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Title: Increasing access to microfluidics for studying fungi and other branched biological structures

Abstract

Background: Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve “ready-to-use microfluidics.”Results: We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we alsomore » demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.Conclusions: This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10]; ORCiD logo [1]; ORCiD logo [11]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center
  2. Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry and Cellular and Molecular Biology
  4. Duke Univ., Durham, NC (United States). Biology Dept.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  5. Duke Univ., Durham, NC (United States). Biology Dept.
  6. Univ. of California, Davis, CA (United States). Center for Neuroscience
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Inst. national de la recherche agronomique (INRA), Centre INRA-Lorraine, Champenoux (France)
  8. Inst. national de la recherche agronomique (INRA), Centre INRA-Lorraine, Champenoux (France)
  9. Fujian Agricultural and Forestry Univ., Fuzhou City (China)
  10. Michigan State Univ., East Lansing, MI (United States). Dept. of Plant, Soil and Microbial Sciences
  11. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1528740
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Fungal Biology and Biotechnology
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2054-3085
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Millet, Larry J., Aufrecht, Jayde, Labbé, Jessy, Uehling, Jessie, Vilgalys, Rytas, Estes, Myka L., Miquel Guennoc, Cora, Deveau, Aurélie, Olsson, Stefan, Bonito, Gregory, Doktycz, Mitchel John, and Retterer, Scott T. Increasing access to microfluidics for studying fungi and other branched biological structures. United States: N. p., 2019. Web. doi:10.1186/s40694-019-0071-z.
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Millet, Larry J., Aufrecht, Jayde, Labbé, Jessy, Uehling, Jessie, Vilgalys, Rytas, Estes, Myka L., Miquel Guennoc, Cora, Deveau, Aurélie, Olsson, Stefan, Bonito, Gregory, Doktycz, Mitchel John, & Retterer, Scott T. Increasing access to microfluidics for studying fungi and other branched biological structures. United States. https://doi.org/10.1186/s40694-019-0071-z
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Millet, Larry J., Aufrecht, Jayde, Labbé, Jessy, Uehling, Jessie, Vilgalys, Rytas, Estes, Myka L., Miquel Guennoc, Cora, Deveau, Aurélie, Olsson, Stefan, Bonito, Gregory, Doktycz, Mitchel John, and Retterer, Scott T. Mon . "Increasing access to microfluidics for studying fungi and other branched biological structures". United States. https://doi.org/10.1186/s40694-019-0071-z. https://www.osti.gov/servlets/purl/1528740.
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@article{osti_1528740,
title = {Increasing access to microfluidics for studying fungi and other branched biological structures},
author = {Millet, Larry J. and Aufrecht, Jayde and Labbé, Jessy and Uehling, Jessie and Vilgalys, Rytas and Estes, Myka L. and Miquel Guennoc, Cora and Deveau, Aurélie and Olsson, Stefan and Bonito, Gregory and Doktycz, Mitchel John and Retterer, Scott T.},
abstractNote = {Background: Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve “ready-to-use microfluidics.”Results: We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.Conclusions: This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.},
doi = {10.1186/s40694-019-0071-z},
journal = {Fungal Biology and Biotechnology},
number = 1,
volume = 6,
place = {United States},
year = {Mon Jun 10 00:00:00 EDT 2019},
month = {Mon Jun 10 00:00:00 EDT 2019}
}
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journal, March 2010

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Nuclear dynamics in a fungal chimera
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Directional memory arises from long-lived cytoskeletal asymmetries in polarized chemotactic cells
journal, January 2016

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  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 5
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Shining a light on the dark world of plant root–microbe interactions
journal, April 2017

The influence of bacterial interaction on the virulence of Cryptococcus neoformans
journal, September 2015

Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: a widespread ability under controls?
journal, May 2018

  • Miquel Guennoc, Cora; Rose, Christophe; Labbé, Jessy
  • FEMS Microbiology Ecology, Vol. 94, Issue 7
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Bacterial–fungal interactions: ecology, mechanisms and challenges
journal, February 2018

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The RootChip: An Integrated Microfluidic Chip for Plant Science
journal, December 2011

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    Growing a circular economy with fungal biotechnology: a white paper
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