1
|
Case N, Johnston N, Nadeau J. Fluorescence Microscopy with Deep UV, Near UV, and Visible Excitation for In Situ Detection of Microorganisms. ASTROBIOLOGY 2024; 24:300-317. [PMID: 38507693 PMCID: PMC10979697 DOI: 10.1089/ast.2023.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 01/02/2024] [Indexed: 03/22/2024]
Abstract
We report a simple, inexpensive design of a fluorescence microscope with light-emitting diode (LED) excitation for detection of labeled and unlabeled microorganisms in mineral substrates. The use of deep UV (DUV) excitation with visible emission requires no specialized optics or slides and can be implemented easily and inexpensively using an oblique illumination geometry. DUV excitation (<280 nm) is preferable to near UV (365 nm) for avoidance of mineral autofluorescence. When excited with DUV, unpigmented bacteria show two emission peaks: one in the near UV ∼320 nm, corresponding to proteins, and another peak in the blue to green range, corresponding to flavins and/or reduced nicotinamide adenine dinucleotide (NADH). Many commonly used dyes also show secondary excitation peaks in the DUV, with identical emission spectra and quantum yields as their primary peak. However, DUV fails to excite key biosignature molecules, especially chlorophyll in cyanobacteria. Visible excitation (violet to blue) also results in less mineral autofluorescence than near UV, and most autofluorescence in the minerals seen here is green, so that red dyes and red autofluorescence of chlorophyll and porphyrins are readily distinguished. The pairing of DUV and near UV or visible excitation, with emission across the visible, represents the most thorough approach to detection of labeled and unlabeled bacteria in soil and rock.
Collapse
Affiliation(s)
- Noel Case
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Nikki Johnston
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jay Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
| |
Collapse
|
2
|
Moreno-Paz M, dos Santos Severino RS, Sánchez-García L, Manchado JM, García-Villadangos M, Aguirre J, Fernández-Martínez MA, Carrizo D, Kobayashi L, Dave A, Warren-Rhodes K, Davila A, Stoker CR, Glass B, Parro V. Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert. ASTROBIOLOGY 2023; 23:1259-1283. [PMID: 37930382 PMCID: PMC10825288 DOI: 10.1089/ast.2021.0174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/02/2023] [Indexed: 11/07/2023]
Abstract
The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.
Collapse
Affiliation(s)
- Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Rita Sofia dos Santos Severino
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Departament of Física y Matemáticas y de Automática, University of Alcalá de Henares (UAH), Madrid, Spain
| | - Laura Sánchez-García
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Juan Manuel Manchado
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | | | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Miguel Angel Fernández-Martínez
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
- Department of Natural Resource Sciences, McGill University, Québec, Canada
| | - Daniel Carrizo
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| | - Linda Kobayashi
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Arwen Dave
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Kim Warren-Rhodes
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
| | - Alfonso Davila
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Carol R. Stoker
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Brian Glass
- Space Science Division and Astrobiology Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CAB), INTA-CSIC, Madrid, Spain
| |
Collapse
|
3
|
Raymond-Bouchard I, Maggiori C, Brennan L, Altshuler I, Manchado JM, Parro V, Whyte LG. Assessment of Automated Nucleic Acid Extraction Systems in Combination with MinION Sequencing As Potential Tools for the Detection of Microbial Biosignatures. ASTROBIOLOGY 2022; 22:87-103. [PMID: 34962136 DOI: 10.1089/ast.2020.2349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The utilization of nanopore technologies for the detection of organic biogenic compounds has garnered significant focus in recent years. Oxford Nanopore Technologies' (ONT) MinION instrument, which can detect and sequence nucleic acids (NAs), is one such example. These technologies have much promise for unambiguous life detection but require significant development in terms of methods for extraction and preparation of NAs for biosignature detection and their feasibility for use in astrobiology-focused field missions. In this study, we tested pre-existing, automated, or semiautomated NA extraction technologies, coupled with automated ONT VolTRAX NA sample preparation, and verification with Nanopore MinION sequencing. All of the extraction systems tested (SuperFastPrep2, ClaremontX1, and SOLID-Sample Preparation Unit) showed potential for extracting DNA from Canadian High Arctic environments analogous to Mars, Europa, and Enceladus, which could subsequently be detected and sequenced with the MinION. However, they differed with regard to efficacy, yield, purity, and sequencing and annotation quality. Overall, bead beating-based systems performed the best for these parameters. In addition, we showed that the MinION could sequence unpurified DNA contained in crude cell lysates. This is valuable from an astrobiology perspective because purification steps are time-consuming and complicate the requirements for an automated extraction and life detection system. Our results indicate that semiautomated NA extraction and preparation technologies hold much promise, and with increased optimization and automation could be coupled to a larger platform incorporating nanopore detection and sequencing of NAs for life detection applications.
Collapse
Affiliation(s)
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | | | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| |
Collapse
|
4
|
Pacelli C, Selbmann L, Zucconi L, Coleine C, de Vera JP, Rabbow E, Böttger U, Dadachova E, Onofri S. Responses of the Black Fungus Cryomyces antarcticus to Simulated Mars and Space Conditions on Rock Analogs. ASTROBIOLOGY 2019; 19:209-220. [PMID: 30067087 DOI: 10.1089/ast.2016.1631] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The BIOMEX (BIOlogy and Mars Experiment) is part of the European Space Agency (ESA) space mission EXPOSE-R2 in Low-Earth Orbit, devoted to exposing microorganisms for 1.5 years to space and simulated Mars conditions on the International Space Station. In preparing this mission, dried colonies of the Antarctic cryptoendolithic black fungus Cryomyces antarcticus CCFEE 515, grown on martian and lunar analog regolith pellets, were subjected to several ground-based preflight tests, Experiment Verification Tests, and Science Verification Tests (SVTs) that were performed to verify (i) the resistance of our model organism to space stressors when grown on extraterrestrial rock analogs and (ii) the possibility of detecting biomolecules as potential biosignatures. Here, the results of the SVTs, the last set of experiments, which were performed in ultraviolet radiation combined with simulated space vacuum or simulated martian conditions, are reported. The results demonstrate that C. antarcticus was able to tolerate the conditions of the SVT experiment, regardless of the substratum in which it was grown. DNA maintained high integrity after treatments and was confirmed as a possible biosignature; melanin, which was chosen to be a target for biosignature detection, was unambiguously detected by Raman spectroscopy.
Collapse
Affiliation(s)
- Claudia Pacelli
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
- 2 Section of Mycology, Italian Antarctic National Museum (MNA), Genoa, Italy
| | - Laura Zucconi
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Claudia Coleine
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Jean-Pierre de Vera
- 3 Institute of Planetary Research, German Aerospace Center (DLR) Berlin, Berlin, Germany
| | - Elke Rabbow
- 4 German Aerospace Centre, Institute of Aerospace Medicine (DLR), Köln, Germany
| | - Ute Böttger
- 5 Institute of Optical Sensor Systems, German Aerospace Center (DLR) Berlin, Berlin, Germany
| | - Ekaterina Dadachova
- 6 College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada
| | - Silvano Onofri
- 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| |
Collapse
|
5
|
"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.
Collapse
|
6
|
Hanczarek I, Kenna AJ, Lindensmith C, Nadeau J. Performance of Fluorescent Cell-Labeling Dyes under Simulated Europa Mission Radiation Doses. Radiat Res 2018; 190:634. [PMID: 30325265 DOI: 10.1667/rr15187.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We investigated the performance of several commonly used fluorescent dyes after exposure to a simulated Europa mission total ionizing radiation dose of 300 krad (3 kGy) applied using a 60Co source. Dyes irradiated in aqueous solution or as lyophilized powders were evaluated for absorbance and emission spectra, quantum yield, and where appropriate, ability to label cells or nucleic acids. Although some dyes showed significant increase or decrease in quantum yield with the dose, their spectra and cell-labeling properties remained essentially unchanged after irradiation in powder form. Irradiation in aqueous solution led to significantly greater changes, including a large blue shift in the DNA intercalator propidium iodide. These results suggest that many fluorescent probes are appropriate for use in astrobiological missions to Europa, but that SYTO9 and propidium iodide should be used with caution or not mixed with each other, as is commonly done in "Live/Dead" labeling applications.
Collapse
Affiliation(s)
- Iulia Hanczarek
- a Department of Physics, Portland State University, Portland, Oregon 97201
| | - Aaron J Kenna
- b Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109
| | - Chris Lindensmith
- b Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109
| | - Jay Nadeau
- a Department of Physics, Portland State University, Portland, Oregon 97201
| |
Collapse
|
7
|
Moreno-Paz M, Gómez-Cifuentes A, Ruiz-Bermejo M, Hofstetter O, Maquieira Á, Manchado JM, Morais S, Sephton MA, Niessner R, Knopp D, Parro V. Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration. ASTROBIOLOGY 2018; 18:1041-1056. [PMID: 29638146 PMCID: PMC6225596 DOI: 10.1089/ast.2017.1747] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/18/2018] [Indexed: 05/05/2023]
Abstract
Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L- aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1-10 ppb level and some even at the ppt level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (c.a., 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside Earth.
Collapse
Affiliation(s)
- Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Ana Gómez-Cifuentes
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Marta Ruiz-Bermejo
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois
| | - Ángel Maquieira
- Department of Chemistry, Instituto Universitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan M. Manchado
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Sergi Morais
- Department of Chemistry, Instituto Universitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universidad Politécnica de Valencia, Valencia, Spain
| | - Mark A. Sephton
- Department of Earth Science and Engineering, Imperial College London, London, United Kingdom
| | | | - Dietmar Knopp
- Department Chemie, Technische Universität München, Munich, Germany
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| |
Collapse
|
8
|
Nicholson WL, Schuerger AC, Douki T. The Photochemistry of Unprotected DNA and DNA inside Bacillus subtilis Spores Exposed to Simulated Martian Surface Conditions of Atmospheric Composition, Temperature, Pressure, and Solar Radiation. ASTROBIOLOGY 2018; 18:393-402. [PMID: 29589975 DOI: 10.1089/ast.2017.1721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA is considered a potential biomarker for life-detection experiments destined for Mars. Experiments were conducted to examine the photochemistry of bacterial DNA, either unprotected or within Bacillus subtilis spores, in response to exposure to simulated martian surface conditions consisting of the following: temperature (-10°C), pressure (0.7 kPa), atmospheric composition [CO2 (95.54%), N2 (2.7%), Ar (1.6%), O2 (0.13%), and H2O (0.03%)], and UV-visible-near IR solar radiation spectrum (200-1100 nm) calibrated to 4 W/m2 of UVC (200-280 nm). While the majority (99.9%) of viable spores deposited in multiple layers on spacecraft-qualified aluminum coupons were inactivated within 5 min, a detectable fraction survived for up to the equivalent of ∼115 martian sols. Spore photoproduct (SP) was the major lesion detected in spore DNA, with minor amounts of cyclobutane pyrimidine dimers (CPD), in the order TT CPD > TC CPD >> CT CPD. In addition, the (6-4)TC, but not the (6-4)TT, photoproduct was detected in spore DNA. When unprotected DNA was exposed to simulated martian conditions, all photoproducts were detected. Surprisingly, the (6-4)TC photoproduct was the major photoproduct, followed by SP ∼ TT CPD > TC CPD > (6-4)TT > CT CPD > CC CPD. Differences in the photochemistry of unprotected DNA and spore DNA in response to simulated martian surface conditions versus laboratory conditions are reviewed and discussed. The results have implications for the planning of future life-detection experiments that use DNA as the target, and for the long-term persistence on Mars of forward contaminants or their DNA. Key Words: Bacillus subtilis-DNA-Mars-Photochemistry-Spore-Ultraviolet. Astrobiology 18, 393-402.
Collapse
Affiliation(s)
- Wayne L Nicholson
- 1 Department of Microbiology and Cell Science, University of Florida , Merritt Island, Florida, USA
| | - Andrew C Schuerger
- 2 Department of Plant Pathology, University of Florida , Merritt Island, Florida, USA
| | - Thierry Douki
- 3 Univ. Grenoble Alpes , CEA, CNRS, INAC, SyMMES/CIBEST, Grenoble, France
| |
Collapse
|
9
|
Blanco Y, Gallardo-Carreño I, Ruiz-Bermejo M, Puente-Sánchez F, Cavalcante-Silva E, Quesada A, Prieto-Ballesteros O, Parro V. Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario. ASTROBIOLOGY 2017; 17:984-996. [PMID: 29016195 PMCID: PMC5655591 DOI: 10.1089/ast.2016.1467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/20/2017] [Indexed: 05/17/2023]
Abstract
The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration-Life detection-Microbial mat-Life detector chip-Thermogravimetry-Raman spectroscopy-NIR-DRIFTS. Astrobiology 17, 984-996.
Collapse
Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | - Marta Ruiz-Bermejo
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | | | - Antonio Quesada
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| |
Collapse
|
10
|
Mathies RA, Razu ME, Kim J, Stockton AM, Turin P, Butterworth A. Feasibility of Detecting Bioorganic Compounds in Enceladus Plumes with the Enceladus Organic Analyzer. ASTROBIOLOGY 2017; 17:902-912. [PMID: 28915087 PMCID: PMC5610425 DOI: 10.1089/ast.2017.1660] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Enceladus presents an excellent opportunity to detect organic molecules that are relevant for habitability as well as bioorganic molecules that provide evidence for extraterrestrial life because Enceladus' plume is composed of material from the subsurface ocean that has a high habitability potential and significant organic content. A primary challenge is to send instruments to Enceladus that can efficiently sample organic molecules in the plume and analyze for the most relevant molecules with the necessary detection limits. To this end, we present the scientific feasibility and engineering design of the Enceladus Organic Analyzer (EOA) that uses a microfluidic capillary electrophoresis system to provide sensitive detection of a wide range of relevant organic molecules, including amines, amino acids, and carboxylic acids, with ppm plume-detection limits (100 pM limits of detection). Importantly, the design of a capture plate that effectively gathers plume ice particles at encounter velocities from 200 m/s to 5 km/s is described, and the ice particle impact is modeled to demonstrate that material will be efficiently captured without organic decomposition. While the EOA can also operate on a landed mission, the relative technical ease of a fly-by mission to Enceladus, the possibility to nondestructively capture pristine samples from deep within the Enceladus ocean, plus the high sensitivity of the EOA instrument for molecules of bioorganic relevance for life detection argue for the inclusion of EOA on Enceladus missions. Key Words: Lab-on-a-chip-Organic biomarkers-Life detection-Planetary exploration. Astrobiology 17, 902-912.
Collapse
Affiliation(s)
- Richard A. Mathies
- Department of Chemistry, University of California at Berkeley, Berkeley, California
| | - Md Enayet Razu
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas
| | - Jungkyu Kim
- Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas
| | - Amanda M. Stockton
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Paul Turin
- Berkeley Space Sciences Lab, University of California at Berkeley, Berkeley, California
| | - Anna Butterworth
- Berkeley Space Sciences Lab, University of California at Berkeley, Berkeley, California
| |
Collapse
|
11
|
Mojarro A, Ruvkun G, Zuber MT, Carr CE. Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection. ASTROBIOLOGY 2017; 17:747-760. [PMID: 28704064 PMCID: PMC5567878 DOI: 10.1089/ast.2016.1535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids. Our initial DNA extraction experiments resulted in low to undetectable amounts of DNA due to soil chemistry-dependent soil-DNA interactions, namely adsorption to mineral surfaces, binding to divalent/trivalent cations, destruction by iron redox cycling, and acidic conditions. Subsequently, we developed soil-specific extraction protocols that increase DNA yields through a combination of desalting, utilization of competitive binders, and promotion of anaerobic conditions. Our results suggest that a combination of desalting and utilizing competitive binders may establish a "universal" nucleic acid extraction protocol suitable for analyzing samples from diverse soils on Mars. Key Words: Life-detection instruments-Nucleic acids-Mars-Panspermia. Astrobiology 17, 747-760.
Collapse
Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher E. Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| |
Collapse
|
12
|
Baqué M, Verseux C, Böttger U, Rabbow E, de Vera JPP, Billi D. Preservation of Biomarkers from Cyanobacteria Mixed with Mars-Like Regolith Under Simulated Martian Atmosphere and UV Flux. ORIGINS LIFE EVOL B 2016; 46:289-310. [PMID: 26530341 DOI: 10.1007/s11084-015-9467-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/27/2015] [Indexed: 02/05/2023]
Abstract
The space mission EXPOSE-R2 launched on the 24th of July 2014 to the International Space Station is carrying the BIOMEX (BIOlogy and Mars EXperiment) experiment aimed at investigating the endurance of extremophiles and stability of biomolecules under space and Mars-like conditions. In order to prepare the analyses of the returned samples, ground-based simulations were carried out in Planetary and Space Simulation facilities. During the ground-based simulations, Chroococcidiopsis cells mixed with two Martian mineral analogues (phyllosilicatic and sulfatic Mars regolith simulants) were exposed to a Martian simulated atmosphere combined or not with UV irradiation corresponding to the dose received during a 1-year-exposure in low Earth orbit (or half a Martian year on Mars). Cell survival and preservation of potential biomarkers such as photosynthetic and photoprotective pigments or DNA were assessed by colony forming ability assays, confocal laser scanning microscopy, Raman spectroscopy and PCR-based assays. DNA and photoprotective pigments (carotenoids) were detectable after simulations of the space mission (570 MJ/m(2) of UV 200-400 nm irradiation and Martian simulated atmosphere), even though signals were attenuated by the treatment. The fluorescence signal from photosynthetic pigments was differently preserved after UV irradiation, depending on the thickness of the samples. UV irradiation caused a high background fluorescence of the Martian mineral analogues, as revealed by Raman spectroscopy. Further investigation will be needed to ensure unambiguous identification and operations of future Mars missions. However, a 3-month exposure to a Martian simulated atmosphere showed no significant damaging effect on the tested cyanobacterial biosignatures, pointing out the relevance of the latter for future investigations after the EXPOSE-R2 mission. Data gathered during the ground-based simulations will contribute to interpret results from space experiments and guide our search for life on Mars.
Collapse
Affiliation(s)
- Mickael Baqué
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Cyprien Verseux
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Ute Böttger
- German Aerospace Center (DLR), Institute of Planetary Research, Berlin, Germany
| | - Elke Rabbow
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
- Dipartimento di Biologia, Università di Roma "Tor Vergata", Rome, Italy.
| |
Collapse
|
13
|
Willis PA, Creamer JS, Mora MF. Implementation of microchip electrophoresis instrumentation for future spaceflight missions. Anal Bioanal Chem 2015; 407:6939-63. [PMID: 26253225 DOI: 10.1007/s00216-015-8903-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 11/27/2022]
Abstract
We present a comprehensive discussion of the role that microchip electrophoresis (ME) instrumentation could play in future NASA missions of exploration, as well as the current barriers that must be overcome to make this type of chemical investigation possible. We describe how ME would be able to fill fundamental gaps in our knowledge of the potential for past, present, or future life beyond Earth. Despite the great promise of ME for ultrasensitive portable chemical analysis, to date, it has never been used on a robotic mission of exploration to another world. We provide a current snapshot of the technology readiness level (TRL) of ME instrumentation, where the TRL is the NASA systems engineering metric used to evaluate the maturity of technology, and its fitness for implementation on missions. We explain how the NASA flight implementation process would apply specifically to ME instrumentation, and outline the scientific and technology development issues that must be addressed for ME analyses to be performed successfully on another world. We also outline research demonstrations that could be accomplished by independent researchers to help advance the TRL of ME instrumentation for future exploration missions. The overall approach described here for system development could be readily applied to a wide range of other instrumentation development efforts having broad societal and commercial impact.
Collapse
Affiliation(s)
- Peter A Willis
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA,
| | | | | |
Collapse
|
14
|
Baqué M, Verseux C, Rabbow E, de Vera JPP, Billi D. Detection of macromolecules in desert cyanobacteria mixed with a lunar mineral analogue after space simulations. ORIGINS LIFE EVOL B 2014; 44:209-21. [PMID: 25351683 PMCID: PMC4669540 DOI: 10.1007/s11084-014-9367-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 09/16/2014] [Indexed: 11/26/2022]
Abstract
In the context of future exposure missions in Low Earth Orbit and possibly on the Moon, two desert strains of the cyanobacterium Chroococcidiopsis, strains CCMEE 029 and 057, mixed or not with a lunar mineral analogue, were exposed to fractionated fluencies of UVC and polychromatic UV (200–400 nm) and to space vacuum. These experiments were carried out within the framework of the BIOMEX (BIOlogy and Mars EXperiment) project, which aims at broadening our knowledge of mineral-microorganism interaction and the stability/degradation of their macromolecules when exposed to space and simulated Martian conditions. The presence of mineral analogues provided a protective effect, preserving survivability and integrity of DNA and photosynthetic pigments, as revealed by testing colony-forming abilities, performing PCR-based assays and using confocal laser scanning microscopy. In particular, DNA and pigments were still detectable after 500 kJ/m2 of polychromatic UV and space vacuum (10−4 Pa), corresponding to conditions expected during one-year exposure in Low Earth Orbit on board the EXPOSE-R2 platform in the presence of 0.1 % Neutral Density (ND) filter. After exposure to high UV fluencies (800 MJ/m2) in the presence of minerals, however, altered fluorescence emission spectrum of the photosynthetic pigments were detected, whereas DNA was still amplified by PCR. The present paper considers the implications of such findings for the detection of biosignatures in extraterrestrial conditions and for putative future lunar missions.
Collapse
Affiliation(s)
- Mickael Baqué
- />Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Cyprien Verseux
- />Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Elke Rabbow
- />Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | | | - Daniela Billi
- />Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| |
Collapse
|
15
|
Carr CE, Rowedder H, Lui CS, Zlatkovsky I, Papalias CW, Bolander J, Myers JW, Bustillo J, Rothberg JM, Zuber MT, Ruvkun G. Radiation resistance of sequencing chips for in situ life detection. ASTROBIOLOGY 2013; 13:560-569. [PMID: 23734755 DOI: 10.1089/ast.2012.0923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Life beyond Earth may be based on RNA or DNA if such life is related to life on Earth through shared ancestry due to meteoritic exchange, such as may be the case for Mars, or if delivery of similar building blocks to habitable environments has biased the evolution of life toward utilizing nucleic acids. In this case, in situ sequencing is a powerful approach to identify and characterize such life without the limitations or expense of returning samples to Earth, and can monitor forward contamination. A new semiconductor sequencing technology based on sensing hydrogen ions released during nucleotide incorporation can enable massively parallel sequencing in a small, robust, optics-free CMOS chip format. We demonstrate that these sequencing chips survive several analogues of space radiation at doses consistent with a 2-year Mars mission, including protons with solar particle event-distributed energy levels and 1 GeV oxygen and iron ions. We find no measurable impact of irradiation at 1 and 5 Gy doses on sequencing quality nor on low-level hardware characteristics. Further testing is required to study the impacts of soft errors as well as to characterize performance under neutron and gamma irradiation and at higher doses, which would be expected during operation in environments with significant trapped energetic particles such as during a mission to Europa. Our results support future efforts to use in situ sequencing to test theories of panspermia and/or whether life has a common chemical basis.
Collapse
Affiliation(s)
- Christopher E Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|