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Becce M, Klöckner A, Higgins SG, Penders J, Hachim D, Bashor CJ, Edwards AM, Stevens MM. Assessing the impact of silicon nanowires on bacterial transformation and viability of Escherichia coli. J Mater Chem B 2021; 9:4906-4914. [PMID: 34100486 PMCID: PMC8221286 DOI: 10.1039/d0tb02762f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/25/2021] [Indexed: 11/21/2022]
Abstract
We investigated the biomaterial interface between the bacteria Escherichia coli DH5α and silicon nanowire patterned surfaces. We optimised the engineering of silicon nanowire coated surfaces using metal-assisted chemical etching. Using a combination of focussed ion beam scanning electron microscopy, and cell viability and transformation assays, we found that with increasing interfacing force, cell viability decreases, as a result of increasing cell rupture. However, despite this aggressive interfacing regime, a proportion of the bacterial cell population remains viable. We found that the silicon nanowires neither resulted in complete loss of cell viability nor partial membrane disruption and corresponding DNA plasmid transformation. Critically, assay choice was observed to be important, as a reduction-based metabolic reagent was found to yield false-positive results on the silicon nanowire substrate. We discuss the implications of these results for the future design and assessment of bacteria-nanostructure interfacing experiments.
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Affiliation(s)
- Michele Becce
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
| | - Anna Klöckner
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College LondonLondonUK
| | - Stuart G. Higgins
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
| | - Jelle Penders
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
| | - Daniel Hachim
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
| | - Caleb J. Bashor
- Department of Bioengineering, Rice UniversityHoustonTexasUSA
| | - Andrew M. Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College LondonLondonUK
| | - Molly M. Stevens
- Department of Materials, Imperial College LondonLondonUK
- Department of Bioengineering, Imperial College LondonLondonUK
- Institute of Biomedical Engineering, Imperial College LondonLondonUK
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Mendes G, Vieira P, Lanceros-Méndez S, Kluskens L, Mota M. Transformation of Escherichia coli JM109 using pUC19 by the Yoshida effect. J Microbiol Methods 2015; 115:1-5. [DOI: 10.1016/j.mimet.2015.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 05/08/2015] [Indexed: 11/25/2022]
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Yuan L, Wang H, Yu Q, Wu Z, Brash JL, Chen H. “Nano-catalyst” for DNA transformation. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm10734h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tan H, Fu L, Seno M. Optimization of bacterial plasmid transformation using nanomaterials based on the Yoshida effect. Int J Mol Sci 2010; 11:4961-72. [PMID: 21614185 PMCID: PMC3100829 DOI: 10.3390/ijms11124962] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 11/15/2010] [Accepted: 12/01/2010] [Indexed: 11/17/2022] Open
Abstract
With the help of sepiolite, a unique method for transforming DNA into bacteria, based on the Yoshida effect, has been developed recently. However, we confronted many problems when this newest method was tried. Only a few transformants could be obtained even when 100 ng of plasmid pET15b was used, and a successful result seemed difficult to repeat. To address this problem, we optimized the operating method and could achieve about 15,000 transformants using the same amount of plasmid, which could match the efficiency gained using the calcium chloride transformation method. Meanwhile, the results could also be reproduced well. In the same way, carbon nanotubes were used to attain more than 15,000 transformants in the same situation. Therefore, the transformation method could be extended to other nanomaterials. Meanwhile, compared with the mechanism previously reported, we verified quite a different principle for the mechanism responsible for such a transformation. In sum, this unique transformation can be developed to become the third widely-used transformation method in laboratories in addition to the chemical method and electroporation.
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Affiliation(s)
- Haidong Tan
- Biotechnology Department, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; E-Mail:
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, State Key Laboratory of Breast Cancer Research, Cancer Hospital of Tianjin Medical University, Tianjin 300060, China; E-Mail:
| | - Masaharu Seno
- Department of Medical and Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
- Author to whom correspondence should be addressed; E-Mail:
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Wilharm G, Lepka D, Faber F, Hofmann J, Kerrinnes T, Skiebe E. A simple and rapid method of bacterial transformation. J Microbiol Methods 2010; 80:215-6. [PMID: 20004690 DOI: 10.1016/j.mimet.2009.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/19/2009] [Accepted: 12/02/2009] [Indexed: 10/20/2022]
Abstract
Recently, a unique method for bacterial transformation using nanofibers to inoculate DNA has been developed by Naoto Yoshida and colleagues. We have verified the principle, transforming Escherichia coli, Yersinia enterocolitica and Acinetobacter baumannii, and have established a user-friendly protocol. A buffered suspension of sepiolite-an inexpensive, fibrous yet inoffensive mineral-is mixed with bacteria and transforming DNA and the mixture directly spread on selective agar.
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Affiliation(s)
- Gottfried Wilharm
- Robert Koch-Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany.
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Yoshida N, Sato M. Plasmid uptake by bacteria: a comparison of methods and efficiencies. Appl Microbiol Biotechnol 2009; 83:791-8. [PMID: 19471921 DOI: 10.1007/s00253-009-2042-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/11/2009] [Accepted: 05/11/2009] [Indexed: 11/29/2022]
Abstract
The ability to introduce individual molecules of plasmid DNA into cells by transformation has been of central importance to the recent rapid advancement of plasmid biology and to the development of DNA cloning methods. Molecular genetic manipulation of bacteria requires the development of plasmid-mediated transformation systems that include (1) chemical transformation, (2) electro-transformation, (3) biolistic transformation, and (4) sonic transformation, leading to the introduction of exogenous plasmid DNA into bacterial cells. In this review, the manipulation properties and transformation efficiencies of these techniques are described. In addition to these methods, a conceptually novel transformation technique, namely the hydrogel exposure method, was developed. The hydrogel exposure method, based on the Yoshida effect, provides a significant advance over chemical means for transforming many strains of Escherichia coli and a variety of other bacterial species. The new term "tribos transformation" has been proposed for this novel technique. We also determined that, compared to conventional methods, the hydrogel exposure method is a novel and convenient method by which to transform bacteria.
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Affiliation(s)
- Naoto Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Gakuen Kibanadai-Nishi, Japan.
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Yoshida N, Fujiura N. Earthquakes promote bacterial genetic exchange in serpentinite crevices. ASTROBIOLOGY 2009; 9:289-295. [PMID: 19368516 DOI: 10.1089/ast.2007.0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the results of our efforts to study the effects of seismic shaking on simulated biofilms within serpentinite fissures. A colloidal solution consisting of recipient bacterial cells (Pseudomonas sp. or Bacillus subtilis), donor plasmid DNA encoded for antibiotic resistance, and chrysotile (an acicular clay mineral that forms in crevices of serpentinite layers) were placed onto an elastic body made from gellan gum, which acted as the biofilm matrix. Silica beads, as rock analogues (i.e., chemically inert mechanical serpentinite), were placed on the gellan surface, which was coated with the colloidal solution. A rolling vibration similar to vibrations generated by earthquakes was applied, and the silica beads moved randomly across the surface of the gellan. This resulted in the recipient cells' acquiring plasmid DNA and thus becoming genetically transformed to demonstrate marked antibiotic resistance. Neither Pseudomonas sp. nor B. subtilis were transformed by plasmid DNA when chrysotile was substituted for by kaolinite or bentonite in the colloidal solution. Tough gellan (1.0%) promoted the introduction of plasmid DNA into Pseudomonas sp., but soft gellan (0.3%) had no such effect. Genetic transformation of bacteria on the surface of gellan by exposure to exogenous plasmid DNA required seismic shaking and exposure to the acicular clay mineral chrysotile. These experimental results suggest that bacterial genetic exchange readily occurs when biofilms that form in crevices of serpentinite are exposed to seismic shaking. Seismic activity may be a key factor in bacterial evolution along with the formation of biofilms within crevices of serpentinite.
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Affiliation(s)
- Naoto Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki-shi, Japan.
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Yoshida N, Ide K. Plasmid DNA is released from nanosized acicular material surface by low molecular weight oligonucleotides: exogenous plasmid acquisition mechanism for penetration intermediates based on the Yoshida effect. Appl Microbiol Biotechnol 2008; 80:813-21. [PMID: 18704395 DOI: 10.1007/s00253-008-1637-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 07/24/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
When a colloidal solution consisting of nanosized acicular material and bacterial cells is stimulated with sliding friction at the interface between the hydrogel and interface-forming material where the frictional coefficient increases rapidly, the nanosized acicular material accompanying the bacterial cells forms a penetration intermediate. This effect is known as the Yoshida effect in honor of its discoverer. Through the Yoshida effect, a novel property in which penetration intermediates incorporate exogenous plasmid DNA has been identified. This report proposes a possible mechanism for exogenous plasmid acquisition by penetration intermediates in the Yoshida effect. Escherichia coli cells, pUC18, and chrysotile were used as recipient cells, plasmid DNA, and nanosized acicular material, respectively. Even when repeatedly washing the mixture consisting of pUC18 and chrysotile, transformation efficiency by pUC18 was stable. Accordingly, pUC18 adsorbed onto chrysotile was introduced into recipient E. coli cells. At saturation, the amount of pUC18 adsorbed onto chrysotile was 0.8-1.2 microg/mg. To investigate whether pUC18 adsorbed on chrysotile is replicated by polymerase, polymerase chain reaction (PCR) was carried out with the chrysotile. Amplification of the beta-lactamase gene coded in pUC18, which was adsorbed onto chrysotile, was strongly inhibited. This suggests that DNA adsorbed onto chrysotile is not replicated in vivo. When we searched for substances to release pUC18 adsorbed onto chrysotile, we found that a 300-bp single- or double-stranded segment of DNA releases pUC18 from chrysotile. Competitive adsorption onto chrysotile between double-stranded DNA and pUC18 was then examined through the Yoshida effect. The 310- and 603-bp double-stranded nucleotides caused 50% competitive inhibition at the same molar ratio with pUC18. Hence, the adsorbed region of pUC18 is about 300 bp in length. As the culture period for recipient cells increases, transformation efficiency decreases while the expression levels of small RNA of 300-600 bp also decrease. These results suggest that pUC18 adsorbed onto chrysotile can be released by 300-bp small RNA, replicated by DNA polymerase, and transferred to daughter cells.
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Affiliation(s)
- N Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Kibanadai-Nishi, Miyazaki, Japan.
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Yoshida N, Takebe K. Quantitative detection of asbestos fiber in gravelly sand using elastic body-exposure method. J Ind Microbiol Biotechnol 2006; 33:827-33. [PMID: 16636778 DOI: 10.1007/s10295-006-0125-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 03/24/2006] [Indexed: 10/24/2022]
Abstract
Chrysotile or crocidolite colloidal solution containing donor plasmid DNA and Escherichia coli cells was subjected to elastic body friction. These acicular clay minerals mediated E. coli antibiotic resistance plasmid transformation. Other clay minerals had no effect on E. coli transformation. The number of E. coli transformants was counted after elastic body exposure with various crocidolite concentrations. There was a correlation between the number of E. coli transformants and crocidolite concentration (between 40 and 1,000 ng/ml). A mixture consisting of sea sand and crocidolite was utilized as a model for quantitative detection of asbestos in gravelly sand. With sea sand containing 0.15-15 mg of crocidolite, a correlation between crocidolite concentration and the number of colonies derived from E. coli transformants was observed. This indicates that measurement of asbestos is possible even when the asbestos sample includes gravelly sand. Fluorescence microscopic observation of crocidolite colloidal solution indicated that crocidolite was present as spherical aggregates having diameters of 6-9 microm. Thus, the number of transformants correlated with that of 6-9 microm crocidolite aggregates.
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Affiliation(s)
- Naoto Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, 1-1Gakuen Kibanadainishi, Miyazaki-shi, 889-2192, Japan.
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