1
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Kocalar S, Miller BM, Huang A, Gleason E, Martin K, Foley K, Copeland DS, Jewett MC, Saavedra EA, Kraves S. Validation of Cell-Free Protein Synthesis Aboard the International Space Station. ACS Synth Biol 2024; 13:942-950. [PMID: 38442491 PMCID: PMC10949350 DOI: 10.1021/acssynbio.3c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand synthesis of peptide-based vaccines and biotherapeutics as well as the development of diagnostic tests for environmental contaminants and infectious agents. Unlike traditional cell-based systems, CFPS platforms do not require the maintenance of living cells and can be deployed with minimal equipment; therefore, they hold promise for applications in low-resource contexts, including spaceflight. Here, we evaluate the performance of the cell-free platform BioBits aboard the International Space Station by expressing RNA-based aptamers and fluorescent proteins that can serve as biological indicators. We validate two classes of biological sensors that detect either the small-molecule DFHBI or a specific RNA sequence. Upon detection of their respective analytes, both biological sensors produce fluorescent readouts that are visually confirmed using a hand-held fluorescence viewer and imaged for quantitative analysis. Our findings provide insights into the kinetics of cell-free transcription and translation in a microgravity environment and reveal that both biosensors perform robustly in space. Our findings lay the groundwork for portable, low-cost applications ranging from point-of-care health monitoring to on-demand detection of environmental hazards in low-resource communities both on Earth and beyond.
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Affiliation(s)
- Selin Kocalar
- Leigh
High School, 5210 Leigh
Ave, San Jose, California 95124, United States
- Massachusetts
Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Bess M. Miller
- Division
of Genetics, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis St, Boston, Massachusetts 02115, United States
| | - Ally Huang
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Emily Gleason
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kathryn Martin
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
| | - Kevin Foley
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - D. Scott Copeland
- Boeing
Defense, Space & Security, 6398 Upper Brandon Dr, Houston, Texas 77058, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | | | - Sebastian Kraves
- miniPCR
bio, 1770 Massachusetts
Ave, Cambridge, Massachusetts 02140, United States
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2
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Misquitta K, Miller BM, Malecek K, Gleason E, Martin K, Walesky CM, Foley K, Copeland DS, Saavedra EA, Kraves S. A fluorescence viewer for rapid molecular assay readout in space and low-resource terrestrial environments. PLoS One 2024; 19:e0291158. [PMID: 38489299 PMCID: PMC10942025 DOI: 10.1371/journal.pone.0291158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/07/2023] [Indexed: 03/17/2024] Open
Abstract
Fluorescence-based assays provide sensitive and adaptable methods for point of care testing, environmental monitoring, studies of protein abundance and activity, and a wide variety of additional applications. Currently, their utility in remote and low-resource environments is limited by the need for technically complicated or expensive instruments to read out fluorescence signal. Here we describe the Genes in Space Fluorescence Viewer (GiS Viewer), a portable, durable viewer for rapid molecular assay readout that can be used to visualize fluorescence in the red and green ranges. The GiS Viewer can be used to visualize any assay run in standard PCR tubes and contains a heating element. Results are visible by eye or can be imaged with a smartphone or tablet for downstream quantification. We demonstrate the capabilities of the GiS Viewer using two case studies-detection of SARS-CoV-2 RNA using RT-LAMP and quantification of drug-induced changes in gene expression via qRT-PCR on Earth and aboard the International Space Station. We show that the GiS Viewer provides a reliable method to visualize fluorescence in space without the need to return samples to Earth and can further be used to assess the results of RT-LAMP and qRT-PCR assays on Earth.
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Affiliation(s)
| | - Bess M. Miller
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Kathryn Malecek
- Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Emily Gleason
- miniPCR bio, Cambridge, MA, United States of America
| | | | - Chad M. Walesky
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Kevin Foley
- Boeing Defense, Space & Security, Berkeley, MO, United States of America
| | - D. Scott Copeland
- Boeing Defense, Space & Security, Berkeley, MO, United States of America
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3
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Spry JA, Siegel B, Bakermans C, Beaty DW, Bell MS, Benardini JN, Bonaccorsi R, Castro-Wallace SL, Coil DA, Coustenis A, Doran PT, Fenton L, Fidler DP, Glass B, Hoffman SJ, Karouia F, Levine JS, Lupisella ML, Martin-Torres J, Mogul R, Olsson-Francis K, Ortega-Ugalde S, Patel MR, Pearce DA, Race MS, Regberg AB, Rettberg P, Rummel JD, Sato KY, Schuerger AC, Sefton-Nash E, Sharkey M, Singh NK, Sinibaldi S, Stabekis P, Stoker CR, Venkateswaran KJ, Zimmerman RR, Zorzano-Mier MP. Planetary Protection Knowledge Gap Closure Enabling Crewed Missions to Mars. ASTROBIOLOGY 2024; 24:230-274. [PMID: 38507695 DOI: 10.1089/ast.2023.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
As focus for exploration of Mars transitions from current robotic explorers to development of crewed missions, it remains important to protect the integrity of scientific investigations at Mars, as well as protect the Earth's biosphere from any potential harmful effects from returned martian material. This is the discipline of planetary protection, and the Committee on Space Research (COSPAR) maintains the consensus international policy and guidelines on how this is implemented. Based on National Aeronautics and Space Administration (NASA) and European Space Agency (ESA) studies that began in 2001, COSPAR adopted principles and guidelines for human missions to Mars in 2008. At that point, it was clear that to move from those qualitative provisions, a great deal of work and interaction with spacecraft designers would be necessary to generate meaningful quantitative recommendations that could embody the intent of the Outer Space Treaty (Article IX) in the design of such missions. Beginning in 2016, COSPAR then sponsored a multiyear interdisciplinary meeting series to address planetary protection "knowledge gaps" (KGs) with the intent of adapting and extending the current robotic mission-focused Planetary Protection Policy to support the design and implementation of crewed and hybrid exploration missions. This article describes the outcome of the interdisciplinary COSPAR meeting series, to describe and address these KGs, as well as identify potential paths to gap closure. It includes the background scientific basis for each topic area and knowledge updates since the meeting series ended. In particular, credible solutions for KG closure are described for the three topic areas of (1) microbial monitoring of spacecraft and crew health; (2) natural transport (and survival) of terrestrial microbial contamination at Mars, and (3) the technology and operation of spacecraft systems for contamination control. The article includes a KG data table on these topic areas, which is intended to be a point of departure for making future progress in developing an end-to-end planetary protection requirements implementation solution for a crewed mission to Mars. Overall, the workshop series has provided evidence of the feasibility of planetary protection implementation for a crewed Mars mission, given (1) the establishment of needed zoning, emission, transport, and survival parameters for terrestrial biological contamination and (2) the creation of an accepted risk-based compliance approach for adoption by spacefaring actors including national space agencies and commercial/nongovernment organizations.
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Affiliation(s)
| | | | - Corien Bakermans
- Department of Biology, Penn. State University (Altoona), Altoona, Pennsylvania, USA
| | - David W Beaty
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | | | - Rosalba Bonaccorsi
- SETI Institute, Mountain View, California, USA
- NASA Ames Research Center, Moffett Field, California, USA
| | | | - David A Coil
- School of Medicine, University of California, Davis, Davis, California, USA
| | | | - Peter T Doran
- Department of Geology & Geophysics, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Lori Fenton
- SETI Institute, Mountain View, California, USA
| | - David P Fidler
- Council on Foreign Relations, Washington, District of Columbia, USA
| | - Brian Glass
- NASA Ames Research Center, Moffett Field, California, USA
| | | | - Fathi Karouia
- NASA Ames Research Center, Moffett Field, California, USA
| | - Joel S Levine
- College of William & Mary, Williamsburg, Virginia, USA
| | | | - Javier Martin-Torres
- School of Geoscience, University of Aberdeen, Aberdeen, United Kingdom
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Armilla, Spain
| | - Rakesh Mogul
- California Polytechnic (Pomona), Pomona, California, USA
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, Open University, Milton Keynes, United Kingdom
| | | | - Manish R Patel
- School of Environment, Earth and Ecosystem Sciences, Open University, Milton Keynes, United Kingdom
| | - David A Pearce
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | | | | | | | - John D Rummel
- Friday Harbor Associates LLC, Friday Harbor, Washington, USA
| | | | - Andrew C Schuerger
- Department of Plant Pathology, University of Florida, Merritt Island, Florida, USA
| | | | - Matthew Sharkey
- US Department of Health & Human Services, Washington, District of Columbia, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | | | - Carol R Stoker
- NASA Ames Research Center, Moffett Field, California, USA
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4
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Alon DM, Mittelman K, Stibbe E, Countryman S, Stodieck L, Doraisingam S, Leal Martin DM, Hamo ER, Pines G, Burstein D. CRISPR-based genetic diagnostics in microgravity. Biosens Bioelectron 2023; 237:115479. [PMID: 37459685 DOI: 10.1016/j.bios.2023.115479] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 08/13/2023]
Abstract
Monitoring astronauts' health during space missions poses many challenges, including rapid assessment of crew health conditions. Sensitive genetic diagnostics are crucial for examining crew members and the spacecraft environment. CRISPR-Cas12a, coupled with isothermal amplification, has proven to be a promising biosensing system for rapid, on-site detection of genomic targets. However, the efficiency and sensitivity of CRISPR-based diagnostics have never been tested in microgravity. We tested the use of recombinase polymerase amplification (RPA) coupled with the collateral cleavage activity of Cas12a for genetic diagnostics onboard the International Space Station. We explored the detection sensitivity of amplified and unamplified target DNA. By coupling RPA with Cas12a, we identified targets in attomolar concentrations. We further assessed the reactions' stability following long-term storage. Our results demonstrate that CRISPR-based detection is a powerful tool for on-site genetic diagnostics in microgravity, and can be further utilized for long-term space endeavors to improve astronauts' health and well-being.
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Affiliation(s)
- Dan Mark Alon
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel; Department of Entomology, Agricultural Research Organization - the Volcani Center, 68 HaMaccabim Rd, Rishon LeZion, 7505101, Israel
| | - Karin Mittelman
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Eytan Stibbe
- The Ramon Foundation, Kaplan 1, Tel Aviv, 6473402, Israel
| | | | - Louis Stodieck
- BioServe Space Technologies, University of Colorado Boulder, CO, 80309, USA
| | | | | | | | - Gur Pines
- Department of Entomology, Agricultural Research Organization - the Volcani Center, 68 HaMaccabim Rd, Rishon LeZion, 7505101, Israel.
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Science, Tel Aviv University, Tel Aviv, 6997801, Israel.
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5
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Siegel B, Spry JA, Broyan J, Castro-Wallace SL, Sato K, Mahoney E, Robinson J. Development of a NASA roadmap for planetary protection to prepare for the first human missions to Mars. LIFE SCIENCES IN SPACE RESEARCH 2023; 38:1-7. [PMID: 37481303 DOI: 10.1016/j.lssr.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 07/24/2023]
Abstract
As part of planning for future space exploration, COSPAR (The Committee on Space Research) together with participating space agencies, organized and held interdisciplinary meetings to consider next steps in addressing knowledge gaps for planetary protection for future human missions to Mars. Beginning with the results of these meetings and earlier work by NASA, ESA, and COSPAR (e.g., Criswell et al., 2005; Hogan et al., 2006; Rummel et al., 2008) as a base the authors of this paper carried out a follow-on NASA planning activity to identify the necessary steps to be accomplished to close knowledge gaps. We identified significant overlap between the planetary protection needs and other sets of Mars preparation roadmaps (1) microbial monitoring requirements for crew health and medical systems, (2) studies of the microbiome of the built environment, (3) environmental control and life support systems (ECLSS), (4) waste management, and (5) planetary surface operations. In many cases, efforts to mature exploration class systems for Mars that are occurring in other domains can be leveraged with minor changes to address planetary protection gaps as well. In other cases, work planned for testing on the International Space Station (ISS) as an analog for crew Mars transit, or on the lunar surface as an analog for Mars surface operations can be used to close planetary protection technology and knowledge gaps. An overall strategic framework that combines these domains has the advantage of being more comprehensive, efficient, and timely for closing gaps. This approach has led to the development of a NASA roadmap for addressing planetary protection integrated with other related roadmaps. NASA's development and execution of the planetary protection is now viewed in an integrated way with related technology development and testing. Key features of the integrated capabilities roadmap include.
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Affiliation(s)
| | - J Andy Spry
- SETI Institute, Silver Spring, MD, United States
| | | | - Sarah L Castro-Wallace
- NASA JSC, Biomedical Research and Environmental Sciences Division, Houston, TX, United States
| | - Kevin Sato
- NASA HQ, Biological and Physical Sciences Division, Science Mission Directorate Washington, DC, United States
| | | | - Julie Robinson
- NASA HQ, Science Mission Directorate, Washington, DC, United States
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6
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Chan K, Arumugam A, Markham C, Jenson R, Wu HW, Wong S. The Development of a 3D Printer-Inspired, Microgravity-Compatible Sample Preparation Device for Future Use Inside the International Space Station. MICROMACHINES 2023; 14:mi14050937. [PMID: 37241562 DOI: 10.3390/mi14050937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
Biological testing on the International Space Station (ISS) is necessary in order to monitor the microbial burden and identify risks to crew health. With support from a NASA Phase I Small Business Innovative Research contract, we have developed a compact prototype of a microgravity-compatible, automated versatile sample preparation platform (VSPP). The VSPP was built by modifying entry-level 3D printers that cost USD 200-USD 800. In addition, 3D printing was also used to prototype microgravity-compatible reagent wells and cartridges. The VSPP's primary function would enable NASA to rapidly identify microorganisms that could affect crew safety. It has the potential to process samples from various sample matrices (swab, potable water, blood, urine, etc.), thus yielding high-quality nucleic acids for downstream molecular detection and identification in a closed-cartridge system. When fully developed and validated in microgravity environments, this highly automated system will allow labor-intensive and time-consuming processes to be carried out via a turnkey, closed system using prefilled cartridges and magnetic particle-based chemistries. This manuscript demonstrates that the VSPP can extract high-quality nucleic acids from urine (Zika viral RNA) and whole blood (human RNase P gene) in a ground-level laboratory setting using nucleic acid-binding magnetic particles. The viral RNA detection data showed that the VSPP can process contrived urine samples at clinically relevant levels (as low as 50 PFU/extraction). The extraction of human DNA from eight replicate samples showed that the DNA extraction yield is highly consistent (there was a standard deviation of 0.4 threshold cycle when the extracted and purified DNA was tested via real-time polymerase chain reaction). Additionally, the VSPP underwent 2.1 s drop tower microgravity tests to determine if its components are compatible for use in microgravity. Our findings will aid future research in adapting extraction well geometry for 1 g and low g working environments operated by the VSPP. Future microgravity testing of the VSPP in the parabolic flights and in the ISS is planned.
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Affiliation(s)
- Kamfai Chan
- AI Biosciences, Inc., College Station, TX 77845, USA
| | | | - Cole Markham
- AI Biosciences, Inc., College Station, TX 77845, USA
| | | | - Hao-Wei Wu
- AI Biosciences, Inc., College Station, TX 77845, USA
| | - Season Wong
- AI Biosciences, Inc., College Station, TX 77845, USA
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7
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Tran QD, Tran V, Toh LS, Williams PM, Tran NN, Hessel V. Space Medicines for Space Health. ACS Med Chem Lett 2022; 13:1231-1247. [PMID: 35978686 PMCID: PMC9377000 DOI: 10.1021/acsmedchemlett.1c00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Scientists from around the world are studying the effects of microgravity and cosmic radiation via the "off-Earth" International Space Station (ISS) laboratory platform. The ISS has helped scientists make discoveries that go beyond the basic understanding of Earth. Over 300 medical experiments have been performed to date, with the goal of extending the knowledge gained for the benefit of humanity. This paper gives an overview of these numerous space medical findings, critically identifies challenges and gaps, and puts the achievements into perspective toward long-term space traveling and also adding benefits to our home planet. The medical contents are trifold structured, starting with the well-being of space travelers (astronaut health studies), followed by medical formulation research under space conditions, and then concluding with a blueprint for space pharmaceutical manufacturing. The review covers essential elements of our Earth-based pharmaceutical research such as drug discovery, drug and formulation stability, drug-organ interaction, drug disintegration/bioavailability/pharmacokinetics, pathogen virulence, genome mutation, and body's resistance. The information compiles clinical, medicinal, biological, and chemical research as well as fundamentals and practical applications.
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Affiliation(s)
- Quy Don Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
| | - Vienna Tran
- Adelaide
Medical School, University of Adelaide, Adelaide 5005, Australia
| | - Li Shean Toh
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Philip M. Williams
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Nam Nghiep Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- Department
of Chemical Engineering, Can Tho University, Can Tho 900000, Vietnam
| | - Volker Hessel
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- School of
Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
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8
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Berliner AJ, Lipsky I, Ho D, Hilzinger JM, Vengerova G, Makrygiorgos G, McNulty MJ, Yates K, Averesch NJH, Cockell CS, Wallentine T, Seefeldt LC, Criddle CS, Nandi S, McDonald KA, Menezes AA, Mesbah A, Arkin AP. Space bioprocess engineering on the horizon. COMMUNICATIONS ENGINEERING 2022; 1:13. [PMCID: PMC10955938 DOI: 10.1038/s44172-022-00012-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/17/2022] [Indexed: 06/04/2024]
Abstract
Space bioprocess engineering (SBE) is an emerging multi-disciplinary field to design, realize, and manage biologically-driven technologies specifically with the goal of supporting life on long term space missions. SBE considers synthetic biology and bioprocess engineering under the extreme constraints of the conditions of space. A coherent strategy for the long term development of this field is lacking. In this Perspective, we describe the need for an expanded mandate to explore biotechnological needs of the future missions. We then identify several key parameters—metrics, deployment, and training—which together form a pathway towards the successful development and implementation of SBE technologies of the future. Space bioprocess engineering integrates synthetic biology and bioprocess engineering with the specific goal to support human life in long term space missions. In this Perspective, Berliner and colleagues describe a pathway towards the development and implementation of space bioprocessing technologies of the future.
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Affiliation(s)
- Aaron J. Berliner
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Isaac Lipsky
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Davian Ho
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Jacob M. Hilzinger
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Gretchen Vengerova
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
| | - Georgios Makrygiorgos
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA USA
| | - Matthew J. McNulty
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical Engineering, University of California, Davis, Davis, CA USA
| | - Kevin Yates
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical Engineering, University of California, Davis, Davis, CA USA
| | - Nils J. H. Averesch
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA USA
| | - Charles S. Cockell
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Tyler Wallentine
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT USA
| | - Lance C. Seefeldt
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT USA
| | - Craig S. Criddle
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA USA
| | - Somen Nandi
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical Engineering, University of California, Davis, Davis, CA USA
- Global HealthShare Initiative, Davis, CA USA
| | - Karen A. McDonald
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical Engineering, University of California, Davis, Davis, CA USA
| | - Amor A. Menezes
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL USA
| | - Ali Mesbah
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA USA
| | - Adam P. Arkin
- Center for the Utilization of Biological Engineering in Space (CUBES), Berkeley, CA USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
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9
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Ly VT, Baudin PV, Pansodtee P, Jung EA, Voitiuk K, Rosen YM, Willsey HR, Mantalas GL, Seiler ST, Selberg JA, Cordero SA, Ross JM, Rolandi M, Pollen AA, Nowakowski TJ, Haussler D, Mostajo-Radji MA, Salama SR, Teodorescu M. Picroscope: low-cost system for simultaneous longitudinal biological imaging. Commun Biol 2021; 4:1261. [PMID: 34737378 PMCID: PMC8569150 DOI: 10.1038/s42003-021-02779-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/05/2021] [Indexed: 01/02/2023] Open
Abstract
Simultaneous longitudinal imaging across multiple conditions and replicates has been crucial for scientific studies aiming to understand biological processes and disease. Yet, imaging systems capable of accomplishing these tasks are economically unattainable for most academic and teaching laboratories around the world. Here, we propose the Picroscope, which is the first low-cost system for simultaneous longitudinal biological imaging made primarily using off-the-shelf and 3D-printed materials. The Picroscope is compatible with standard 24-well cell culture plates and captures 3D z-stack image data. The Picroscope can be controlled remotely, allowing for automatic imaging with minimal intervention from the investigator. Here, we use this system in a range of applications. We gathered longitudinal whole organism image data for frogs, zebrafish, and planaria worms. We also gathered image data inside an incubator to observe 2D monolayers and 3D mammalian tissue culture models. Using this tool, we can measure the behavior of entire organisms or individual cells over long-time periods.
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Affiliation(s)
- Victoria T Ly
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
| | - Pierre V Baudin
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Pattawong Pansodtee
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Erik A Jung
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Kateryna Voitiuk
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Yohei M Rosen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Gary L Mantalas
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Spencer T Seiler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - John A Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sergio A Cordero
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Jayden M Ross
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Marco Rolandi
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Tomasz J Nowakowski
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mohammed A Mostajo-Radji
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94143, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
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10
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Phuakrod A, Sripumkhai W, Jeamsaksiri W, Pattamang P, Loymek S, Brindley PJ, Sarasombath PT, Wongkamchai S. A miniPCR-Duplex Lateral Flow Dipstick Platform for Rapid and Visual Diagnosis of Lymphatic Filariae Infection. Diagnostics (Basel) 2021; 11:diagnostics11101855. [PMID: 34679553 PMCID: PMC8534866 DOI: 10.3390/diagnostics11101855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/18/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphatic filariasis (LF) is a neglected major tropical disease that is a leading cause of permanent and long-term disability worldwide. Significant progress made by the Global Programme to Eliminate Lymphatic Filariasis (GPELF) has led to a substantial decrease in the levels of infection. In this limitation, DNA detection of lymphatic filariae could be useful due to it capable of detecting low level of the parasites. In the present study, we developed a diagnostic assay that combines a miniPCR with a duplex lateral flow dipstick (DLFD). The PCR primers were designed based on the HhaI and SspI repetitive noncoding DNA sequences of Brugia malayi and Wuchereria bancrofti, respectively. The limits of detection and crossreactivity of the assay were evaluated. In addition, blood samples were provided by Thais living in a brugian filariasis endemic area. The miniPCR-DLFD assay exhibited a detection limit of 2 and 4 mf per milliliter (mL) of blood for B. malayi as well as W. bancrofti, respectively, and crossamplification was not observed with 11 other parasites. The result obtained from the present study was in accordance with the thick blood smear staining for the known cases. Thus, a miniPCR-DLFD is an alternative tool for the diagnosis of LF in point-of-collection settings with a modest cost (~USD 5) per sample.
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Affiliation(s)
- Achinya Phuakrod
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Witsaroot Sripumkhai
- Thai Microelectronic Center, National Electronics and Computer Technology Center, Thailand Science Park, Pathum Thani 12110, Thailand; (W.S.); (W.J.); (P.P.)
| | - Wutthinan Jeamsaksiri
- Thai Microelectronic Center, National Electronics and Computer Technology Center, Thailand Science Park, Pathum Thani 12110, Thailand; (W.S.); (W.J.); (P.P.)
| | - Pattaraluck Pattamang
- Thai Microelectronic Center, National Electronics and Computer Technology Center, Thailand Science Park, Pathum Thani 12110, Thailand; (W.S.); (W.J.); (P.P.)
| | - Sumat Loymek
- Office of Disease Prevention and Control, Region 12, Department of Disease Control, The Ministry of Public Health, Songkhla 9000, Thailand;
| | - Paul J. Brindley
- Immunology & Tropical Medicine & Research Center for Neglected Diseases of Poverty, Department of Microbiology, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA;
| | - Patsharaporn T. Sarasombath
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Correspondence: (P.T.S.); (S.W.); Tel.: +66-2-419-6468 (P.T.S. & S.W.); Fax: +66-2-419-6470 (P.T.S. & S.W.)
| | - Sirichit Wongkamchai
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Correspondence: (P.T.S.); (S.W.); Tel.: +66-2-419-6468 (P.T.S. & S.W.); Fax: +66-2-419-6470 (P.T.S. & S.W.)
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11
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Stahl-Rommel S, Li D, Sung M, Li R, Vijayakumar A, Atabay KD, Bushkin GG, Castro CL, Foley KD, Copeland DS, Castro-Wallace SL, Alvarez Saavedra E, Gleason EJ, Kraves S. A CRISPR-based assay for the study of eukaryotic DNA repair onboard the International Space Station. PLoS One 2021; 16:e0253403. [PMID: 34191829 PMCID: PMC8244870 DOI: 10.1371/journal.pone.0253403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
As we explore beyond Earth, astronauts may be at risk for harmful DNA damage caused by ionizing radiation. Double-strand breaks are a type of DNA damage that can be repaired by two major cellular pathways: non-homologous end joining, during which insertions or deletions may be added at the break site, and homologous recombination, in which the DNA sequence often remains unchanged. Previous work suggests that space conditions may impact the choice of DNA repair pathway, potentially compounding the risks of increased radiation exposure during space travel. However, our understanding of this problem has been limited by technical and safety concerns, which have prevented integral study of the DNA repair process in space. The CRISPR/Cas9 gene editing system offers a model for the safe and targeted generation of double-strand breaks in eukaryotes. Here we describe a CRISPR-based assay for DNA break induction and assessment of double-strand break repair pathway choice entirely in space. As necessary steps in this process, we describe the first successful genetic transformation and CRISPR/Cas9 genome editing in space. These milestones represent a significant expansion of the molecular biology toolkit onboard the International Space Station.
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Affiliation(s)
| | - David Li
- Woodbury High School, Woodbury, Minnesota, United States of America
| | - Michelle Sung
- Mounds View High School, Arden Hills, Minnesota, United States of America
| | - Rebecca Li
- Mounds View High School, Arden Hills, Minnesota, United States of America
| | - Aarthi Vijayakumar
- Mounds View High School, Arden Hills, Minnesota, United States of America
| | - Kutay Deniz Atabay
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - G. Guy Bushkin
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | | | - Kevin D. Foley
- Boeing Defense, Space & Security, Berkley, Michigan, United States of America
| | - D. Scott Copeland
- Boeing Defense, Space & Security, Berkley, Michigan, United States of America
| | - Sarah L. Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, Texas, United States of America
| | | | - Emily J. Gleason
- MiniPCR Bio, Cambridge, Massachusetts, United States of America
- * E-mail: (EJG); (SK)
| | - Sebastian Kraves
- MiniPCR Bio, Cambridge, Massachusetts, United States of America
- * E-mail: (EJG); (SK)
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12
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Solis-Marcano NE, Morales-Cruz M, Vega-Hernández G, Gómez-Moreno R, Binder C, Baerga-Ortiz A, Priest C, Cabrera CR. PCR-assisted impedimetric biosensor for colibactin-encoding pks genomic island detection in E. coli samples. Anal Bioanal Chem 2021; 413:4673-4680. [PMID: 34046698 PMCID: PMC8159250 DOI: 10.1007/s00216-021-03404-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/03/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
A fast PCR-assisted impedimetric biosensor was developed for the selective detection of the clbN gene from the polyketide synthase (pks) genomic island in real Escherichia coli samples. This genomic island is responsible for the production of colibactin, a harmful genotoxin that has been associated with colorectal cancer. The experimental protocol consisted of immobilizing the designated forward primer onto an Au electrode surface to create the sensing probe, followed by PCR temperature cycling in blank, positive, and negative DNA controls. Target DNA identification was possible by monitoring changes in the system’s charge transfer resistance values (Rct) before and after PCR treatment through electrochemical impedance spectroscopy (EIS) analysis. Custom-made, flexible gold electrodes were fabricated using chemical etching optical lithography. A PCR cycle study determined the optimum conditions to be at 6 cycles providing fast results while maintaining a good sensitivity. EIS data for the DNA recognition process demonstrated the successful distinction between target interaction resulting in an increase in resistance to charge transfer (Rct) percentage change of 176% for the positive DNA control vs. 21% and 20% for the negative and non-DNA-containing controls, respectively. Results showed effective fabrication of a fast, PCR-based electrochemical biosensor for the detection of pks genomic island with a calculated limit of detection of 17 ng/μL.
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Affiliation(s)
- Nadja E Solis-Marcano
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Myreisa Morales-Cruz
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Gabriela Vega-Hernández
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico
| | - Ramón Gómez-Moreno
- Department of Biochemistry, Molecular Sciences Research Center, University of Puerto Rico, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Claudia Binder
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Abel Baerga-Ortiz
- Department of Biochemistry, Molecular Sciences Research Center, University of Puerto Rico, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Craig Priest
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Carlos R Cabrera
- Department of Chemistry, Molecular Sciences Research Center, University of Puerto Rico, Río Piedras Campus, San Juan, 00925-2537, Puerto Rico.
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13
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Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Audouard M, Ponce-Rojas JC, Costello MS, Baxter NJ, Kosik KS, Arias C, Acosta-Alvear D, Wilson MZ. A Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. J Clin Microbiol 2021; 59:e02402-20. [PMID: 33478979 PMCID: PMC8092748 DOI: 10.1128/jcm.02402-20] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment. Here, we showcase an orthogonal pipeline we call CREST (Cas13-based, rugged, equitable, scalable testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows a binary interpretation of results. CREST may provide a point-of-care solution to increase the distribution of COVID-19 surveillance.
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Affiliation(s)
- Jennifer N Rauch
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Eric Valois
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Sabrina C Solley
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Friederike Braig
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Ryan S Lach
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Morgane Audouard
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Jose Carlos Ponce-Rojas
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Michael S Costello
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Naomi J Baxter
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Kenneth S Kosik
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Carolina Arias
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Diego Acosta-Alvear
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Maxwell Z Wilson
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
- Center for BioEngineering, University of California, Santa Barbara, Santa Barbara, California, USA
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14
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Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Audouard M, Ponce-Rojas JC, Costello MS, Baxter NJ, Kosik KS, Arias C, Acosta-Alvear D, Wilson MZ. A Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. J Clin Microbiol 2021; 59:JCM.02402-20. [PMID: 33478979 DOI: 10.1101/2020.04.20.052159] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/10/2021] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic has created massive demand for widespread, distributed tools for detecting SARS-CoV-2 genetic material. The hurdles to scalable testing include reagent and instrument accessibility, availability of highly trained personnel, and large upfront investment. Here, we showcase an orthogonal pipeline we call CREST (Cas13-based, rugged, equitable, scalable testing) that addresses some of these hurdles. Specifically, CREST pairs commonplace and reliable biochemical methods (PCR) with low-cost instrumentation, without sacrificing detection sensitivity. By taking advantage of simple fluorescence visualizers, CREST allows a binary interpretation of results. CREST may provide a point-of-care solution to increase the distribution of COVID-19 surveillance.
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Affiliation(s)
- Jennifer N Rauch
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Eric Valois
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Sabrina C Solley
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Friederike Braig
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Ryan S Lach
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Morgane Audouard
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Jose Carlos Ponce-Rojas
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Michael S Costello
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Naomi J Baxter
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
| | - Kenneth S Kosik
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Carolina Arias
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Diego Acosta-Alvear
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Maxwell Z Wilson
- University of California, Santa Barbara, Department of Molecular, Cellular, and Developmental Biology, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, USA
- Center for BioEngineering, University of California, Santa Barbara, Santa Barbara, California, USA
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15
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Stahl-Rommel S, Jain M, Nguyen HN, Arnold RR, Aunon-Chancellor SM, Sharp GM, Castro CL, John KK, Juul S, Turner DJ, Stoddart D, Paten B, Akeson M, Burton AS, Castro-Wallace SL. Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station Using Nanopore Sequencing. Genes (Basel) 2021; 12:genes12010106. [PMID: 33467183 PMCID: PMC7830261 DOI: 10.3390/genes12010106] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/23/2022] Open
Abstract
For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.
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Affiliation(s)
| | - Miten Jain
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Hang N. Nguyen
- JES Tech, Houston, TX 77058, USA; (S.S.-R.); (H.N.N.); (C.L.C.)
| | - Richard R. Arnold
- Astronaut Office, NASA Johnson Space Center, Houston, TX 77058, USA; (R.R.A.); (S.M.A.-C.)
| | | | | | | | - Kristen K. John
- Project Management and Systems Engineering Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY 10013, USA;
| | - Daniel J. Turner
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - David Stoddart
- Oxford Nanopore Technologies, Oxford Science Park, Oxford OX4 4DQ, UK; (D.J.T.); (D.S.)
| | - Benedict Paten
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Mark Akeson
- UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA; (M.J.); (B.P.); (M.A.)
| | - Aaron S. Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Sarah L. Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX 77058, USA
- Correspondence: ; Tel.: +1-281-483-7254
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16
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Guerrini CJ, Contreras JL. Credit for and Control of Research Outputs in Genomic Citizen Science. Annu Rev Genomics Hum Genet 2020; 21:465-489. [PMID: 32873078 DOI: 10.1146/annurev-genom-083117-021812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Citizen science encompasses activities with scientific objectives in which members of the public participate as more than passive research subjects from whom personal data or biospecimens are collected and analyzed by others. Citizen science is increasingly common in the biomedical sciences, including the fields of genetics and human genomics. Genomic citizen science initiatives are diverse and involve citizen scientists in collecting genetic data, solving genetic puzzles, and conducting experiments in community laboratories. At the same time that genomic citizen science is presenting new opportunities for individuals to participate in scientific discovery, it is also challenging norms regarding the manner in which scientific research outputs are managed. In this review, we present a typology of genomic citizen science initiatives, describe ethical and legal foundations for recognizing genomic citizen scientists' claims of credit for and control of research outputs, and detail how such claims are or might be addressed in practice across a variety of initiatives.
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Affiliation(s)
- Christi J Guerrini
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas 77030, USA;
| | - Jorge L Contreras
- S.J. Quinney College of Law and School of Medicine, University of Utah, Salt Lake City, Utah 84112, USA;
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17
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Urbaniak C, Wong S, Tighe S, Arumugam A, Liu B, Parker CW, Wood JM, Singh NK, Skorupa DJ, Peyton BM, Jenson R, Karouia F, Dragon J, Venkateswaran K. Validating an Automated Nucleic Acid Extraction Device for Omics in Space Using Whole Cell Microbial Reference Standards. Front Microbiol 2020; 11:1909. [PMID: 32973700 PMCID: PMC7472602 DOI: 10.3389/fmicb.2020.01909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 11/13/2022] Open
Abstract
NASA has made great strides in the past five years to develop a suite of instruments for the International Space Station in order to perform molecular biology in space. However, a key piece of equipment that has been lacking is an instrument that can extract nucleic acids from an array of complex human and environmental samples. The Omics in Space team has developed the μTitan (simulated micro(μ) gravity tested instrument for automated nucleic acid) system capable of automated, streamlined, nucleic acid extraction that is adapted for use under microgravity. The μTitan system was validated using a whole cell microbial reference (WCMR) standard comprised of a suspension of nine bacterial strains, titrated to concentrations that would challenge the performance of the instrument, as well as to determine the detection limits for isolating DNA. Quantitative assessment of system performance was measured by comparing instrument input challenge dose vs recovery by Qubit spectrofluorometry, qPCR, Bioanalyzer, and Next Generation Sequencing. Overall, results indicate that the μTitan system performs equal to or greater than a similar commercially available, earth-based, automated nucleic acid extraction device. The μTitan system was also tested in Yellowstone National Park (YNP) with the WCMR, to mimic a remote setting, with limited resources. The performance of the device at YNP was comparable to that in a laboratory setting. Such a portable, field-deployable, nucleic extraction system will be valuable for environmental microbiology, as well as in health care diagnostics.
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Affiliation(s)
- Camilla Urbaniak
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Season Wong
- AI Biosciences, College Station, TX, United States
| | - Scott Tighe
- University of Vermont, Burlington, VT, United States
| | | | - Bo Liu
- AI Biosciences, College Station, TX, United States
| | - Ceth W Parker
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M Wood
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K Singh
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | | | | | | | - Fathi Karouia
- NASA Ames Research Center, Moffett Field, CA, United States
| | - Julie Dragon
- University of Vermont, Burlington, VT, United States
| | - Kasthuri Venkateswaran
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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18
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González-González E, Trujillo-de Santiago G, Lara-Mayorga IM, Martínez-Chapa SO, Alvarez MM. Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection. PLoS One 2020; 15:e0237418. [PMID: 32790779 PMCID: PMC7425953 DOI: 10.1371/journal.pone.0237418] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/27/2020] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has crudely demonstrated the need for massive and rapid diagnostics. By the first week of July, more than 10,000,000 positive cases of COVID-19 have been reported worldwide, although this number could be greatly underestimated. In the case of an epidemic emergency, the first line of response should be based on commercially available and validated resources. Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. We used the miniPCR to detect and amplify SARS-CoV-2 DNA sequences using the sets of initiators recommended by the World Health Organization (WHO) for targeting three different regions that encode for the N protein. Prior to amplification, samples were combined with a DNA intercalating reagent (i.e., EvaGreen Dye). Sample fluorescence after amplification was then read using a commercial 96-well plate reader. This straightforward method allows the detection and amplification of SARS-CoV-2 nucleic acids in the range of ~625 to 2×105 DNA copies. The accuracy and simplicity of this diagnostics strategy may provide a cost-efficient and reliable alternative for COVID-19 pandemic testing, particularly in underdeveloped regions where RT-QPCR instrument availability may be limited. The portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for deployment in point-of-care SARS-CoV-2 detection efforts during pandemics.
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Affiliation(s)
- Everardo González-González
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Sergio Omar Martínez-Chapa
- Departamento de Ingeniería Mecátrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo León, México
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Amalfitano S, Levantesi C, Copetti D, Stefani F, Locantore I, Guarnieri V, Lobascio C, Bersani F, Giacosa D, Detsis E, Rossetti S. Water and microbial monitoring technologies towards the near future space exploration. WATER RESEARCH 2020; 177:115787. [PMID: 32315899 DOI: 10.1016/j.watres.2020.115787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.
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Affiliation(s)
- Stefano Amalfitano
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy.
| | - Caterina Levantesi
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
| | - Diego Copetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Fabrizio Stefani
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Ilaria Locantore
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Vincenzo Guarnieri
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Cesare Lobascio
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Francesca Bersani
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Donatella Giacosa
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Emmanouil Detsis
- European Science Foundation, 1 quai Lezay Marnésia, BP 90015, 67080, Strasbourg Cedex, France
| | - Simona Rossetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
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Rubinfien J, Atabay KD, Nichols NM, Tanner NA, Pezza JA, Gray MM, Wagner BM, Poppin JN, Aken JT, Gleason EJ, Foley KD, Copeland DS, Kraves S, Alvarez Saavedra E. Nucleic acid detection aboard the International Space Station by colorimetric loop-mediated isothermal amplification (LAMP). FASEB Bioadv 2020; 2:160-165. [PMID: 32161905 PMCID: PMC7059625 DOI: 10.1096/fba.2019-00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/22/2022] Open
Abstract
Human spaceflight endeavors present an opportunity to expand our presence beyond Earth. To this end, it is crucial to understand and diagnose effects of long‐term space travel on the human body. Developing tools for targeted, on‐site detection of specific DNA sequences will allow us to establish research and diagnostics platforms that will benefit space programs. We describe a simple DNA diagnostic method that utilizes colorimetric loop‐mediated isothermal amplification (LAMP) to enable detection of a repetitive telomeric DNA sequence in as little as 30 minutes. A proof of concept assay for this method was carried out using existing hardware on the International Space Station and the results were read instantly by an astronaut through a simple color change of the reaction mixture. LAMP offers a novel platform for on‐orbit DNA‐based diagnostics that can be deployed on the International Space Station and to the broader benefit of space programs.
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Affiliation(s)
| | - Kutay D Atabay
- Whitehead Institute for Biomedical Research Massachusetts Institute of Technology Cambridge MA USA
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Cortesão M, Schütze T, Marx R, Moeller R, Meyer V. Fungal Biotechnology in Space: Why and How? GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [DOI: 10.1007/978-3-030-29541-7_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Dietary intervention of mice using an improved Multiple Artificial-gravity Research System (MARS) under artificial 1 g. NPJ Microgravity 2019; 5:16. [PMID: 31312718 PMCID: PMC6614370 DOI: 10.1038/s41526-019-0077-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/16/2019] [Indexed: 11/24/2022] Open
Abstract
Japan Aerospace Exploration Agency (JAXA) has developed mouse habitat cage units equipped with an artificial gravity-producing centrifuge, called the Multiple Artificial-gravity Research System (MARS), that enables single housing of a mouse under artificial gravity (AG) in orbit. This is a report on a hardware evaluation. The MARS underwent improvement in water leakage under microgravity (MG), and was used in the second JAXA mouse mission to evaluate the effect of AG and diet on mouse biological system simultaneously. Twelve mice were divided into four groups of three, with each group fed a diet either with or without fructo-oligosaccharide and housed singly either at 1 g AG or MG for 30 days on the International Space Station, then safely returned to the Earth. Body weight tended to increase in AG mice and decrease in MG mice after spaceflight, but these differences were not significant. This indicates that the improved MARS may be useful in evaluating AG and dietary intervention for space flown mice.
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González-González E, Mendoza-Ramos JL, Pedroza SC, Cuellar-Monterrubio AA, Márquez-Ipiña AR, Lira-Serhan D, Trujillo-de Santiago G, Alvarez MM. Validation of use of the miniPCR thermocycler for Ebola and Zika virus detection. PLoS One 2019; 14:e0215642. [PMID: 31071117 PMCID: PMC6508694 DOI: 10.1371/journal.pone.0215642] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 04/07/2019] [Indexed: 01/16/2023] Open
Abstract
The development of point-of-care (POC) diagnostic systems has received well-deserved attention in recent years in the scientific literature, and many experimental systems show great promise in real settings. However, in the case of an epidemic emergency (or a natural disaster), the first line of response should be based on commercially available and validated resources. Here, we compare the performance and ease of use of the miniPCR, a recently commercially available compact and portable PCR device, and a conventional thermocycler for the diagnostics of viral nucleic acids. We used both thermocyclers to detect and amplify Ebola and Zika DNA sequences of different lengths (in the range of 91 to 300 nucleotides) at different concentrations (in the range of ~50 to 4.0 x 108 DNA copies). Our results suggest that the performance of both thermocyclers is quite similar. Moreover, the portability, ease of use, and reproducibility of the miniPCR makes it a reliable alternative for point-of-care nucleic acid detection and amplification.
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Affiliation(s)
- Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Jackelin Lizeth Mendoza-Ramos
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Sara Cristina Pedroza
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Aimé Alexandra Cuellar-Monterrubio
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Alan Roberto Márquez-Ipiña
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Daniel Lira-Serhan
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Ingeniería Mecátrónica y Eléctrica, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
- Departamento de Bioingeniería, Tecnologico de Monterrey, CP, Monterrey, Nuevo León, México
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Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. MICROBIOME 2019; 7:50. [PMID: 30955503 PMCID: PMC6452512 DOI: 10.1186/s40168-019-0666-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring and observational studies of spacecraft and space stations have been conducted by traditional culture methods, although it is known that many microbes cannot be cultured with standard techniques. To fully appreciate the true number and diversity of microbes that survive in the ISS, molecular and culture-based methods were used to assess microbial communities on ISS surfaces. Samples were taken at eight pre-defined locations during three flight missions spanning 14 months and analyzed upon return to Earth. RESULTS The cultivable bacterial and fungal population ranged from 104 to 109 CFU/m2 depending on location and consisted of various bacterial (Actinobacteria, Firmicutes, and Proteobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Amplicon sequencing detected more bacterial phyla when compared to the culture-based analyses, but both methods identified similar numbers of fungal phyla. Changes in bacterial and fungal load (by culture and qPCR) were observed over time but not across locations. Bacterial community composition changed over time, but not across locations, while fungal community remained the same between samplings and locations. There were no significant differences in community composition and richness after propidium monoazide sample treatment, suggesting that the analyzed DNA was extracted from intact/viable organisms. Moreover, approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured. CONCLUSIONS The results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.
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Affiliation(s)
- Aleksandra Checinska Sielaff
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
- Washington State University Extension - Youth and Families Program Unit, Washington State University, Pullman, WA, USA
| | - Camilla Urbaniak
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Ganesh Babu Malli Mohan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Jeremiah Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Teresa Mayer
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Fathi Karouia
- NASA Ames Research Center, Space Bioscience Division, Moffett Field, Mountain View, CA, USA
- Research Center, Moffett Field, Mountain View, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA.
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Montague TG, Almansoori A, Gleason EJ, Copeland DS, Foley K, Kraves S, Alvarez Saavedra E. Gene expression studies using a miniaturized thermal cycler system on board the International Space Station. PLoS One 2018; 13:e0205852. [PMID: 30379894 PMCID: PMC6209215 DOI: 10.1371/journal.pone.0205852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/02/2018] [Indexed: 02/02/2023] Open
Abstract
The distance and duration of human spaceflight missions is set to markedly increase over the coming decade as we prepare to send astronauts to Mars. However, the health impact of long-term exposure to cosmic radiation and microgravity is not fully understood. In order to identify the molecular mechanisms underpinning the effects of space travel on human health, we must develop the capacity to monitor changes in gene expression and DNA integrity in space. Here, we report successful implementation of three molecular biology procedures on board the International Space Station (ISS) using a miniaturized thermal cycler system and C. elegans as a model organism: first, DNA extraction–the initial step for any type of DNA analysis; second, reverse transcription of RNA to generate complementary DNA (cDNA); and third, the subsequent semi-quantitative PCR amplification of cDNA to analyze gene expression changes in space. These molecular procedures represent a significant expansion of the budding molecular biology capabilities of the ISS and will permit more complex analyses of space-induced genetic changes during spaceflight missions aboard the ISS and beyond.
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Affiliation(s)
- Tessa G. Montague
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | | | | | - Kevin Foley
- Boeing, Houston, TX, United States of America
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"The Smartphone's Guide to the Galaxy": In Situ Analysis in Space. BIOSENSORS-BASEL 2018; 8:bios8040096. [PMID: 30347742 PMCID: PMC6316803 DOI: 10.3390/bios8040096] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/05/2018] [Accepted: 10/13/2018] [Indexed: 01/02/2023]
Abstract
A human mission to Mars can be viewed as the apex of human technological achievement. However, to make this dream a reality several obstacles need to be overcome. One is devising practical ways to safeguard the crew health during the mission through the development of easy operable and compact sensors. Lately, several smartphone-based sensing devices (SBDs) with the purpose to enable the immediate sensitive detection of chemicals, proteins or pathogens in remote settings have emerged. In this critical review, the potential to piggyback these systems for in situ analysis in space has been investigated on application of a systematic keyword search whereby the most relevant articles were examined comprehensively and existing SBDs were divided into 4 relevant groups for the monitoring of crew health during space missions. Recently developed recognition elements (REs), which could offer the enhanced ability to tolerate those harsh conditions in space, have been reviewed with recommendations offered. In addition, the potential use of cell free synthetic biology to obtain long-term shelf-stable reagents was reviewed. Finally, a synopsis of the possibilities of combining novel SBD, RE and nanomaterials to create a compact sensor-platform ensuring adequate crew health monitoring has been provided.
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