Biology subjects

Zuber, M. T.

Publications and source records attributed to Zuber, M. T..

6 recordsLinked to original sources

bioRxiv2024

Nanogap Solid-State Single-Molecule Detection at Mars, Europa, and Microgravity Conditions

Solid-state nanogap systems are an emerging technology for in-situ life detection due to their single-molecule resolution of a wide range of biomolecules, including amino acids and informational polymers, at the parts per billion to trillion level. By targeting the abundance distributions of organic molecules, this technology is a candidate for detecting ancient and extant life and discriminating between biotic and abiotic organics on future planetary missions to Mars and icy moons such as Enceladus and Europa. A benchtop system developed at Osaka University has a proven ability to detect and discriminate among single amino acids, RNA, and DNA using nanogap chips. The Electronic Life-detection Instrument for Enceladus/Europa (ELIE) prototype was subsequently developed to make this technology viable for space instrumentation through the simplification of electronics, reduction of size and weight, and automation of gap formation. Initial ground testing using a manually formed nanogap with the first ELIE prototype detected the amino acid L-proline. However, this manual adjustment approach posed limitations in maintaining a consistent gap size. To address this challenge, we integrated an automated piezo actuator to enable real-time gap control, permitting single-molecule identification of a target amino acid, L-proline, under reduced gravity (g), including Mars (g = 0.378), Europa or Lunar (g = 0.166), and microgravity conditions (g = 0.03-0.06), as validated through parabolic flight testing. Power supply noise and experimental constraints of the experiment design limited data collection to short segments of good-quality data. Nevertheless, the subsequent analysis of detected events within these segments revealed a consistent system performance and a controlled gap size across the different accelerations. This finding highlights the systems resilience to physical vibrations. Future goals are to progress the instrument towards technology readiness level 4 with further reductions of size and mass, lower noise, and additional system automation. With further development, ELIE has the potential to be an autonomous and sensitive single-molecule detection instrument for deployment throughout the solar system.

biophysics↗

bioRxiv2022

Solid-State Single-Molecule Sensing with the Electronic Life-detection Instrument for Enceladus/Europa (ELIE)

Growing evidence of the potential habitability of Ocean Worlds across our Solar System is motivating the advancement of technologies capable of detecting life as we know it - sharing a common ancestry or common physicochemical origin to life on Earth - or dont know it, representing a distinct genesis event of life quite different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of- principle in a laboratory environment, we demonstrate single-molecule detection of the amino acid L-proline at a 10 {micro}M concentration in a compact system. Based on ELIEs solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecules highest energy occupied molecular orbital and lowest energy unoccupied molecular orbital) as a novel approach to measure amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived (-amino acids in order to reduce false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in the plume, surface, or subsurface of ice moons such as Enceladus or Europa. One Sentence SummaryA solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we dont.

biophysics↗

bioRxiv2020

In search of the RNA world on Mars

Advances in origins of life research and prebiotic chemistry suggest that life as we know it may have emerged from an earlier RNA World. However, it has been difficult to reconcile the conditions used in laboratory experiments with real-world geochemical environments that may have existed on the early Earth and hosted the origin(s) of life. This challenge is in part due to geologic resurfacing and recycling that have erased the overwhelming majority of the Earths prebiotic history. We therefore propose that Mars, a planet frozen in time, comprised of many surfaces that have remained relatively unchanged since their formation >4 Gya, is the best alternative to search for environments consistent with geochemical requirements imposed by the RNA world. In this study we synthesize in situ and orbital observations of Mars and modeling of its early atmosphere into solutions containing a range of pHs and concentrations of prebiotically relevant metals (Fe2+, Mg2+, and Mn2+), spanning various candidate aqueous environments. We then experimentally determine RNA degradation kinetics due to metal-catalyzed hydrolysis and evaluate whether early Mars could have been permissive towards the accumulation of long-lived RNA polymers. Our results indicate that a Mg2+-rich basalt sourcing metals to a slightly acidic (pH 5.4) aqueous environment mediates the slowest rates of metal-catalyzed RNA hydrolysis, though geologic evidence and modeling of basalt weathering suggest that aquifers on Mars would be near neutral (pH [~]7). Moreover, oxidizing conditions on Mars have major consequences regarding the availability oxygen-sensitive prebiotic metals (i.e., Fe2+ and Mn2+) very early in its history due to increased RNA degradation rates and precipitation. Overall, 1) low pH better preserves RNA than basic conditions at high concentrations; 2) acidic to neutral pH environments with Fe2+ or Mn2+ will hydrolyze more RNA; and 3) alkaline environments with Mg2+ dramatically hydrolyze more RNA.

molecular biology↗

bioRxiv2020

Nanopore Sequencing at Mars, Europa and Microgravity Conditions

Nanopore sequencing, as represented by Oxford Nanopore Technologies MinION, is a promising technology for in situ life detection and for microbial monitoring including in support of human space exploration, due to its small size, low mass ([~]100 g) and low power ([~]1W). Now ubiquitous on Earth and previously demonstrated on the International Space Station (ISS), nanopore sequencing involves translocation of DNA through a biological nanopore on timescales of milliseconds per base. Nanopore sequencing is now being done in both controlled lab settings as well as in diverse environments that include ground, air and space vehicles. Future space missions may also utilize nanopore sequencing in reduced gravity environments, such as in the search for life on Mars (Earth-relative gravito-inertial acceleration (GIA) g = 0.378), or at icy moons such as Europa (g = 0.134) or Enceladus (g = 0.012). We confirm the ability to sequence at Mars as well as near Europa or Lunar (g = 0.166) and lower g levels, demonstrate the functionality of updated chemistry and sequencing protocols under parabolic flight, and reveal consistent performance across g level, during dynamic accelerations, and despite vibrations with significant power at translocation-relevant frequencies. Our work strengthens the use case for nanopore sequencing in dynamic environments on Earth and in space, including as part of the search for nucleic-acid based life beyond Earth.

genomics↗

bioRxiv2018

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

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 metagenomics-based 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.

molecular biology↗

bioRxiv2017

CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing

MotivationLong-read nanopore sequencing technology is of particular significance for taxonomic identification at or below the species level. For many environmental samples, the total extractable DNA is far below the current input requirements of nanopore sequencing, preventing \"sample to sequence\" metagenomics from low-biomass or recalcitrant samples.\n\nResultsHere we address this problem by employing carrier sequencing, a method to sequence low-input DNA by preparing the target DNA with a genomic carrier to achieve ideal library preparation and sequencing stoichiometry without amplification. We then use CarrierSeq, a sequence analysis workflow to identify the low-input target reads from the genomic carrier. We tested CarrierSeq experimentally by sequencing from a combination of 0.2 ng Bacillus subtilis ATCC 6633 DNA in a background of 1 g Enterobacteria phage {lambda} DNA. After filtering of carrier, low quality, and low complexity reads, we detected target reads (B. subtilis), contamination reads, and \"high quality noise reads\" (HQNRs) not mapping to the carrier, target or known lab contaminants. These reads appear to be artifacts of the nanopore sequencing process as they are associated with specific channels (pores). By treating reads as a Poisson arrival process, we implement a statistical test to reject data from channels dominated by HQNRs while retaining target reads.\n\nAvailabilityCarrierSeq is an open-source bash script with supporting python scripts which leverage a variety of bioinformatics software packages on macOS and Ubuntu. Supplemental documentation is available from Github - https://github.com/amojarro/carrierseq. In addition, we have compiled all required dependencies in a Docker image available from - https://hub.docker.com/r/mojarro/carrierseq.

bioinformatics↗