Towards in situ sequencing for life detection

Carr, Christopher E.; Mojarro, Angel; Hachey, Julie; Saboda, Kendall N.; Tani, Jacopo; Bhattaru, Srinivasa A.; Smith, Alex; Pontefract, A.; Zuber, M. T.; Doebler, Robert; Brown, Mark J.; Herrington, Keith; Talbot, Ryan; Nguyen, Vinh; Bailey, Ryan C.; Ferguson, Tanya M.; Finney, Michael; Church, George M.; Ruvkun, Gary

doi:10.1109/aero.2017.7943896

Cited by 27 publications

(33 citation statements)

References 57 publications

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“…Raw data is then basecalled by applying algorithms such as Hidden Markov Models (Simpson et al, 2016) or Recurrent Neural Networks (Boža et al, 2017) that translate the collection of k-mers into consensus nucleic acid sequences. In previous work, we have demonstrated the capacity for these algorithms to detect non-standard bases by sequencing Poly(deoxyinosinic-deoxycytidylic) acid, a synthetic DNA polymer composed of alternating deoxy-inosine (I) and deoxy-cytosine (C) bases (Carr et al, 2017). This proof of principle demonstrates the detection of the non-standard inosine nucleoside, the nucleobase (hypoxanthine) of which which has been identified within meteorites (Martins et al, 2008); furthermore, work by others has demonstrated the ability to detect base modification such as methylation (Simpson et al, 2016) using novel basecalling algorithms.…”

Section: Detecting Non-standard Basesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…To test these hypotheses, we are developing the Search for Extra-Terrestrial Genomes (SETG) life-detection instrument for in-situ extraction and nanopore sequencing of nucleic acids (Carr et al, 2017 from extant or preserved life on Mars. Assuming a convergent adoption of nucleic acids as the unitary solution of genetic information storage and transmission (e.g., DNA or RNA), long-read nanopore sequencing could be capable of detecting non-standard nucleic acids (Carr, 2016;Carr et al, 2017) possibly endemic to Mars . Furthermore, longread sequencing is of particular significance for taxonomic identification at or below the species level (Benítez-Páez et al, 2016;Brown et al, 2017;Greninger et al, 2015;Quick et al, 2015) which would permit the detection of microbial forward contamination.…”

Section: Introductionmentioning

confidence: 99%

“…These experiments stress the importance of the mitigation strategies used to reduce detrimental soil-DNA interactions (e.g., adsorption to mineral surfaces, DNA destruction) and conclude in the development of a 'near-universal' extraction protocol for low-biomass Mars analog soils. As in our previous experiments (Carr et al, 2017, we require DNA extraction yields of at least 5% in order to achieve a minimum sensitivity target of 1 ppb for life-detection (i.e., 10 4 cells in 50 mg of soil).…”

Section: Introductionmentioning

confidence: 99%

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Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection

Mojarro

Hachey

Bailey

et al. 2018

Preprint

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Recent studies regarding the origin of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomicsbased life-detection instrument which integrates nucleic acid extraction and nanopore sequencing:The Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly-related to life on Earth indicating a shared-ancestry due to lithological exchange, or (2) is unrelated to life on Earth suggesting a convergent origin of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results equivalent to 1 ppb life-detection sensitivity achieved by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier.

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Section: Detecting Non-standard Basesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection

Mojarro

Hachey

Bailey

et al. 2018

Preprint

Self Cite

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“…It has been hypothesized that the water may have originated from the melting of subsurface ice, the discharge of shallow aquifers, or the deliquescence of regolith salts by atmospheric water vapor (Grimm et al, ; Kannan et al, ; Ojha et al, ). Of course, attempts have been made to confirm the source of the liquid water (Carr et al, ), and sampling locations on Mars have included subsurface regions (Byrne et al, ; Dundas et al, ; Jones et al, ). These subsurface regions can be accessed by drilling or via geological features such as lava tubes, within which the search for Extra‐Terrestrial Genomes can be used to target extant or recently dead life (Ciarletti et al, ), given the limited lifetime of DNA on Earth (~106 years, due to hydrolysis) and on Mars (~107 years, due to self‐radiation) under otherwise protected conditions (Carr et al, ; Hays et al, ).…”

Section: Discussionmentioning

confidence: 99%

Contemporary Liquid Brine Exploration on Mars: From Spectral Unmixing to Subpixel Mapping

Zhong

Luo

et al. 2019

Earth and Space Science

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Water is a critical symbol for the existence of life in deep space exploration, and thus, the confirmation of the existence of liquid water on the contemporary Martian surface is important for the future studies of the hydrologic cycle and potential life on Mars. The main Mars observation system at a global scale is the Mars Reconnaissance Orbiter; however, this system has several drawbacks, that is, it cannot simultaneously resolve the features narrower than a few meters and scrutinize the surface composition both physically and chemically, leading to deficient and unsophisticated aqueous activity detection. Therefore, in this study, a joint endmember extraction, spectral analysis, and subpixel mapping technique, which we refer to as a joint processing pipeline, was applied to accommodate the detailed spatial information with the composition information in the physical and chemical aspects through luxuriant spectra. The validation of the proposed joint processing pipeline is described in the experimental part, with a case study of the megadune in the Russell Crater of Mars. The experimental results not only confirm the superior performance of the proposed pipeline in the accurate mapping and retrieval of Mars surface geology but also provide spectral evidence for the confirmation that hydrated material existed in the Russell Crater.

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Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa

Sutton

Burton

Zaikova

et al. 2019

Sci Rep

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The search for life beyond Earth is a key motivator in space exploration. Informational polymers, like DNA and RNA, are key biosignatures for life as we know it. The MinION is a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future planetary missions. A critical unanswered question is whether the MinION and its protein-based nanopores can withstand increased radiation exposure outside Earth’s shielding magnetic field. We evaluated the effects of ionizing radiation on the MinION platform – including flow cells, reagents, and hardware – and discovered limited performance loss when exposed to ionizing doses comparable to a mission to Mars. Targets with harsher radiation environments, like Europa, would require improved radiation resistance via additional shielding or design refinements.

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Towards in situ sequencing for life detection

Cited by 27 publications

References 57 publications

Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection

Nucleic acid extraction and sequencing from low-biomass synthetic Mars analog soils for in situ life detection

Contemporary Liquid Brine Exploration on Mars: From Spectral Unmixing to Subpixel Mapping

Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa

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