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  1. AU="Nielsen, David R"
  2. AU="Natsui, Hiroaki"
  3. AU="Ziv Ben-Ari"
  4. AU="Gönen, Murat"
  5. AU="Soliman, Essam S"
  6. AU="Poenisch, Falk"
  7. AU="Ng C."
  8. AU="Cabaton, Nicolas J"

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  1. Article ; Online: Editorial overview: Energy biotechnology as an integral solution to global challenges.

    Park, Junyoung O / Nielsen, David R

    Current opinion in biotechnology

    2023  Volume 84, Page(s) 103006

    MeSH term(s) Biotechnology ; Renewable Energy
    Language English
    Publishing date 2023-10-02
    Publishing country England
    Document type Editorial
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2023.103006
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3071: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Systematic Engineering of

    Dookeran, Zachary A / Nielsen, David R

    ACS synthetic biology

    2021  Volume 10, Issue 12, Page(s) 3561–3575

    Abstract: Amino acids and related targets are typically produced by well-characterized heterotrophs ... ...

    Abstract Amino acids and related targets are typically produced by well-characterized heterotrophs including
    MeSH term(s) Cadaverine/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Glutarates/metabolism ; Lysine/metabolism ; Metabolic Engineering ; Synechococcus/metabolism
    Chemical Substances Glutarates ; Lysine (K3Z4F929H6) ; Cadaverine (L90BEN6OLL)
    Language English
    Publishing date 2021-12-01
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.1c00492
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  3. Article ; Online: Exploiting Polyploidy for Markerless and Plasmid-Free Genome Engineering in Cyanobacteria.

    Jones, Christopher M / Parrish, Sydney / Nielsen, David R

    ACS synthetic biology

    2021  Volume 10, Issue 9, Page(s) 2371–2382

    Abstract: Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being ... ...

    Abstract Here we describe a universal approach for plasmid-free genome engineering in cyanobacteria that exploits the polyploidy of their chromosomes as a natural counterselection system. Rather than being delivered
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Genetic Engineering/methods ; Genome, Bacterial ; Polyploidy ; Recombination, Genetic ; Synechococcus/genetics ; Synechocystis/genetics
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2021-08-17
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.1c00269
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  4. Article ; Online: Optimization of a T7-RNA polymerase system in Synechococcus sp. PCC 7002 mirrors the protein overproduction phenotype from E. coli BL21(DE3).

    Jones, Christopher M / Korosh, Travis C / Nielsen, David R / Pfleger, Brian F

    Applied microbiology and biotechnology

    2021  Volume 105, Issue 3, Page(s) 1147–1158

    Abstract: With the goal of expanding the diversity of tools available for controlling gene expression in cyanobacteria, the T7-RNA polymerase gene expression system from E. coli BL21(DE3) was adapted and systematically engineered for robust function Synechococcus ... ...

    Abstract With the goal of expanding the diversity of tools available for controlling gene expression in cyanobacteria, the T7-RNA polymerase gene expression system from E. coli BL21(DE3) was adapted and systematically engineered for robust function Synechococcus sp. PCC 7002, a fast-growing saltwater strain. Expression of T7-RNA polymerase was controlled via LacI regulation, while functionality was optimized by both further tuning its expression level along with optimizing the translation initiation region of the expressed gene, in this case an enhanced YFP reporter. Under high CO
    MeSH term(s) DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Phenotype ; Synechococcus/genetics ; Synechococcus/metabolism
    Chemical Substances DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2021-01-14
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-020-11085-x
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2229: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article: Applying a ‘Metabolic Funnel’ for Phenol Production in Escherichia coli

    Thompson, Brian / Machas, Michael / Abed, Omar / Nielsen, David R.

    Fermentation. 2021 Oct. 05, v. 7, no. 4

    2021  

    Abstract: Phenol is an important petrochemical that is conventionally used as a precursor for synthesizing an array of plastics and fine chemicals. As an emerging alternative to its traditional petrochemical production, multiple enzyme pathways have been ... ...

    Abstract Phenol is an important petrochemical that is conventionally used as a precursor for synthesizing an array of plastics and fine chemicals. As an emerging alternative to its traditional petrochemical production, multiple enzyme pathways have been engineered to date to enable its renewable biosynthesis from biomass feedstocks, each incorporating unique enzyme chemistries and intermediate molecules. Leveraging all three of the unique phenol biosynthesis pathways reported to date, a series of synthetic ‘metabolic funnels’ was engineered, each with the goal of maximizing net precursor assimilation and flux towards phenol via the parallel co-expression of multiple distinct pathways within the same Escherichia coli host. By constructing and evaluating all possible binary and tertiary pathway combinations, one ‘funnel’ was ultimately identified, which supported enhanced phenol production relative to all three individual pathways by 16 to 69%. Further host engineering to increase endogenous precursor availability then allowed for 26% greater phenol production, reaching a final titer of 554 ± 19 mg/L and 28.8 ± 0.34 mg/g yield on glucose. Lastly, using a diphasic culture including dibutyl phthalate for in situ phenol extraction, final titers were further increased to a maximum of 812 ± 145 mg/L at a yield of 40.6 ± 7.2 mg/g. The demonstrated ‘funneling’ pathway holds similar promise in support of phenol production by other, non-E. coli hosts, while this general approach can be readily extended towards a diversity of other value-added bioproducts of interest.
    Keywords Escherichia coli ; biobased products ; biomass ; biosynthesis ; dibutyl phthalate ; enzymes ; feedstocks ; fermentation ; glucose ; phenol ; value added
    Language English
    Dates of publication 2021-1005
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2813985-9
    ISSN 2311-5637
    ISSN 2311-5637
    DOI 10.3390/fermentation7040216
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  6. Article: Optimization of a T7-RNA polymerase system in Synechococcus sp. PCC 7002 mirrors the protein overproduction phenotype from E. coli BL21(DE3)

    Jones, Christopher M / Korosh, Travis C / Nielsen, David R / Pfleger, Brian F

    Applied microbiology and biotechnology. 2021 Feb., v. 105, no. 3

    2021  

    Abstract: With the goal of expanding the diversity of tools available for controlling gene expression in cyanobacteria, the T7-RNA polymerase gene expression system from E. coli BL21(DE3) was adapted and systematically engineered for robust function Synechococcus ... ...

    Abstract With the goal of expanding the diversity of tools available for controlling gene expression in cyanobacteria, the T7-RNA polymerase gene expression system from E. coli BL21(DE3) was adapted and systematically engineered for robust function Synechococcus sp. PCC 7002, a fast-growing saltwater strain. Expression of T7-RNA polymerase was controlled via LacI regulation, while functionality was optimized by both further tuning its expression level along with optimizing the translation initiation region of the expressed gene, in this case an enhanced YFP reporter. Under high CO₂ conditions, the resulting system displayed a 60-fold dynamic range in expression levels. Furthermore, when maximally induced, T7-RNA polymerase-dependent protein production constituted up to two-thirds of total cellular protein content in Synechococcus sp. PCC 7002. Ultimately, however, this came at the cost of 40% reductions in both biomass and pigmentation levels. Taken together, the developed T7-RNA polymerase gene expression system is effective for controlling and achieving high-level expression of heterologous genes in Synechococcus sp. PCC 7002, making it a valuable tool for cyanobacterial research. KEY POINTS: • Promoter driving T7-RNA polymerase was optimized. • Up to 60-fold dynamic range in expression, depending on CO₂ conditions. • Two-thirds of total protein is T7-RNA polymerase dependent.
    Keywords Escherichia coli ; biomass ; biotechnology ; carbon dioxide ; gene expression ; genes ; microbiology ; phenotype ; pigmentation ; protein content ; protein synthesis ; saline water
    Language English
    Dates of publication 2021-02
    Size p. 1147-1158.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-020-11085-x
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    In stock of ZB MED Bonn / Germany

    Z 79/727: Show issues

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  7. Article: Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production

    Flores, Andrew / Wang, Xuan / Nielsen, David R

    Current opinion in biotechnology. 2019 June, v. 57

    2019  

    Abstract: Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ ... ...

    Abstract Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ product separation are poised to help address this intrinsic problem, but suffer their own unique shortcomings. To improve and expand the utility of this versatile bioprocessing strategy, recent innovations have focused on developing more effective separation materials and novel process configurations, as well as adapting designs to accommodate semi-continuous modes of operation. As a result, integrated bioprocesses are finding new applications to aid the biosynthesis of an ever-growing list of bioproducts. Emerging applications, meanwhile, are exploring the further expansion of such designs to interface microbial and chemical catalysts, leading to new and versatile routes for the one-pot synthesis of an even greater diversity of renewable products.
    Keywords biofuels ; bioprocessing ; biosynthesis ; catalysts ; synthesis ; toxicity
    Language English
    Dates of publication 2019-06
    Size p. 82-87.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2019.02.007
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3071: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Soluble and stable cyanophycin synthetase expression enhances heterologous cyanophycin production in Escherichia coli

    Swain, Kyle / Sharon, Itai / Blackson, Wyatt / Parrish, Sydney / Tekel, Stefan / Schmeing, T. Martin / Nielsen, David R. / Nannenga, Brent L.

    Biochemical Engineering Journal. 2023 June, v. 195 p.108916-

    2023  

    Abstract: Microbial production of biopolymers represents a promising, sustainable alternative to current approaches for plastic production. Cyanophycin synthetase 1 (CphA1) produces cyanophycin - an attractive biopolymer consisting of a poly-L-aspartic acid ... ...

    Abstract Microbial production of biopolymers represents a promising, sustainable alternative to current approaches for plastic production. Cyanophycin synthetase 1 (CphA1) produces cyanophycin - an attractive biopolymer consisting of a poly-L-aspartic acid backbone decorated with L-arginine side groups. In this work, a series of CphA1 enzymes from different bacteria that were each previously identified to express as soluble and stable enzymes in Escherichia coli were screened for heterologous cyanophycin production in engineered E. coli. In each case, expression of stable CphA1 enzymes resulted in greater insoluble cyanophycin production, and it was found that CphA1 from Tatumella morbirosei (TmCphA1) was especially productive. Under these conditions, TmCphA1 was capable of supporting up to ∼2-fold greater yields of insoluble cyanophycin than any other tested CphA1 enzymes, including 10.8-times more than CphA1 from Synechocystis sp. PCC6308. Finally, using a bench-scale bioreactor, cyanophycin production by TmCphA1-expressing E. coli reached up to 1.9 g per liter of culture by 48 h.
    Keywords Escherichia coli ; Synechocystis ; Tatumella ; arginine ; biopolymers ; bioreactors ; Cyanophycin ; Cyanophycin synthetase
    Language English
    Dates of publication 2023-06
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 2012139-8
    ISSN 1369-703X
    ISSN 1369-703X
    DOI 10.1016/j.bej.2023.108916
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  9. Article ; Online: Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production.

    Flores, Andrew / Wang, Xuan / Nielsen, David R

    Current opinion in biotechnology

    2019  Volume 57, Page(s) 82–87

    Abstract: Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ ... ...

    Abstract Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ product separation are poised to help address this intrinsic problem, but suffer their own unique shortcomings. To improve and expand the utility of this versatile bioprocessing strategy, recent innovations have focused on developing more effective separation materials and novel process configurations, as well as adapting designs to accommodate semi-continuous modes of operation. As a result, integrated bioprocesses are finding new applications to aid the biosynthesis of an ever-growing list of bioproducts. Emerging applications, meanwhile, are exploring the further expansion of such designs to interface microbial and chemical catalysts, leading to new and versatile routes for the one-pot synthesis of an even greater diversity of renewable products.
    MeSH term(s) Bioelectric Energy Sources ; Biofuels ; Biotechnology/trends ; Catalysis
    Chemical Substances Biofuels
    Language English
    Publishing date 2019-03-13
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2019.02.007
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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  10. Article ; Online: Tetragonal crystal form of the cyanobacterial bicarbonate-transporter regulator SbtB from Synechocystis sp. PCC 6803.

    Bu, Guanhong / Simmons, Chad R / Nielsen, David R / Nannenga, Brent L

    Acta crystallographica. Section F, Structural biology communications

    2020  Volume 76, Issue Pt 9, Page(s) 438–443

    Abstract: ... The ... ...

    Abstract The P
    MeSH term(s) Amino Acid Sequence ; Anion Transport Proteins/chemistry ; Anion Transport Proteins/genetics ; Anion Transport Proteins/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bicarbonates/chemistry ; Bicarbonates/metabolism ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Synechocystis/chemistry ; Synechocystis/metabolism
    Chemical Substances Anion Transport Proteins ; Bacterial Proteins ; Bicarbonates ; Recombinant Proteins
    Language English
    Publishing date 2020-08-19
    Publishing country United States
    Document type Journal Article
    ISSN 2053-230X
    ISSN (online) 2053-230X
    DOI 10.1107/S2053230X20010523
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