Georgia R.",
                "orcid": "0000-0002-8717-2897",
                "clpid": "Squyres-Georgia-R"
            },
            {
                "family_name": "Duong",
                "given_name": "Kathy"
            },
            {
                "family_name": "Reichhardt",
                "given_name": "Courtney",
                "orcid": "0000-0002-1022-5110"
            },
            {
                "family_name": "Parsek",
                "given_name": "Matthew R.",
                "orcid": "0000-0003-2932-7966"
            },
            {
                "family_name": "Newman",
                "given_name": "Dianne K.",
                "orcid": "0000-0003-1647-1918",
                "clpid": "Newman-D-K"
            }
        ],
        "abstract": "Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior across all domains of life. But how has evolution optimized these materials to ensure the success of multicellular communities? Inspired by the well-established composition\u2013properties\u2013function relationships in engineered materials, we hypothesized that analogous relationships exist in extracellular matrices, where the composition and interactions among various matrix components govern material properties and cellular physiology. Here, we examine\n                    Pseudomonas aeruginosa\n                    biofilms\u2014representative of ubiquitous multicellular microbial assemblies in nature and disease. We show that electrostatic interactions between the cationic polysaccharide Pel and extracellular DNA (eDNA) compete with eDNA binding to pyocyanin (PYO), a diffusible redox-active metabolite that supports anaerobic metabolism via extracellular electron transfer (EET). From a materials perspective, biofilm-mimetic hydrogels and natural biofilms revealed that altering Pel's charge via pH adjustment or chemical acetylation, or tuning the Pel:eDNA ratio, directly and predictably modulates PYO retention and EET efficiency. Biologically, a lower Pel:eDNA ratio enhances biofilm metabolism under oxygen limitation, whereas a higher ratio promotes survival under antibiotic stress. Notably, these perturbations (pH, Pel structure, and abundance) can be achieved directly or indirectly through biological activities. Together, these findings highlight how biologically regulated matrix chemistry encodes tunable material properties that, in turn, affect cellular responses that confer biofilm fitness advantages. They further suggest cells might actively fine-tune the surrounding matrix chemistry to maximize survival across diverse environments. More broadly, our work establishes a materials-based framework for a mechanistic understanding of the biological functions of extracellular matrix components in multicellular communities.",
        "doi": "10.1073/pnas.2528666123",
        "pmcid": "PMC13055754",
        "issn": "0027-8424",
        "publisher": "National Academy of Sciences",
        "publication": "Proceedings of the National Academy of Sciences",
        "publication_date": "2026-04-14",
        "series_number": "15",
        "volume": "123",
        "issue": "15",
        "pages": "e2528666123"
    },
    {
        "id": "authors:40rx5-vek70",
        "collection": "authors",
        "collection_id": "40rx5-vek70",
        "cite_using_url": "https://authors.library.caltech.edu/records/40rx5-vek70",
        "type": "article",
        "title": "Biomimetic Redox Capacitor To Control the Flow of Electrons",
        "author": [
            {
                "family_name": "Kim",
                "given_name": "Eunkyoung",
                "orcid": "0000-0003-2566-4041"
            },
            {
                "family_name": "Zhao",
                "given_name": "Zhiling"
            },
            {
                "family_name": "Wu",
                "given_name": "Si",
                "orcid": "0000-0001-6325-3951"
            },
            {
                "family_name": "Li",
                "given_name": "Jinyang",
                "orcid": "0000-0003-3190-4021",
                "clpid": "Li-Jinyang"
            },
            {
                "family_name": "Bentley",
                "given_name": "William E.",
                "orcid": "0000-0002-4855-7866"
            },
            {
                "family_name": "Payne",
                "given_name": "Gregory F.",
                "orcid": "0000-0001-6638-9459"
            }
        ],
        "abstract": "<p>In biological systems, electrons, energy, and information &ldquo;flow&rdquo; through the redox modality, and we ask, does biology have redox capacitor capabilities for storing electrons? We describe emerging evidence indicating that biological phenolic/catecholic materials possess such redox capacitor properties. We further describe results that show biomimetic catecholic materials are reversibly redox-active with redox potentials in the midphysiological range and can repeatedly accept electrons (from various reductants), store electrons, and donate electrons (to various oxidants). Importantly, catechol-containing films that are assembled onto electrode surfaces can enhance the flow of electrons, energy, and information. Further, catechol-containing films can serve as redox-based interactive materials capable of actuating biological responses by turning on gene expression from redox-responsive genetic circuits. Looking forward, we envision that the emerging capabilities for measuring dynamic redox processes and reversible redox states will provide new insights into redox biology and will also catalyze new technological opportunities for information processing and energy harvesting.</p>",
        "doi": "10.1021/acsami.4c13032",
        "issn": "1944-8244",
        "publisher": "American Chemical Society",
        "publication": "ACS Applied Materials & Interfaces",
        "publication_date": "2024-11-13",
        "series_number": "45",
        "volume": "16",
        "issue": "45",
        "pages": "61495\u201361502"
    },
    {
        "id": "authors:s9y1r-vce93",
        "collection": "authors",
        "collection_id": "s9y1r-vce93",
        "cite_using_url": "https://authors.library.caltech.edu/records/s9y1r-vce93",
        "type": "article",
        "title": "Redox active plant phenolic, acetosyringone, for electrogenetic signaling",
        "author": [
            {
                "family_name": "Zakaria",
                "given_name": "Fauziah Rahma",
                "clpid": "Zakaria-Fauziah-Rahma"
            },
            {
                "family_name": "Chen",
                "given_name": "Chen-Yu",
                "orcid": "0000-0001-6500-6970",
                "clpid": "Chen-Chen-Yu"
            },
            {
                "family_name": "Li",
                "given_name": "Jinyang",
                "orcid": "0000-0003-3190-4021",
                "clpid": "Li-Jinyang"
            },
            {
                "family_name": "Wang",
                "given_name": "Sally",
                "orcid": "0000-0001-9668-888X",
                "clpid": "Wang-Sally"
            },
            {
                "family_name": "Payne",
                "given_name": "Gregory F.",
                "orcid": "0000-0001-6638-9459",
                "clpid": "Payne-Gregory-F"
            },
            {
                "family_name": "Bentley",
                "given_name": "William E.",
                "orcid": "0000-0002-4855-7866",
                "clpid": "Bentley-William-E"
            }
        ],
        "abstract": "<div class=\"c-article-section\">\n<div class=\"c-article-section__content\">\n<p>Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the&nbsp;<em>E. coli</em>&nbsp;redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a &ldquo;pro-signaling molecule&rdquo; that can be activated by its oxidation&mdash;in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O<sub>2</sub>&nbsp;to form H<sub>2</sub>O<sub>2</sub> or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed &ldquo;pro-signal&rdquo; dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.</p>\n</div>\n</div>",
        "doi": "10.1038/s41598-024-60191-7",
        "pmcid": "PMC11053109",
        "issn": "2045-2322",
        "publisher": "Nature",
        "publication": "Scientific Reports",
        "publication_date": "2024-04-26",
        "volume": "14",
        "pages": "9666"
    },
    {
        "id": "authors:hdspq-37956",
        "collection": "authors",
        "collection_id": "hdspq-37956",
        "cite_using_url": "https://authors.library.caltech.edu/records/hdspq-37956",
        "type": "article",
        "title": "Electronic inputs to cue the emergence of hydrogel structure and to confer function",
        "author": [
            {
                "family_name": "Liu",
                "given_name": "Yi",
                "orcid": "0000-0001-9936-4688"
            },
            {
                "family_name": "Lei",
                "given_name": "Miao",
                "orcid": "0000-0001-6414-4773"
            },
            {
                "family_name": "Li",
                "given_name": "Jinyang",
                "orcid": "0000-0003-3190-4021",
                "clpid": "Li-Jinyang"
            },
            {
                "family_name": "Kim",
                "given_name": "Eunkyoung",
                "orcid": "0000-0003-2566-4041"
            },
            {
                "family_name": "Yan",
                "given_name": "Kun"
            },
            {
                "family_name": "Bentley",
                "given_name": "William E.",
                "orcid": "0000-0002-4855-7866"
            },
            {
                "family_name": "Shi",
                "given_name": "Xiaowen",
                "orcid": "0000-0001-8294-2920"
            },
            {
                "family_name": "Qu",
                "given_name": "Xue"
            },
            {
                "family_name": "Payne",
                "given_name": "Gregory F.",
                "orcid": "0000-0001-6638-9459"
            }
        ],
        "abstract": "<p>Electrode-imposed electronic inputs can generate various cues that can control the emergence of hierarchical structure and confer function to hydrogel systems. Here we describe three such top-down cues. Electrolytic reactions can create pH cues that can induce the&nbsp;<a class=\"topic-link\" title=\"Learn more about electrodeposition from ScienceDirect's AI-generated Topic Pages\" href=\"https://www.sciencedirect.com/topics/materials-science/electrodeposition\">electrodeposition</a>&nbsp;of pH-responsive self-assembling polymers (e.g., chitosan and alginate). The electric field provides a long-range cue that can induce polymer chains to migrate toward (or away from) the electrode and can align the polymer chains within the assembling hydrogel network (e.g., collagen). The electrochemical generation of diffusible oxidants provides a molecular cue that can induce oxidative assembly - typically through the formation of covalent bonds (e.g., disulfide bonds). Here, we review recent results on the use of these three cues for the electrofabrication of hydrogels and we illustrate how complementary capabilities from biotechnology allow the creation of functional hydrogel systems. Overall, we envision that electro-bio-fabrication could emerge as a scalable&nbsp;<a class=\"topic-link\" title=\"Learn more about additive manufacturing from ScienceDirect's AI-generated Topic Pages\" href=\"https://www.sciencedirect.com/topics/materials-science/three-dimensional-printing\">additive manufacturing</a> method as well as a flexible approach for distributed manufacturing in public maker spaces.</p>",
        "doi": "10.1016/j.matlet.2023.135497",
        "issn": "0167-577X",
        "publisher": "Elsevier",
        "publication": "Materials Letters",
        "publication_date": "2024-01-15",
        "volume": "355",
        "pages": "135497"
    }
]