1
|
Xiao M, Lv S, Zhu C. Bacterial Patterning: A Promising Biofabrication Technique. ACS APPLIED BIO MATERIALS 2024. [PMID: 38408887 DOI: 10.1021/acsabm.4c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacterial patterning has emerged as a pivotal biofabrication technique in the biomedical field. In the past 2 decades, a diverse array of bacterial patterning approaches have been developed to enable the precise manipulation of the spatial distribution of bacterial patterns for various applications. Despite the significance of these advancements, there is a deficiency of review articles providing an overview of bacterial patterning technologies. In this mini-review, we systematically summarize the progress of bacterial patterning over the past 2 decades. This review commences with an elucidation of the definition and fundamental principles of bacterial patterning. Subsequently, we introduce the established bacterial patterning strategies, accompanied by discussions about the advantages and limitations of each approach. Furthermore, we showcase the biomedical applications of these strategies, highlighting their efficacy in spatial control of biofilms, biosensing, and biointervention. Finally, this mini-review is concluded with a summary and an outlook on future challenges and opportunities. It is anticipated that this mini-review can serve as a concise guide for those who are interested in this exciting and rapidly evolving research area.
Collapse
Affiliation(s)
- Minghui Xiao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Functional Polymer Materials, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shuyi Lv
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Functional Polymer Materials, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Functional Polymer Materials, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
| |
Collapse
|
2
|
Submicron polymer particles may mask the presence of toxicants in wastewater effluents probed by reporter gene containing bacteria. Sci Rep 2021; 11:7424. [PMID: 33795746 PMCID: PMC8016889 DOI: 10.1038/s41598-021-86672-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/11/2021] [Indexed: 11/08/2022] Open
Abstract
Microplastics are ubiquitous in aquatic systems and break down into submicron particles that can interact with aquatic toxic chemicals. These interactions may affect the detection of toxicants when using bacteria as a biomonitoring tool. This study examined the effects of model polystyrene (PS)-based submicron particles on the detection of aqueous geno- and cytotoxicity by genetically modified bioluminescent (GMB) bacteria. The toxicities were tested in three treated wastewater (TWW) effluents before and after chlorination. The PS plastics included negatively charged sulfate-coated (S-PS) and pristine (P-PS) particles of different sizes (0.1, 0.5, and 1.0 µm) that were present at different concentrations. Chlorinated or not, the S-PS and P-PS particles per se were not toxic to the GMB bacteria. However, exposure of PS particles to TWW effluents can significantly reduce the measured geno- and cytotoxicity. Adsorption of toxic compounds to polymer particles can limit the ability of the bacteria to detect those compounds. This masking effect may be mitigated by TWW chlorination, possibly due to the formation of new toxic material. Due to interactions between toxic TWW constituents and the plastics particles, water samples containing particle-associated contaminants and/or their transformation products may be declared non-toxic, based on bacterial tests as a biomonitoring tool.
Collapse
|
3
|
Alsharif N, Uzarski JR, Lawton TJ, Brown KA. High-Throughput Multiobjective Optimization of Patterned Multifunctional Surfaces. ACS APPLIED MATERIALS & INTERFACES 2020; 12:32069-32077. [PMID: 32551476 DOI: 10.1021/acsami.0c04202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The realization and optimization of multifunctional materials is difficult, especially when the functionalities are directly incompatible. For example, it is challenging to make surfaces both enzymatically active and water repellent, as these two properties are directly competitive because of the hydrophilic nature of the enzyme-laden surfaces. Patterning discrete domains of distinct functionalities can represent a path to multifunctionality, but the innumerable possible domain permutations present a major barrier to optimizing performance. Here, we develop a high-throughput approach for exploring patterned multifunctional surfaces that is inspired by the microtiter plate architecture. As a model system, patterned surfaces are realized with horseradish peroxidase-decorated domains amidst a background of hydrophobic fluorinated self-assembled monolayers. In experiments exploring effects of pattern geometry, the measured enzyme activity is dependent only on the surface coverage. In contrast, roll-off behavior strongly depends on the parameters of the pattern geometry. Importantly, this finding enables the precise tailoring of distinct wetting behavior of the surfaces in a manner that is independent of their enzymatic activity. The high-throughput nature of the platform facilitates multiobjective optimization of surface functionalities in a general and flexible manner.
Collapse
Affiliation(s)
- Nourin Alsharif
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Joshua R Uzarski
- Soldier Protection and Survivability Directorate, US Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- Soldier Protection and Survivability Directorate, US Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Keith A Brown
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Physics Department and Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| |
Collapse
|
4
|
Hicks M, Bachmann TT, Wang B. Synthetic Biology Enables Programmable Cell-Based Biosensors. Chemphyschem 2020; 21:132-144. [PMID: 31585026 PMCID: PMC7004036 DOI: 10.1002/cphc.201900739] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/03/2019] [Indexed: 01/10/2023]
Abstract
Cell-based biosensors offer cheap, portable and simple methods of detecting molecules of interest but have yet to be truly adopted commercially. Issues with their performance and specificity initially slowed the development of cell-based biosensors. With the development of rational approaches to tune response curves, the performance of biosensors has rapidly improved and there are now many biosensors capable of sensing with the required performance. This has stimulated an increased interest in biosensors and their commercial potential. However the reliability, long term stability and biosecurity of these sensors are still barriers to commercial application and public acceptance. Research into overcoming these issues remains active. Here we present the state-of-the-art tools offered by synthetic biology to allow construction of cell-based biosensors with customisable performance to meet the real world requirements in terms of sensitivity and dynamic range and discuss the research progress to overcome the challenges in terms of the sensor stability and biosecurity fears.
Collapse
Affiliation(s)
- Maggie Hicks
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
| | - Till T. Bachmann
- Infection MedicineEdinburgh Medical School: Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Baojun Wang
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
| |
Collapse
|
5
|
Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition. Cell Host Microbe 2019; 25:128-139.e5. [PMID: 30629913 DOI: 10.1016/j.chom.2018.12.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/20/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022]
Abstract
Neonates are highly susceptible to infection with enteric pathogens, but the underlying mechanisms are not resolved. We show that neonatal chick colonization with Salmonella enterica serovar Enteritidis requires a virulence-factor-dependent increase in epithelial oxygenation, which drives pathogen expansion by aerobic respiration. Co-infection experiments with an Escherichia coli strain carrying an oxygen-sensitive reporter suggest that S. Enteritidis competes with commensal Enterobacteriaceae for oxygen. A combination of Enterobacteriaceae and spore-forming bacteria, but not colonization with either community alone, confers colonization resistance against S. Enteritidis in neonatal chicks, phenocopying germ-free mice associated with adult chicken microbiota. Combining spore-forming bacteria with a probiotic E. coli isolate protects germ-free mice from pathogen colonization, but the protection is lost when the ability to respire oxygen under micro-aerophilic conditions is genetically ablated in E. coli. These results suggest that commensal Enterobacteriaceae contribute to colonization resistance by competing with S. Enteritidis for oxygen, a resource critical for pathogen expansion.
Collapse
|
6
|
Chang B, Kivinen O, Pini I, Levkin PA, Ras RHA, Zhou Q. Nanoliter deposition on star-shaped hydrophilic-superhydrophobic patterned surfaces. SOFT MATTER 2018; 14:7500-7506. [PMID: 30152827 DOI: 10.1039/c8sm01288a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanoliter sized droplet deposition has gained increasing importance in many biomedical, chemical, and microfluidic applications and in materials synthesis. In this paper, we report a simple method for rapid and high-throughput deposition of nanoliter-sized droplets by dragging a larger droplet on star-shaped hydrophilic-superhydrophobic patterned surfaces. Dragging a droplet on the patterned surface causes water to adhere to hydrophilic patterns. As the larger mother droplet detaches from a star-shaped pattern, a small daughter droplet is deposited on the pattern. Star-shaped hydrophilic patterns with a distinct number of spikes are fabricated and investigated. Systematic tests are carried out to study the influence of different process parameters including the volume of a mother droplet, the dragging velocity, the number of spikes and the dragging directions to the deposition process. The results indicate that creating microarrays by dragging large droplets on patterned hydrophilic-superhydrophobic surfaces yield a reliable, cost-efficient, high-accuracy and easily scalable deposition. The volume of the daughter droplet grows with the velocity of the mother droplet and the number of spikes in a pattern, and decreases with the volume of the mother droplet.
Collapse
Affiliation(s)
- Bo Chang
- College of Mechanical and Electrical Engineering, Shaanxi University of Science and Technology, Xi'An 710021, P. R. China
| | | | | | | | | | | |
Collapse
|
7
|
Roggo C, van der Meer JR. Miniaturized and integrated whole cell living bacterial sensors in field applicable autonomous devices. Curr Opin Biotechnol 2017; 45:24-33. [PMID: 28088093 DOI: 10.1016/j.copbio.2016.11.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 11/19/2022]
Abstract
Live-cell based bioreporters are increasingly being deployed in microstructures, which facilitates their handling and permits the development of instruments that could perform autonomous environmental monitoring. Here we review recent developments of on-chip integration of live-cell bioreporters, the coupling of their reporter signal to the devices, their longer term preservation and multi-analyte capacity. We show examples of instruments that have attempted to fully integrate bioreporters as their sensing elements.
Collapse
Affiliation(s)
- Clémence Roggo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | | |
Collapse
|
8
|
van der Meer JR. Towards improved biomonitoring tools for an intensified sustainable multi-use environment. Microb Biotechnol 2016; 9:658-65. [PMID: 27468753 PMCID: PMC4993185 DOI: 10.1111/1751-7915.12395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 07/10/2016] [Indexed: 11/28/2022] Open
Abstract
The increasing use of our environment for multiple contrasting activities (e.g. fisheries, tourism) will have to be accompanied by improved monitoring of environmental quality, to avoid transboundary conflicts and ensure long-term sustainable intensified usage. Biomonitoring approaches are appropriate for this, since they can integrate biological effects of environmental exposure rather than measure individual compound concentrations. Recent advances in biomonitoring concepts and tools focus on single-cell assays and purified biological components that can be miniaturized and integrated in automated systems. Despite these advances, we are still very far from being able to deploy bioassays routinely in environmental monitoring, mostly because of lack of experience in interpreting responses and insufficient robustness of the biosensors for their environmental application. Further future challenges include broadening the spectrum of detectable compounds by biosensors, accelerate response times and combining sample pretreatment strategies with bioassays.
Collapse
|
9
|
Derkus B. Applying the miniaturization technologies for biosensor design. Biosens Bioelectron 2016; 79:901-13. [DOI: 10.1016/j.bios.2016.01.033] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 12/11/2022]
|
10
|
Abstract
There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.
Collapse
|
11
|
Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays. BIOMED RESEARCH INTERNATIONAL 2015; 2015:182107. [PMID: 26436087 PMCID: PMC4576000 DOI: 10.1155/2015/182107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/26/2015] [Indexed: 11/21/2022]
Abstract
Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes.
Collapse
|
12
|
Velema WA, van der Berg JP, Szymanski W, Driessen AJM, Feringa BL. Bacterial patterning controlled by light exposure. Org Biomol Chem 2015; 13:1639-42. [PMID: 25530471 DOI: 10.1039/c4ob02483d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Patterning of multiple bacterial strains in one system is achieved by employing a single photo-activated antibiotic. Varying the light-exposure time results in zones with mixed and single populations.
Collapse
Affiliation(s)
- Willem A Velema
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | | | | | | | | |
Collapse
|
13
|
Jia K, Ionescu RE. Measurement of Bacterial Bioluminescence Intensity and Spectrum: Current Physical Techniques and Principles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 154:19-45. [PMID: 25981856 DOI: 10.1007/10_2015_324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed.
Collapse
Affiliation(s)
- Kun Jia
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France
| | - Rodica Elena Ionescu
- Laboratoire de Nanotechnologie et d'Instrumentation Optique, Institut Charles Delaunay, Université de Technologie de Troyes, UMR CNRS 6281, 12 rue Marie Curie CS 42060, TROYES, 10004 Cedex, France.
| |
Collapse
|
14
|
Yagur-Kroll S, Schreuder E, Ingham CJ, Heideman R, Rosen R, Belkin S. A miniature porous aluminum oxide-based flow-cell for online water quality monitoring using bacterial sensor cells. Biosens Bioelectron 2015; 64:625-32. [DOI: 10.1016/j.bios.2014.09.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
|
15
|
Pannier A, Soltmann U, Soltmann B, Altenburger R, Schmitt-Jansen M. Alginate/silica hybrid materials for immobilization of green microalgae Chlorella vulgaris for cell-based sensor arrays. J Mater Chem B 2014; 2:7896-7909. [DOI: 10.1039/c4tb00944d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Ge X, Eleftheriou NM, Dahoumane SA, Brennan JD. Sol–Gel-Derived Materials for Production of Pin-Printed Reporter Gene Living-Cell Microarrays. Anal Chem 2013; 85:12108-17. [DOI: 10.1021/ac403220g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xin Ge
- Biointerfaces
Institute and Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada L8S 4L8
- Department
of Chemical and Environmental Engineering, University of California, Riverside, CA 92521
| | - Nikolas M. Eleftheriou
- Biointerfaces
Institute and Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada L8S 4L8
- Department
of Laboratory Medicine, Lund University, Lund, Sweden
| | - Si Amar Dahoumane
- Biointerfaces
Institute and Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada L8S 4L8
| | - John D. Brennan
- Biointerfaces
Institute and Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada L8S 4L8
| |
Collapse
|
17
|
Improved detection of antibiotic compounds by bacterial reporter strains achieved by manipulations of membrane permeability and efflux capacity. Appl Microbiol Biotechnol 2013; 98:2267-77. [PMID: 23963273 DOI: 10.1007/s00253-013-5176-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/20/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
The occurrence of pharmaceuticals, including antibacterial compounds, in the environment has been acknowledged as an emerging and troubling issue in environmental safety; their usage is constantly on the rise, and their effects on the environment are only partially understood. Such compounds can accumulate, contaminate the ecosystem, and contribute to the spreading of antibiotic resistance among bacteria, hindering human health. Bioluminescent Escherichia coli reporter strains, engineered to detect antibiotic compounds by fusing the promoter of the global regulator soxS to the Photorhabdus luminescens luxCDABE cassette, were further modified by altering their membrane permeability and efflux capabilities. This was accomplished by introducing several mutations in the efflux system (ΔemrE, ΔacrB, and ΔtolC) and by overexpressing OmpF, a porin located in the outer membrane that allows passive diffusion of molecules. Combinations of these alterations had a cumulative effect in lowering the detection threshold of several antibiotics, in some of the cases to concentrations reported from pharmaceutical-polluted environments.
Collapse
|
18
|
Nwankire CE, Donohoe GG, Zhang X, Siegrist J, Somers M, Kurzbuch D, Monaghan R, Kitsara M, Burger R, Hearty S, Murrell J, Martin C, Rook M, Barrett L, Daniels S, McDonagh C, O’Kennedy R, Ducrée J. At-line bioprocess monitoring by immunoassay with rotationally controlled serial siphoning and integrated supercritical angle fluorescence optics. Anal Chim Acta 2013; 781:54-62. [DOI: 10.1016/j.aca.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/28/2013] [Accepted: 04/08/2013] [Indexed: 12/25/2022]
|
19
|
Merulla D, Buffi N, Beggah S, Truffer F, Geiser M, Renaud P, van der Meer JR. Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem. Curr Opin Biotechnol 2013; 24:534-41. [DOI: 10.1016/j.copbio.2012.09.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 08/17/2012] [Accepted: 09/02/2012] [Indexed: 11/28/2022]
|
20
|
Drogue B, Thomas P, Balvay L, Prigent-Combaret C, Dorel C. Engineering adherent bacteria by creating a single synthetic curli operon. J Vis Exp 2012. [PMID: 23183588 DOI: 10.3791/4176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The method described here consists in redesigning E. coli adherence properties by assembling the minimum number of curli genes under the control of a strong and metal-overinducible promoter, and in visualizing and quantifying the resulting gain of bacterial adherence. This method applies appropriate engineering principles of abstraction and standardization of synthetic biology, and results in the BBa_K540000 Biobrick (Best new Biobrick device, engineered, iGEM 2011). The first step consists in the design of the synthetic operon devoted to curli overproduction in response to metal, and therefore in increasing the adherence abilities of the wild type strain. The original curli operon was modified in silico in order to optimize transcriptional and translational signals and escape the "natural" regulation of curli. This approach allowed to test with success our current understanding of curli production. Moreover, simplifying the curli regulation by switching the endogenous complex promoter (more than 10 transcriptional regulators identified) to a simple metal-regulated promoter makes adherence much easier to control. The second step includes qualitative and quantitative assessment of adherence abilities by implementation of simple methods. These methods are applicable to a large range of adherent bacteria regardless of biological structures involved in biofilm formation. Adherence test in 24-well polystyrene plates provides a quick preliminary visualization of the bacterial biofilm after crystal violet staining. This qualitative test can be sharpened by the quantification of the percentage of adherence. Such a method is very simple but more accurate than only crystal violet staining as described previously with both a good repeatability and reproducibility. Visualization of GFP-tagged bacteria on glass slides by fluorescence or laser confocal microscopy allows to strengthen the results obtained with the 24-well plate test by direct observation of the phenomenon.
Collapse
Affiliation(s)
- Benoît Drogue
- UMR CNRS 5557 Ecologie Microbienne, Université Lyon 1, Université de Lyon
| | | | | | | | | |
Collapse
|
21
|
Melamed S, Lalush C, Elad T, Yagur‐Kroll S, Belkin S, Pedahzur R. A bacterial reporter panel for the detection and classification of antibiotic substances. Microb Biotechnol 2012; 5:536-48. [PMID: 22385678 PMCID: PMC3815330 DOI: 10.1111/j.1751-7915.2012.00333.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/25/2012] [Indexed: 12/05/2022] Open
Abstract
The ever-growing use of pharmaceutical compounds, including antibacterial substances, poses a substantial pollution load on the environment. Such compounds can compromise water quality, contaminate soils, livestock and crops, enhance resistance of microorganisms to antibiotic substances, and hamper human health. We report the construction of a novel panel of genetically engineered Escherichia coli reporter strains for the detection and classification of antibiotic substances. Each of these strains harbours a plasmid that carries a fusion of a selected gene promoter to bioluminescence (luxCDABE) reporter genes and an alternative tryptophan auxotrophy-based non-antibiotic selection system. The bioreporter panel was tested for sensitivity and responsiveness to diverse antibiotic substances by monitoring bioluminescence as a function of time and of antibiotic concentrations. All of the tested antibiotics were detected by the panel, which displayed different response patterns for each substance. These unique responses were analysed by several algorithms that enabled clustering the compounds according to their functional properties, and allowed the classification of unknown antibiotic substances with a high degree of accuracy and confidence.
Collapse
Affiliation(s)
- Sahar Melamed
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chaim Lalush
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tal Elad
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Sharon Yagur‐Kroll
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rami Pedahzur
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Environmental Sciences, Hadassah Academic College, Jerusalem, Israel
| |
Collapse
|
22
|
Hesselman MC, Odoni DI, Ryback BM, de Groot S, van Heck RGA, Keijsers J, Kolkman P, Nieuwenhuijse D, van Nuland YM, Sebus E, Spee R, de Vries H, Wapenaar MT, Ingham CJ, Schroën K, Martins dos Santos VAP, Spaans SK, Hugenholtz F, van Passel MWJ. A multi-platform flow device for microbial (co-) cultivation and microscopic analysis. PLoS One 2012; 7:e36982. [PMID: 22606321 PMCID: PMC3351485 DOI: 10.1371/journal.pone.0036982] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/11/2012] [Indexed: 01/06/2023] Open
Abstract
Novel microbial cultivation platforms are of increasing interest to researchers in academia and industry. The development of materials with specialized chemical and geometric properties has opened up new possibilities in the study of previously unculturable microorganisms and has facilitated the design of elegant, high-throughput experimental set-ups. Within the context of the international Genetically Engineered Machine (iGEM) competition, we set out to design, manufacture, and implement a flow device that can accommodate multiple growth platforms, that is, a silicon nitride based microsieve and a porous aluminium oxide based microdish. It provides control over (co-)culturing conditions similar to a chemostat, while allowing organisms to be observed microscopically. The device was designed to be affordable, reusable, and above all, versatile. To test its functionality and general utility, we performed multiple experiments with Escherichia coli cells harboring synthetic gene circuits and were able to quantitatively study emerging expression dynamics in real-time via fluorescence microscopy. Furthermore, we demonstrated that the device provides a unique environment for the cultivation of nematodes, suggesting that the device could also prove useful in microscopy studies of multicellular microorganisms.
Collapse
Affiliation(s)
| | - Dorett I. Odoni
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Brendan M. Ryback
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Suzette de Groot
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Ruben G. A. van Heck
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Jaap Keijsers
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Pim Kolkman
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - David Nieuwenhuijse
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Youri M. van Nuland
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Erik Sebus
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Rob Spee
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Hugo de Vries
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Marten T. Wapenaar
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | | | - Karin Schroën
- Food Process Engineering, Wageningen University, Wageningen, The Netherlands
| | | | - Sebastiaan K. Spaans
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Floor Hugenholtz
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Mark W. J. van Passel
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| |
Collapse
|
23
|
Melamed S, Elad T, Belkin S. Microbial sensor cell arrays. Curr Opin Biotechnol 2012; 23:2-8. [DOI: 10.1016/j.copbio.2011.11.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 11/16/2011] [Accepted: 11/23/2011] [Indexed: 11/29/2022]
|
24
|
Staying alive: new perspectives on cell immobilization for biosensing purposes. Anal Bioanal Chem 2011; 402:1785-97. [PMID: 21922308 DOI: 10.1007/s00216-011-5364-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/10/2011] [Accepted: 08/24/2011] [Indexed: 01/09/2023]
|