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  1. Book: Synthetic metabolic pathways

    Krogh Jensen, Michael / Keasling, Jay D.

    methods and protocols

    (Methods in molecular biology ; 1671 ; Springer protocols ; Biomedicine)

    2018  

    Author's details edited by Michael Krogh Jensen (The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark), Jay D. Keasling (Joint BioEnergy Institute, Emeryville, CA, USA)
    Series title Methods in molecular biology ; 1671
    Springer protocols
    Biomedicine
    Collection
    Keywords cell factory ; Genome-scale ; metabolism ; prototyping ; Prokaryote
    Subject code 610
    Language English
    Size xii, 354 Seiten, Illustrationen, Diagramme, 25.4 cm x 17.8 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT019404657
    ISBN 978-1-4939-7294-4 ; 1-4939-7294-4 ; 9781493972951 ; 1493972952
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -1671- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Carbene chemistry for unnatural biosynthesis.

    Huang, Jing / Keasling, Jay D

    Science China. Life sciences

    2023  Volume 67, Issue 1, Page(s) 204–207

    MeSH term(s) Protein Engineering ; Methane
    Chemical Substances carbene (2465-56-7) ; Methane (OP0UW79H66)
    Language English
    Publishing date 2023-11-08
    Publishing country China
    Document type Journal Article
    ZDB-ID 2546732-3
    ISSN 1869-1889 ; 1674-7305
    ISSN (online) 1869-1889
    ISSN 1674-7305
    DOI 10.1007/s11427-023-2470-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Sustainable manufacturing with synthetic biology.

    Scown, Corinne D / Keasling, Jay D

    Nature biotechnology

    2022  Volume 40, Issue 3, Page(s) 304–307

    MeSH term(s) Commerce ; Synthetic Biology
    Language English
    Publishing date 2022-02-21
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-022-01248-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2167: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 137: Show issues
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  4. Article ; Online: Triumphs and Challenges of Natural Product Discovery in the Postgenomic Era.

    Cano-Prieto, Carolina / Undabarrena, Agustina / de Carvalho, Ana Calheiros / Keasling, Jay D / Cruz-Morales, Pablo

    Annual review of biochemistry

    2024  

    Abstract: Natural products have played significant roles as medicine and food throughout human history. Here, we first provide a brief historical overview of natural products, their classification, biosynthetic origins, and the microbiological and genetic methods ... ...

    Abstract Natural products have played significant roles as medicine and food throughout human history. Here, we first provide a brief historical overview of natural products, their classification, biosynthetic origins, and the microbiological and genetic methods used for their discovery. We also describe and discuss the technologies that revolutionized the field, which transitioned from classic genetics to genome-centric discovery approximately two decades ago. We then highlight the most recent advancements and approaches in the current postgenomic era, in which genome mining is a standard operation and high-throughput analytical methods allow parallel discovery of genes and molecules at an unprecedented pace. Finally, we discuss the new challenges faced by the field of natural products and the future of systematic heterologous expression and strain-independent discovery, which promises to deliver more molecules in vials than ever before.
    Language English
    Publishing date 2024-04-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 207924-0
    ISSN 1545-4509 ; 0066-4154
    ISSN (online) 1545-4509
    ISSN 0066-4154
    DOI 10.1146/annurev-biochem-032620-104731
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  5. Article ; Online: Expanding the structural diversity of terpenes by synthetic biology approaches.

    Chen, Rong / Wang, Ming / Keasling, Jay D / Hu, Tianyuan / Yin, Xiaopu

    Trends in biotechnology

    2024  

    Abstract: Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible ... ...

    Abstract Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.
    Language English
    Publishing date 2024-01-16
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 47474-5
    ISSN 1879-3096 ; 0167-7799
    ISSN (online) 1879-3096
    ISSN 0167-7799
    DOI 10.1016/j.tibtech.2023.12.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2750: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Heterologous production of polycyclopropanated fatty acids and their methyl esters in Streptomyces.

    Yin, Kevin / Cruz-Morales, Pablo / Whitford, Christopher M / Keasling, Jay D

    STAR protocols

    2023  Volume 4, Issue 2, Page(s) 102190

    Abstract: Polycyclopropanated (POP) compounds show promise as fuels as their energy density can be greater than jet and rocket fuels in current use, but realizing their full potential requires significant development. This protocol guides the production of ... ...

    Abstract Polycyclopropanated (POP) compounds show promise as fuels as their energy density can be greater than jet and rocket fuels in current use, but realizing their full potential requires significant development. This protocol guides the production of polycyclopropanated fatty acids in Streptomyces; POP production in another host remains to be demonstrated. This method can serve as a baseline for further development of POP as well as other polyketide products. For complete details on the use and execution of this protocol, please refer to Cruz-Morales et al. (2022).
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2023.102190
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: CasPER: A CRISPR/Cas9-Based Method for Directed Evolution in Genomic Loci in Saccharomyces cerevisiae.

    Jakočiūnas, Tadas / Jensen, Michael K / Keasling, Jay D

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2513, Page(s) 23–37

    Abstract: Here, in this chapter, we describe a detailed protocol for the method named Cas9-mediated protein evolution reaction or short CasPER. CasPER is based on the generation of large 300-600-bp mutagenized linear DNA fragments by error-prone PCR which are used ...

    Abstract Here, in this chapter, we describe a detailed protocol for the method named Cas9-mediated protein evolution reaction or short CasPER. CasPER is based on the generation of large 300-600-bp mutagenized linear DNA fragments by error-prone PCR which are used as a donor for repair of double-strand break mediated by Cas9 and subsequently integrated to the genome. This method can be efficiently used for directed evolution of desired essential or nonessential genes in the genome and most importantly can be multiplexed. Altogether, the described method allows for heterogeneous DNA integration with successful transformation efficiencies of 98-100% for both single and multiplex targeting.
    MeSH term(s) CRISPR-Associated Protein 9 ; CRISPR-Cas Systems/genetics ; Genomics ; Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics
    Chemical Substances CRISPR-Associated Protein 9 (EC 3.1.-)
    Language English
    Publishing date 2022-06-30
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2399-2_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Medicinal terpenoid UDP-glycosyltransferases in plants: recent advances and research strategies.

    Lu, Xu / Huang, Lijin / Scheller, Henrik V / Keasling, Jay D

    Journal of experimental botany

    2022  Volume 74, Issue 5, Page(s) 1343–1357

    Abstract: Terpenoid glycosides have significant curative effects on many kinds of diseases. Most of these compounds are derived from medicinal plants. Glycosylation is a key step in the biosynthesis of medicinal terpenoids. In plants, UDP-dependent ... ...

    Abstract Terpenoid glycosides have significant curative effects on many kinds of diseases. Most of these compounds are derived from medicinal plants. Glycosylation is a key step in the biosynthesis of medicinal terpenoids. In plants, UDP-dependent glycosyltransferases comprise a large family of enzymes that catalyze the transfer of sugars from donor to acceptor to form various bioactive glycosides. In recent years, numerous terpenoid UDP-glycosyltransferases (UGTs) have been cloned and characterized in medicinal plants. We review the typical characteristics and evolution of terpenoid-related UGTs in plants and summarize the advances and research strategies of terpenoid UGTs in medicinal plants over the past 20 years. We provide a reference for the study of glycosylation of terpenoid skeletons and the biosynthetic pathways for medicinal terpenoids in plants.
    MeSH term(s) Glycosyltransferases/genetics ; Glycosyltransferases/metabolism ; Terpenes/metabolism ; Uridine Diphosphate/metabolism ; Research Design ; Plants/metabolism ; Glycosides
    Chemical Substances Glycosyltransferases (EC 2.4.-) ; Terpenes ; Uridine Diphosphate (58-98-0) ; Glycosides
    Language English
    Publishing date 2022-12-24
    Publishing country England
    Document type Review ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2976-2
    ISSN 1460-2431 ; 0022-0957
    ISSN (online) 1460-2431
    ISSN 0022-0957
    DOI 10.1093/jxb/erac505
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 55/29: Show issues

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  9. Article ; Online: UniKP: a unified framework for the prediction of enzyme kinetic parameters.

    Yu, Han / Deng, Huaxiang / He, Jiahui / Keasling, Jay D / Luo, Xiaozhou

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 8211

    Abstract: Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical ... ...

    Abstract Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (k
    MeSH term(s) Temperature ; Catalysis ; Biotechnology ; Kinetics
    Language English
    Publishing date 2023-12-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44113-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Foldy: An open-source web application for interactive protein structure analysis.

    Roberts, Jacob B / Nava, Alberto A / Pearson, Allison N / Incha, Matthew R / Valencia, Luis E / Ma, Melody / Rao, Abhay / Keasling, Jay D

    PLoS computational biology

    2024  Volume 20, Issue 2, Page(s) e1011171

    Abstract: Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, ... ...

    Abstract Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy's interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy's interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.
    MeSH term(s) Humans ; Software ; Proteins ; Amino Acids
    Chemical Substances Proteins ; Amino Acids
    Language English
    Publishing date 2024-02-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1011171
    Database MEDical Literature Analysis and Retrieval System OnLINE

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