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  1. Article ; Online: The microbial food revolution.

    Graham, Alicia E / Ledesma-Amaro, Rodrigo

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2231

    Abstract: Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention ... ...

    Abstract Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
    MeSH term(s) Diet ; Food ; Nutritional Status
    Language English
    Publishing date 2023-04-19
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37891-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Author Correction: Inducible expression of large gRNA arrays for multiplexed CRISPRai applications.

    Shaw, William M / Studená, Lucie / Roy, Kyler / Hapeta, Piotr / McCarty, Nicholas S / Graham, Alicia E / Ellis, Tom / Ledesma-Amaro, Rodrigo

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 137

    Language English
    Publishing date 2023-01-10
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-35867-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Inducible expression of large gRNA arrays for multiplexed CRISPRai applications.

    Shaw, William M / Studená, Lucie / Roy, Kyler / Hapeta, Piotr / McCarty, Nicholas S / Graham, Alicia E / Ellis, Tom / Ledesma-Amaro, Rodrigo

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4984

    Abstract: CRISPR gene activation and inhibition (CRISPRai) has become a powerful synthetic tool for influencing the expression of native genes for foundational studies, cellular reprograming, and metabolic engineering. Here we develop a method for near leak-free, ... ...

    Abstract CRISPR gene activation and inhibition (CRISPRai) has become a powerful synthetic tool for influencing the expression of native genes for foundational studies, cellular reprograming, and metabolic engineering. Here we develop a method for near leak-free, inducible expression of a polycistronic array containing up to 24 gRNAs from two orthogonal CRISPR/Cas systems to increase CRISPRai multiplexing capacity and target gene flexibility. To achieve strong inducibility, we create a technology to silence gRNA expression within the array in the absence of the inducer, since we found that long gRNA arrays for CRISPRai can express themselves even without promoter. Using this method, we create a highly tuned and easy-to-use CRISPRai toolkit in the industrially relevant yeast, Saccharomyces cerevisiae, establishing the first system to combine simultaneous activation and repression, large multiplexing capacity, and inducibility. We demonstrate this toolkit by targeting 11 genes in central metabolism in a single transformation, achieving a 45-fold increase in succinic acid, which could be precisely controlled in an inducible manner. Our method offers a highly effective way to regulate genes and rewire metabolism in yeast, with principles of gRNA array construction and inducibility that should extend to other chassis organisms.
    MeSH term(s) CRISPR-Cas Systems ; Gene Editing/methods ; RNA, Guide, CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Transcriptional Activation
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2022-08-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-32603-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Multiplexed CRISPR technologies for gene editing and transcriptional regulation.

    McCarty, Nicholas S / Graham, Alicia E / Studená, Lucie / Ledesma-Amaro, Rodrigo

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 1281

    Abstract: Multiplexed CRISPR technologies, in which numerous gRNAs or Cas enzymes are expressed at once, have facilitated powerful biological engineering applications, vastly enhancing the scope and efficiencies of genetic editing and transcriptional regulation. ... ...

    Abstract Multiplexed CRISPR technologies, in which numerous gRNAs or Cas enzymes are expressed at once, have facilitated powerful biological engineering applications, vastly enhancing the scope and efficiencies of genetic editing and transcriptional regulation. In this review, we discuss multiplexed CRISPR technologies and describe methods for the assembly, expression and processing of synthetic guide RNA arrays in vivo. Applications that benefit from multiplexed CRISPR technologies, including cellular recorders, genetic circuits, biosensors, combinatorial genetic perturbations, large-scale genome engineering and the rewiring of metabolic pathways, are highlighted. We also offer a glimpse of emerging challenges and emphasize experimental considerations for future studies.
    MeSH term(s) Animals ; Biosensing Techniques ; CRISPR-Cas Systems/genetics ; Gene Editing ; Gene Expression Regulation ; Humans ; RNA, Guide, CRISPR-Cas Systems/genetics ; Transcription, Genetic
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2020-03-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-15053-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Engineered cell-to-cell signalling within growing bacterial cellulose pellicles.

    Walker, Kenneth T / Goosens, Vivianne J / Das, Akashaditya / Graham, Alicia E / Ellis, Tom

    Microbial biotechnology

    2018  Volume 12, Issue 4, Page(s) 611–619

    Abstract: Bacterial cellulose is a strong and flexible biomaterial produced at high yields by Acetobacter species and has applications in health care, biotechnology and electronics. Naturally, bacterial cellulose grows as a large unstructured polymer network ... ...

    Abstract Bacterial cellulose is a strong and flexible biomaterial produced at high yields by Acetobacter species and has applications in health care, biotechnology and electronics. Naturally, bacterial cellulose grows as a large unstructured polymer network around the bacteria that produce it, and tools to enable these bacteria to respond to different locations are required to grow more complex structured materials. Here, we introduce engineered cell-to-cell communication into a bacterial cellulose-producing strain of Komagataeibacter rhaeticus to enable different cells to detect their proximity within growing material and trigger differential gene expression in response. Using synthetic biology tools, we engineer Sender and Receiver strains of K. rhaeticus to produce and respond to the diffusible signalling molecule, acyl-homoserine lactone. We demonstrate that communication can occur both within and between growing pellicles and use this in a boundary detection experiment, where spliced and joined pellicles sense and reveal their original boundary. This work sets the basis for synthetic cell-to-cell communication within bacterial cellulose and is an important step forward for pattern formation within engineered living materials.
    MeSH term(s) Acetobacteraceae/genetics ; Acetobacteraceae/growth & development ; Acetobacteraceae/metabolism ; Acyl-Butyrolactones/metabolism ; Biofilms/growth & development ; Cellulose/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Quorum Sensing
    Chemical Substances Acyl-Butyrolactones ; Cellulose (9004-34-6)
    Language English
    Publishing date 2018-11-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.13340
    Database MEDical Literature Analysis and Retrieval System OnLINE

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