A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis
Publication Date
May 14, 2012
Journal
PLOS ONE
Authors
Matthijn C. Hesselman, Dorett I. Odoni, Brendan M. Ryback, Suzette De Groot, et al
Volume
7
Issue
5
Pages
e36982
DOI
https://dx.plos.org/10.1371/journal.pone.0036982
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0036982
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22606321
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351485
Europe PMC
http://europepmc.org/abstract/MED/22606321
Web of Science
000305339400050
Scopus
84861008844
Mendeley
http://www.mendeley.com/research/multiplatform-flow-device-microbial-co-cultivation-microscopic-analysis
Events
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Mendeley | Further Information

{"title"=>"A multi-platform flow device for microbial (co-) cultivation and microscopic analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Matthijn C.", "last_name"=>"Hesselman", "scopus_author_id"=>"55216562800"}, {"first_name"=>"Dorett I.", "last_name"=>"Odoni", "scopus_author_id"=>"55216562600"}, {"first_name"=>"Brendan M.", "last_name"=>"Ryback", "scopus_author_id"=>"55216767400"}, {"first_name"=>"Suzette", "last_name"=>"de Groot", "scopus_author_id"=>"55216613900"}, {"first_name"=>"Ruben G A", "last_name"=>"van Heck", "scopus_author_id"=>"55216728600"}, {"first_name"=>"Jaap", "last_name"=>"Keijsers", "scopus_author_id"=>"41561594400"}, {"first_name"=>"Pim", "last_name"=>"Kolkman", "scopus_author_id"=>"55216726200"}, {"first_name"=>"David", "last_name"=>"Nieuwenhuijse", "scopus_author_id"=>"55216562900"}, {"first_name"=>"Youri M.", "last_name"=>"van Nuland", "scopus_author_id"=>"55216830500"}, {"first_name"=>"Erik", "last_name"=>"Sebus", "scopus_author_id"=>"55216563000"}, {"first_name"=>"Rob", "last_name"=>"Spee", "scopus_author_id"=>"55216365200"}, {"first_name"=>"Hugo", "last_name"=>"de Vries", "scopus_author_id"=>"55216474700"}, {"first_name"=>"Marten T.", "last_name"=>"Wapenaar", "scopus_author_id"=>"55216605400"}, {"first_name"=>"Colin J.", "last_name"=>"Ingham", "scopus_author_id"=>"7004372711"}, {"first_name"=>"Karin", "last_name"=>"Schroën", "scopus_author_id"=>"6603871712"}, {"first_name"=>"Vítor A P", "last_name"=>"Martins dos Santos", "scopus_author_id"=>"6506726905"}, {"first_name"=>"Sebastiaan K.", "last_name"=>"Spaans", "scopus_author_id"=>"55216563300"}, {"first_name"=>"Floor", "last_name"=>"Hugenholtz", "scopus_author_id"=>"37121914900"}, {"first_name"=>"Mark W J", "last_name"=>"van Passel", "scopus_author_id"=>"9640076400"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84861008844", "sgr"=>"84861008844", "pui"=>"364803142", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22606321", "doi"=>"10.1371/journal.pone.0036982"}, "id"=>"d6925e92-b36e-32e5-ad6d-47c3f0b40631", "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.", "link"=>"http://www.mendeley.com/research/multiplatform-flow-device-microbial-co-cultivation-microscopic-analysis", "reader_count"=>58, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>12, "Student > Doctoral Student"=>2, "Student > Ph. D. 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Student"=>22, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>3, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>28, "Design"=>1, "Chemical Engineering"=>2, "Physics and Astronomy"=>2, "Chemistry"=>7, "Computer Science"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>7}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>4, "Portugal"=>1, "Switzerland"=>1, "Germany"=>1, "Spain"=>1}, "group_count"=>6}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/639932"], "description"=>"<p>Fluorescent <i>E. coli</i> cells in the wells of the microdish showing variations in signal strength over time. The graph depicts variations plotted with the image analysis and processing tool ImageJ. The x-axis represents time, and the y-axis represents fluorescence (in arbitrary units and with a variance of maximally 0.01 for the normalised data of 5 wells). Below the graph are microscopic images of fluorescent bacteria in the cultivation chip wells at different intervals using identical illumination conditions and CCD camera exposure times. The time points at which the images were taken are indicated with an asterisk.</p>", "links"=>[], "tags"=>["gfp", "observed", "microdish"], "article_id"=>310398, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.g003", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oscillating_GFP_expression_observed_in_microdish_wells_/310398", "title"=>"Oscillating GFP expression observed in microdish wells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-14 00:06:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/640016"], "description"=>"<p>Increase of GFP expression of inducible cells on the sieve after inoculation of inducer cells below. Graph plotted with the image analysis and processing tool ImageJ. The x-axis corresponds to time and the y-axis shows the detected GFP signal (in arbitrary units). Below: a number of representative images of the microsieve. The time points at which the images were taken are indicated with an asterisk.</p>", "links"=>[], "tags"=>["cells", "separated"], "article_id"=>310491, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.g004", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Co_cultivation_of_cells_separated_by_a_microsieve_/310491", "title"=>"Co-cultivation of cells separated by a microsieve.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-14 00:08:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/640358"], "description"=>"*<p>co-cultivated with RFP containing BioBrick part as control for leakage.</p>", "links"=>[], "tags"=>["biobrick", "parts"], "article_id"=>310825, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.t001", "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_BioBrick_parts_used_/310825", "title"=>"Overview of the BioBrick parts used.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-14 00:13:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/329811"], "description"=>"<div><p>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 <em>Escherichia coli</em> 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.</p> </div>", "links"=>[], "tags"=>["multi-platform", "microbial", "cultivation", "microscopic"], "article_id"=>125108, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Multi_Platform_Flow_Device_for_Microbial_Co_Cultivation_and_Microscopic_Analysis/125108", "title"=>"A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-14 01:25:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/640251"], "description"=>"<p>A) Nematodes floating over the wells while the chamber is filled with liquid. The fluorescent oesophagus in the front side of the nematode is clearly visible. B) Nematode trapped in a well filled with fluorescent <i>E. coli</i> cells after removing the liquid from the chamber. C) Next day: A nematode after consuming all fluorescent bacteria from the well, resulting in observable fluorescence in the nematode intestine.</p>", "links"=>[], "tags"=>["nematodes", "observed"], "article_id"=>310718, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.g006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fluorescent_nematodes_observed_in_the_flow_device_/310718", "title"=>"Fluorescent nematodes observed in the flow device.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-14 00:11:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/639845"], "description"=>"<p>Retained clusters of fluorescent <i>E. coli</i> cells on the sieve (100x magnification). The diagonal light grey bands are the permeable areas of the microsieve that contain the pores.</p>", "links"=>[], "tags"=>["retention"], "article_id"=>310315, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cell_retention_on_the_microsieve_/310315", "title"=>"Cell retention on the microsieve.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-14 00:05:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/639744"], "description"=>"<p>A) Schematic representation of the flow device, with the dimensions in mm. Depicted in red and blue are the in- and outflow channels of the top compartment (light green). The respective in- and outflow channels of the lower compartment (yellow) are given in purple and dark green. B) Electron microscopy image of a microsieve. C) Electron microscopy image of a microdish. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036982#pone.0036982.s001\" target=\"_blank\">File S1</a> for more views of the device.</p>", "links"=>[], "tags"=>["microbiology", "biotechnology", "ecology", "developmental biology"], "article_id"=>310209, "categories"=>["Microbiology", "Biotechnology", "Ecology", "Developmental Biology"], "users"=>["Matthijn C. Hesselman", "Dorett I. Odoni", "Brendan M. Ryback", "Suzette de Groot", "Ruben G. A. van Heck", "Jaap Keijsers", "Pim Kolkman", "David Nieuwenhuijse", "Youri M. van Nuland", "Erik Sebus", "Rob Spee", "Hugo de Vries", "Marten T. Wapenaar", "Colin J. Ingham", "Karin Schroën", "Vítor A. P. Martins dos Santos", "Sebastiaan K. Spaans", "Floor Hugenholtz", "Mark W. J. van Passel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036982.g001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_flow_device_/310209", "title"=>"Schematic representation of the flow device.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-14 00:03:29"}

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Relative Metric

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