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Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip.

Biosensors & bioelectronics

Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H.
PMID: 21855314
Biosens Bioelectron. 2011 Nov 15;29(1):34-9. doi: 10.1016/j.bios.2011.07.047. Epub 2011 Aug 05.

We describe analysis and control of 50S ribosomal subunits by a solid-state 45nm diameter nanopore incorporated in a microfluidic chip. When used as a resistive pulse sensor, translocation of single 50S subunits through the nanopore produces current blockades that...

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Rudenko MI, Holmes MR, Ermolenko DN, et al. Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron. 2011;29(1):34-9doi: 10.1016/j.bios.2011.07.047.
Rudenko, M. I., Holmes, M. R., Ermolenko, D. N., Lunt, E. J., Gerhardt, S., Noller, H. F., Deamer, D. W., Hawkins, A., & Schmidt, H. (2011). Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosensors & bioelectronics, 29(1), 34-9. https://doi.org/10.1016/j.bios.2011.07.047
Rudenko, Mikhail I, et al. "Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip." Biosensors & bioelectronics vol. 29,1 (2011): 34-9. doi: https://doi.org/10.1016/j.bios.2011.07.047
Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H. Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron. 2011 Nov 15;29(1):34-9. doi: 10.1016/j.bios.2011.07.047. Epub 2011 Aug 05. PMID: 21855314.
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Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli.

Biomacromolecules

Matsumoto K, Hori C, Fujii R, Takaya M, Ooba T, Ooi T, Isono T, Satoh T, Taguchi S.
PMID: 29323923
Biomacromolecules. 2018 Feb 12;19(2):662-671. doi: 10.1021/acs.biomac.7b01768. Epub 2018 Jan 22.

Biological polymer synthetic systems, which utilize no template molecules, normally synthesize random copolymers. We report an exception, a synthesis of block polyhydroxyalkanoates (PHAs) in an engineered Escherichia coli. Using an engineered PHA synthase, block copolymers poly[(R)-2-hydroxybutyrate(2HB)-b-(R)-3-hydroxybutyrate(3HB)] were produced in...

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Matsumoto K, Hori C, Fujii R, et al. Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli. Biomacromolecules. 2018;19(2):662-671doi: 10.1021/acs.biomac.7b01768.
Matsumoto, K., Hori, C., Fujii, R., Takaya, M., Ooba, T., Ooi, T., Isono, T., Satoh, T., & Taguchi, S. (2018). Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli. Biomacromolecules, 19(2), 662-671. https://doi.org/10.1021/acs.biomac.7b01768
Matsumoto, Ken'ichiro, et al. "Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli." Biomacromolecules vol. 19,2 (2018): 662-671. doi: https://doi.org/10.1021/acs.biomac.7b01768
Matsumoto K, Hori C, Fujii R, Takaya M, Ooba T, Ooi T, Isono T, Satoh T, Taguchi S. Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli. Biomacromolecules. 2018 Feb 12;19(2):662-671. doi: 10.1021/acs.biomac.7b01768. Epub 2018 Jan 22. PMID: 29323923.
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Parallel substrate supply and pH stabilization for optimal screening of E. coli with the membrane-based fed-batch shake flask.

Microbial cell factories

Philip P, Kern D, Goldmanns J, Seiler F, Schulte A, Habicher T, Büchs J.
PMID: 29743073
Microb Cell Fact. 2018 May 09;17(1):69. doi: 10.1186/s12934-018-0917-8.

BACKGROUND: Screening in the fed-batch operation mode is essential for biological cultivations facing challenges as oxygen limitation, osmotic inhibition, catabolite repression, substrate inhibition or overflow metabolism. As a screening tool on shake flask level, the membrane-based fed-batch shake flask...

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Philip P, Kern D, Goldmanns J, et al. Parallel substrate supply and pH stabilization for optimal screening of E. coli with the membrane-based fed-batch shake flask. Microb Cell Fact. 2018;17(1):69doi: 10.1186/s12934-018-0917-8.
Philip, P., Kern, D., Goldmanns, J., Seiler, F., Schulte, A., Habicher, T., & Büchs, J. (2018). Parallel substrate supply and pH stabilization for optimal screening of E. coli with the membrane-based fed-batch shake flask. Microbial cell factories, 17(1), 69. https://doi.org/10.1186/s12934-018-0917-8
Philip, P, et al. "Parallel substrate supply and pH stabilization for optimal screening of E. coli with the membrane-based fed-batch shake flask." Microbial cell factories vol. 17,1 (2018): 69. doi: https://doi.org/10.1186/s12934-018-0917-8
Philip P, Kern D, Goldmanns J, Seiler F, Schulte A, Habicher T, Büchs J. Parallel substrate supply and pH stabilization for optimal screening of E. coli with the membrane-based fed-batch shake flask. Microb Cell Fact. 2018 May 09;17(1):69. doi: 10.1186/s12934-018-0917-8. PMID: 29743073; PMCID: PMC5941677.
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Structural biology: solving the T4SS structural mystery.

Nature reviews. Microbiology

Kåhrström CT.
PMID: 24686411
Nat Rev Microbiol. 2014 May;12(5):312. doi: 10.1038/nrmicro3254. Epub 2014 Apr 01.

No abstract available.

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Kåhrström CT. Structural biology: solving the T4SS structural mystery. Nat Rev Microbiol. 2014;12(5):312doi: 10.1038/nrmicro3254.
Kåhrström, C. T. (2014). Structural biology: solving the T4SS structural mystery. Nature reviews. Microbiology, 12(5), 312. https://doi.org/10.1038/nrmicro3254
Kåhrström, Christina Tobin. "Structural biology: solving the T4SS structural mystery." Nature reviews. Microbiology vol. 12,5 (2014): 312. doi: https://doi.org/10.1038/nrmicro3254
Kåhrström CT. Structural biology: solving the T4SS structural mystery. Nat Rev Microbiol. 2014 May;12(5):312. doi: 10.1038/nrmicro3254. Epub 2014 Apr 01. PMID: 24686411.
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Effect of the volume-to-surface ratio of cultures on Escherichia coli growth: an experimental and theoretical analysis.

Current microbiology

Martínez H, Buhse T, Rivera M, Ayala G, Parmananda P, Sánchez J.
PMID: 22532396
Curr Microbiol. 2012 Jul;65(1):60-5. doi: 10.1007/s00284-012-0128-1. Epub 2012 Apr 25.

The growth dynamics of bacterial populations are usually represented by the classical S-shaped profiles composed of lag, exponential and stationary growth phases. Although exceptions to this classical behavior occur, they are normally produced under non-standard conditions such as supply...

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Martínez H, Buhse T, Rivera M, et al. Effect of the volume-to-surface ratio of cultures on Escherichia coli growth: an experimental and theoretical analysis. Curr Microbiol. 2012;65(1):60-5doi: 10.1007/s00284-012-0128-1.
Martínez, H., Buhse, T., Rivera, M., Ayala, G., Parmananda, P., & Sánchez, J. (2012). Effect of the volume-to-surface ratio of cultures on Escherichia coli growth: an experimental and theoretical analysis. Current microbiology, 65(1), 60-5. https://doi.org/10.1007/s00284-012-0128-1
Martínez, Haydee, et al. "Effect of the volume-to-surface ratio of cultures on Escherichia coli growth: an experimental and theoretical analysis." Current microbiology vol. 65,1 (2012): 60-5. doi: https://doi.org/10.1007/s00284-012-0128-1
Martínez H, Buhse T, Rivera M, Ayala G, Parmananda P, Sánchez J. Effect of the volume-to-surface ratio of cultures on Escherichia coli growth: an experimental and theoretical analysis. Curr Microbiol. 2012 Jul;65(1):60-5. doi: 10.1007/s00284-012-0128-1. Epub 2012 Apr 25. PMID: 22532396.
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Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media.

Rapid communications in mass spectrometry : RCM

Chippendale TW, Španěl P, Smith D.
PMID: 21710596
Rapid Commun Mass Spectrom. 2011 Aug 15;25(15):2163-72. doi: 10.1002/rcm.5099.

Preliminary measurements have been made of the volatile compounds emitted by the bacterium E. coli JM109 cultured in the commonly used media Dulbecco's modified Eagle's medium (DMEM) and lysogeny broth (LB) using selected ion flow tube mass spectrometry, SIFT-MS,...

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Chippendale TW, Španěl P, Smith D. Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid Commun Mass Spectrom. 2011;25(15):2163-72doi: 10.1002/rcm.5099.
Chippendale, T. W., Španěl, P., & Smith, D. (2011). Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid communications in mass spectrometry : RCM, 25(15), 2163-72. https://doi.org/10.1002/rcm.5099
Chippendale, Thomas W E, et al. "Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media." Rapid communications in mass spectrometry : RCM vol. 25,15 (2011): 2163-72. doi: https://doi.org/10.1002/rcm.5099
Chippendale TW, Španěl P, Smith D. Time-resolved selected ion flow tube mass spectrometric quantification of the volatile compounds generated by E. coli JM109 cultured in two different media. Rapid Commun Mass Spectrom. 2011 Aug 15;25(15):2163-72. doi: 10.1002/rcm.5099. PMID: 21710596.
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Isolation of detergent-resistant membranes (DRMs) from Escherichia coli.

Analytical biochemistry

Guzmán-Flores JE, Alvarez AF, Poggio S, Gavilanes-Ruiz M, Georgellis D.
PMID: 27984012
Anal Biochem. 2017 Feb 01;518:1-8. doi: 10.1016/j.ab.2016.10.025. Epub 2016 Oct 29.

Lipid rafts or membrane microdomains have been proposed to compartmentalize cellular processes by spatially organizing diverse molecules/proteins in eukaryotic cells. Such membrane microdomains were recently reported to also exist in a few bacterial species. In this work, we report...

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Guzmán-Flores JE, Alvarez AF, Poggio S, et al. Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Anal Biochem. 2016;518:1-8doi: 10.1016/j.ab.2016.10.025.
Guzmán-Flores, J. E., Alvarez, A. F., Poggio, S., Gavilanes-Ruiz, M., & Georgellis, D. (2017). Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Analytical biochemistry, 5181-8. https://doi.org/10.1016/j.ab.2016.10.025
Guzmán-Flores, José E, et al. "Isolation of detergent-resistant membranes (DRMs) from Escherichia coli." Analytical biochemistry vol. 518 (2017): 1-8. doi: https://doi.org/10.1016/j.ab.2016.10.025
Guzmán-Flores JE, Alvarez AF, Poggio S, Gavilanes-Ruiz M, Georgellis D. Isolation of detergent-resistant membranes (DRMs) from Escherichia coli. Anal Biochem. 2017 Feb 01;518:1-8. doi: 10.1016/j.ab.2016.10.025. Epub 2016 Oct 29. PMID: 27984012.
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Exploration of the Tolerance Ability of a Cell-Free Biosynthesis System to Toxic Substances.

Applied biochemistry and biotechnology

Zhang P, Wang J, Ding X, Lin J, Jiang H, Zhou H, Lu Y.
PMID: 31161383
Appl Biochem Biotechnol. 2019 Dec;189(4):1096-1107. doi: 10.1007/s12010-019-03039-5. Epub 2019 Jun 04.

Cell-free synthetic biology has become a robust technology platform for synthesizing proteins and chemicals in recent years. Cell-free synthetic biology system activates biological machinery without the use of living cells, which opens new opportunities for the addition or synthesis...

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Zhang P, Wang J, Ding X, et al. Exploration of the Tolerance Ability of a Cell-Free Biosynthesis System to Toxic Substances. Appl Biochem Biotechnol. 2019;189(4):1096-1107doi: 10.1007/s12010-019-03039-5.
Zhang, P., Wang, J., Ding, X., Lin, J., Jiang, H., Zhou, H., & Lu, Y. (2019). Exploration of the Tolerance Ability of a Cell-Free Biosynthesis System to Toxic Substances. Applied biochemistry and biotechnology, 189(4), 1096-1107. https://doi.org/10.1007/s12010-019-03039-5
Zhang, Peng, et al. "Exploration of the Tolerance Ability of a Cell-Free Biosynthesis System to Toxic Substances." Applied biochemistry and biotechnology vol. 189,4 (2019): 1096-1107. doi: https://doi.org/10.1007/s12010-019-03039-5
Zhang P, Wang J, Ding X, Lin J, Jiang H, Zhou H, Lu Y. Exploration of the Tolerance Ability of a Cell-Free Biosynthesis System to Toxic Substances. Appl Biochem Biotechnol. 2019 Dec;189(4):1096-1107. doi: 10.1007/s12010-019-03039-5. Epub 2019 Jun 04. PMID: 31161383.
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Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis.

Metabolomics : Official journal of the Metabolomic Society

Putri SP, Nakayama Y, Shen C, Noguchi S, Nitta K, Bamba T, Pontrelli S, Liao J, Fukusaki E.
PMID: 30830363
Metabolomics. 2018 Jul 04;14(7):96. doi: 10.1007/s11306-018-1386-0.

INTRODUCTION: Previously constructed Escherichia coli strains that produce 1-propanol use the native threonine pathway, or a heterologous citramalate pathway. However, based on the energy and cofactor requirements of each pathway, a combination of the two pathways produces synergistic effects...

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Putri SP, Nakayama Y, Shen C, et al. Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis. Metabolomics. 2018;14(7):96doi: 10.1007/s11306-018-1386-0.
Putri, S. P., Nakayama, Y., Shen, C., Noguchi, S., Nitta, K., Bamba, T., Pontrelli, S., Liao, J., & Fukusaki, E. (2018). Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis. Metabolomics : Official journal of the Metabolomic Society, 14(7), 96. https://doi.org/10.1007/s11306-018-1386-0
Putri, Sastia Prama, et al. "Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis." Metabolomics : Official journal of the Metabolomic Society vol. 14,7 (2018): 96. doi: https://doi.org/10.1007/s11306-018-1386-0
Putri SP, Nakayama Y, Shen C, Noguchi S, Nitta K, Bamba T, Pontrelli S, Liao J, Fukusaki E. Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis. Metabolomics. 2018 Jul 04;14(7):96. doi: 10.1007/s11306-018-1386-0. PMID: 30830363.
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The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.

Nucleic acids research

Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS.
PMID: 14681416
Nucleic Acids Res. 2004 Jan 01;32:D293-5. doi: 10.1093/nar/gkh108.

The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous...

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Sundararaj S, Guo A, Habibi-Nazhad B, et al. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004;32:D293-5doi: 10.1093/nar/gkh108.
Sundararaj, S., Guo, A., Habibi-Nazhad, B., Rouani, M., Stothard, P., Ellison, M., & Wishart, D. S. (2004). The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic acids research, 32D293-5. https://doi.org/10.1093/nar/gkh108
Sundararaj, Shan, et al. "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli." Nucleic acids research vol. 32 (2004): D293-5. doi: https://doi.org/10.1093/nar/gkh108
Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 2004 Jan 01;32:D293-5. doi: 10.1093/nar/gkh108. PMID: 14681416; PMCID: PMC308842.
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The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers.

The Journal of general and applied microbiology

Mizuno S, Sakurai T, Nabasama M, Kawakami K, Hiroe A, Taguchi S, Tsuge T.
PMID: 33952784
J Gen Appl Microbiol. 2021 Oct 22;67(4):134-141. doi: 10.2323/jgam.2020.09.002. Epub 2021 May 01.

With the aid of a chain transfer (CT) reaction, hydroxyalkanoate (HA) oligomers can be secreted by recombinant Escherichia coli carrying the gene encoding a lactate-polymerizing enzyme (PhaC1

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Mizuno S, Sakurai T, Nabasama M, et al. The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers. J Gen Appl Microbiol. 2021;67(4):134-141doi: 10.2323/jgam.2020.09.002.
Mizuno, S., Sakurai, T., Nabasama, M., Kawakami, K., Hiroe, A., Taguchi, S., & Tsuge, T. (2021). The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers. The Journal of general and applied microbiology, 67(4), 134-141. https://doi.org/10.2323/jgam.2020.09.002
Mizuno, Shoji, et al. "The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers." The Journal of general and applied microbiology vol. 67,4 (2021): 134-141. doi: https://doi.org/10.2323/jgam.2020.09.002
Mizuno S, Sakurai T, Nabasama M, Kawakami K, Hiroe A, Taguchi S, Tsuge T. The influence of medium composition on the microbial secretory production of hydroxyalkanoate oligomers. J Gen Appl Microbiol. 2021 Oct 22;67(4):134-141. doi: 10.2323/jgam.2020.09.002. Epub 2021 May 01. PMID: 33952784.
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