Article
Food Science & Technology
Robert G. Hatfield, David Ryder, Annabel M. Tidy, David M. Hartnell, Karl J. Dean, Frederico M. Batista
Summary: The armoured dinoflagellate Alexandrium is commonly found in temperate and tropical marine environments worldwide. It produces potent neurotoxins called saxitoxins, which pose a significant threat to animal, environmental, and human health. This study presents a novel assay that combines recombinase polymerase amplification with nanopore sequencing to accurately identify individual species of Alexandrium in sea water samples, allowing for the detection and monitoring of toxic variants.
Article
Environmental Sciences
Xiang Li, Miao Zhang, Chenyuan Dang, Ziqi Wu, Yu Xia
Summary: Nanopore metagenomic sequencing allows for rapid analysis of microbiological ecosystems. By studying high-altitude glacier meltwater at Qilian Mountain, China, it was found that microbial communities and functionalities varied significantly based on vertical alpine distribution. The Qilian meltwater microbiome displayed metabolic functions such as sulfur oxidation, selenite decomposition, photosynthesis, energy production, enzymic activity, and UV tolerance. The classification and functionalities of Qilian meltwater were consistent with other glacial microbiomes, indicating stable molecular adaptations and lifestyles across the globe.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Sophie A. Simon, Katharina Schmidt, Lea Griesdorn, Andre R. Soares, Till L. V. Bornemann, Alexander J. Probst
Summary: This study evaluated the use of lower-than-recommended DNA quantities for Nanopore library preparation and found that high-quality MAGs could still be recovered when the input level reached 35ng. Furthermore, Nanopore reads from input quantities as low as 1ng improved the quality of hybrid assemblies when combined with short-read data.
Article
Immunology
Yinghu Chen, Lingfeng Mao, Dengming Lai, Weize Xu, Yuebai Zhang, Sihao Wu, Di Yang, Shaobo Zhao, Zhicong Liu, Yi Xiao, Yi Tang, Xiaofang Meng, Min Wang, Jueliang Shi, Qixing Chen, Qiang Shu
Summary: We developed a rapid and low-cost method for 16S rDNA nanopore sequencing by adding barcodes to the 16S primer. The accuracy rate for identifying common pulmonary pathogens was 100% and the turnaround time was shortened to 6-8 hours. By comparing the results with culture or PCR, the method showed high consistency in terms of sensitivity and specificity.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Yupei You, Michael B. Clark, Heejung Shim
Summary: In this study, a method called "NanoSplicer" was developed to accurately identify RNA splice junctions using raw nanopore sequencing data. By comparing the observed signal with candidate signals, the method is able to determine the most likely splice junction. Testing on both synthetic and biological mRNA datasets showed that NanoSplicer improves splice junction identification, especially in cases with high basecalling error rates near the splice junction.
Article
Microbiology
Adriel Latorre-Perez, Helena Gimeno-Valero, Kristie Tanner, Javier Pascual, Cristina Vilanova, Manuel Porcar
Summary: This study evaluated the use of Nanopore sequencing during an expedition to the Tabernas Desert in Spain, finding a strong correlation between Nanopore and culturing data. Portable sequencers have the potential to be key tools for in situ-informed bioprospecting strategies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Ryan R. R. Wick, Louise M. M. Judd, Kathryn E. E. Holt
Summary: A perfect bacterial genome assembly requires improved long-read sequencing, assemblers, and polishers. By combining Oxford Nanopore Technologies long reads and Illumina short reads, we suggest using Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, and additional short-read polishing tools and manual curation. We also discuss potential challenges and provide an online tutorial for reference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Pei-Ling Yu, James C. Fulton, Owen H. Hudson, Jose C. Huguet-Tapia, Jeremy T. Brawner
Summary: This study developed a broad-spectrum fungal identification tool using high-throughput Nanopore sequencing and enrichment probes. It provides a fast and accurate method for fungal identification, and also offers a platform for identifying other plant pathogens.
Article
Biotechnology & Applied Microbiology
Haley Sanderson, Madeline C. Mccarthy, Chinenye R. Nnajide, Jessica Sparrow, Joseph E. Rubin, Jo-Anne R. Dillon, Aaron P. White
Summary: This study determined the impact of sequencing and assembly factors on plasmid detection in E. coli. Hybrid assembly combined with plasmid DNA extractions was found to reliably detect plasmids in E. coli. Long read sequencing is sufficient for plasmid detection, but more prone to errors when analyzing a large number of isolates.
Article
Ecology
Nicholas LeBlanc
Summary: The incorporation of plant biomass as green manures into soil can improve crop and soil health by reducing soilborne diseases. This study found that different types of green manures had diverse effects on the taxonomic composition and functional traits of soil bacterial communities. These changes may have implications for the beneficial effects of green manures on plant and soil health.
Article
Biochemical Research Methods
Xiaoyu Guan, Yuqin Wang, Wei Shao, Zhongnian Li, Shuo Huang, Daoqiang Zhang
Summary: This study proposes a sequence-to-sequence (S2S) module to address the issue of unequal length in RNA structural events, and utilizes a sequence-to-sequence neural network based on deep learning to automatically extract features. The experimental results demonstrate a performance increase of about 2% compared to previous methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Immunology
Laura T. Phillips, Adam A. Witney, Martina Furegato, Ken G. Laing, Liqing Zhou, S. Tariq Sadiq
Summary: Early versions of nanopore technology show promise as a real-time surveillance tool, capable of accurately identifying closely related Neisseria gonorrhoeae strains and important antimicrobial resistance markers from cultured isolates, with very short sequencing times.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Maria G. Khrenova, Tatiana Panova, Vladimir A. Rodin, Maxim A. Kryakvin, Dmitrii A. Lukyanov, Ilya A. Osterman, Maria Zvereva
Summary: Nanopore sequencing is a new method for determining nucleotide sequences, and in this study, it was used to assemble the genome of an E. coli strain with antibiotic resistance. The Flye program showed the best assembly results compared to other programs. The required coverage depth for successful assembly depends on the read length, with 30x coverage depth sufficient for long reads and 50x needed for shorter reads. Mechanical mixing should be avoided during sample preparation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Zhao Chen, David L. Erickson, Jianghong Meng
Summary: Oxford Nanopore sequencing is widely used for bacterial pathogen genome assembly, but high error rates in long reads necessitate polishing with Illumina short reads. NextPolish outperformed Pilon in improving genomic analyses of bacterial pathogens, requiring varying numbers of rounds for different strains. Simulated and real reads showed that the accuracy of genomic analyses depended on the optimization tool and the specific bacterial strain.
Article
Chemistry, Multidisciplinary
Jinbo Zhu, Ran Tivony, Filip Boskovic, Joana Pereira-Dias, Sarah E. Sandler, Stephen Baker, Ulrich F. Keyser
Summary: In this study, a nanopore sensor based on DNA dumbbell nanoswitches was established for multiplexed nucleic acid detection and bacterial identification. By assembling four DNA dumbbell nanoswitches on one carrier, simultaneous detection of four different sequences of nucleic acids was achieved. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using barcoded DNA carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, different bacterial species could be identified even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Microbiology
Pilar Junier, Guillaume Cailleau, Ilona Palmieri, Celine Vallotton, Olivia C. Trautschold, Thomas Junier, Christophe Paul, Danae Bregnard, Fabio Palmieri, Aislinn Estoppey, Matteo Buffi, Andrea Lohberger, Aaron Robinson, Julia M. Kelliher, Karen Davenport, Geoffrey L. House, Demosthenes Morales, La Verne Gallegos-Graves, Armand E. K. Dichosa, Simone Lupini, Hang N. Nguyen, Jamey D. Young, Debora F. Rodrigues, A. Nicholas G. Parra-Vasquez, Saskia Bindschedler, Patrick S. G. Chain
Summary: Interactions between bacteria and fungi play a crucial role in ecosystem functioning, with some bacteria using fungal hyphae to disperse in unsaturated soil conditions. Developing tools to investigate these interactions is important for understanding how BFIs affect processes in unsaturated environments.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Instruments & Instrumentation
Kyle Uckert, Rohit Bhartia, Luther W. Beegle, Brian Monacelli, Sanford A. Asher, Aaron S. Burton, Sergei Bykov, Kristine Davis, Marc D. Fries, Ryan S. Jakubek, Joseph Razzell Hollis, Ryan D. Roppel, Yen-Hung Wu
Summary: The translation describes the wavelength calibration process and principles of the SHERLOC spectrometer for analyzing samples on the surface of Mars, as well as the working principle and main parameters of the instrument. It details how SHERLOC uses deep ultraviolet Raman and fluorescence spectroscopy to analyze samples on the Martian surface, and highlights the characteristics and design of the spectrometer.
APPLIED SPECTROSCOPY
(2021)
Article
Multidisciplinary Sciences
Jae Young Choi, Xiaoguang Dai, Ornob Alam, Julie Z. Peng, Priyesh Rughani, Scott Hickey, Eoghan Harrington, Sissel Juul, Julien F. Ayroles, Michael D. Purugganan, Elizabeth A. Stacy
Summary: The study conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant adaptive radiation of woody plants in Hawaii. It was found that Hawaiian Metrosideros originated from a single colonization event and showed evidence of extensive reticulation and admixture between taxa. Divergent selection was identified as driving the formation of differentiation outliers in early stages of speciation/divergence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Astronomy & Astrophysics
Rohit Bhartia, Luther W. Beegle, Lauren DeFlores, William Abbey, Joseph Razzell Hollis, Kyle Uckert, Brian Monacelli, Kenneth S. Edgett, Megan R. Kennedy, Margarite Sylvia, David Aldrich, Mark Anderson, Sanford A. Asher, Zachary Bailey, Kerry Boyd, Aaron S. Burton, Michael Caffrey, Michael J. Calaway, Robert Calvet, Bruce Cameron, Michael A. Caplinger, Brandi L. Carrier, Nataly Chen, Amy Chen, Matthew J. Clark, Samuel Clegg, Pamela G. Conrad, Moogega Cooper, Kristine N. Davis, Bethany Ehlmann, Linda Facto, Marc D. Fries, Dan H. Garrison, Denine Gasway, F. Tony Ghaemi, Trevor G. Graff, Kevin P. Hand, Cathleen Harris, Jeffrey D. Hein, Nicholas Heinz, Harrison Herzog, Eric Hochberg, Andrew Houck, William F. Hug, Elsa H. Jensen, Linda C. Kah, John Kennedy, Robert Krylo, Johnathan Lam, Mark Lindeman, Justin McGlown, John Michel, Ed Miller, Zachary Mills, Michelle E. Minitti, Fai Mok, James Moore, Kenneth H. Nealson, Anthony Nelson, Raymond Newell, Brian E. Nixon, Daniel A. Nordman, Danielle Nuding, Sonny Orellana, Michael Pauken, Glen Peterson, Randy Pollock, Heather Quinn, Claire Quinto, Michael A. Ravine, Ray D. Reid, Joe Riendeau, Amy J. Ross, Joshua Sackos, Jacob A. Schaffner, Mark Schwochert, Molly O. Shelton, Rufus Simon, Caroline L. Smith, Pablo Sobron, Kimberly Steadman, Andrew Steele, Dave Thiessen, Vinh D. Tran, Tony Tsai, Michael Tuite, Eric Tung, Rami Wehbe, Rachel Weinberg, Ryan H. Weiner, Roger C. Wiens, Kenneth Williford, Chris Wollonciej, Yen-Hung Wu, R. Aileen Yingst, Jason Zan
Summary: SHERLOC is a robotic arm-mounted instrument on NASA's Perseverance rover, equipped with two primary boresights for generating chemical maps and capturing color images. By utilizing fluorescence and Raman spectroscopy, along with a deep UV laser, SHERLOC is able to analyze organics, minerals, and chemicals important for potential biogenicity on Mars. With the ability to cover areas up to 7x7 mm and acquire data in under 10 minutes, SHERLOC provides a microscopic view of the organic geochemistry at the Perseverance field site, enabling unprecedented analysis of geological materials for scientific research and Mars sample return missions.
SPACE SCIENCE REVIEWS
(2021)
Article
Geochemistry & Geophysics
Katharina Kaiser, Fabian Schulz, Julien F. Maillard, Felix Hermann, Iago Pozo, Diego Pena, H. James Cleaves, Aaron S. Burton, Gregoire Danger, Carlos Afonso, Scott Sandford, Leo Gross
Summary: Researchers used high-resolution atomic force microscopy to atomically resolve individual molecules from Murchison meteorite samples. They also proposed a method for extracting and preparing meteorite samples for investigation. By processing the samples, they were able to increase the fraction of molecules that could be resolved by atomic force microscopy and identify organic constituents and molecular moieties.
METEORITICS & PLANETARY SCIENCE
(2022)
Article
Astronomy & Astrophysics
Gerhard Kminek, James N. Benardini, Frank E. Brenker, Timothy Brooks, Aaron S. Burton, Suresh Dhaniyala, Jason P. Dworkin, Jeffrey L. Fortman, Mihaela Glamoclija, Monica M. Grady, Heather Graham, Junichi Haruyama, Thomas L. Kieft, Marion Koopmans, Francis M. McCubbin, Michael A. Meyer, Christian Mustin, Tullis C. Onstott, Neil Pearce, Lisa M. Pratt, Mark A. Sephton, Sandra Siljestrom, Haruna Sugahara, Shino Suzuki, Yohey Suzuki, Mark van Zuilen, Michel Viso
Summary: The Committee on Space Research (COSPAR) has developed the Sample Safety Assessment Framework (SSAF) to evaluate the potential harm of samples returned from Mars. The framework is based on a positive hypothesis that seeks to exclude the presence of Martian life in the samples. Further work is needed to determine the level of assurance, conduct analogue tests, and gather relevant contamination knowledge. The framework can be applied to other Mars sample return missions.
Article
Multidisciplinary Sciences
Carina Lee, Jessica M. Weber, Laura E. Rodriguez, Rachel Y. Sheppard, Laura M. Barge, Eve L. Berger, Aaron S. Burton
Summary: Chirality plays a central role in the evolution of biological systems, but why biology has a strong preference for specific chiralities remains controversial. The chirality of organic compounds and minerals affects the preservation and detection of organic molecules. This paper reviews the properties and processes involved, and discusses laboratory reactions and analytical techniques, as well as current and future technologies in planetary missions.
Editorial Material
Biochemical Research Methods
Miten Jain, Robin Abu-Shumays, Hugh E. Olsen, Mark Akeson
Summary: Nanopore direct RNA sequencing is a valuable technology for reading continuous native RNA strands. It has been used to document nucleotide modifications and 3' polyadenosine tails without the need for additional chemistry steps. The success of this technology depends on improving basecall accuracy and reducing RNA input requirements, which will drive its broader adoption in the field of molecular biology and cell biology.
Article
Multidisciplinary Sciences
K. A. Farley, K. M. Stack, D. L. Shuster, B. H. N. Horgan, J. A. Hurowitz, J. D. Tarnas, J. I. Simon, V. Z. Sun, E. L. Scheller, K. R. Moore, S. M. McLennan, P. M. Vasconcelos, R. C. Wiens, A. H. Treiman, L. E. Mayhew, O. Beyssac, T. V. Kizovski, N. J. Tosca, K. H. Williford, L. S. Crumpler, L. W. Beegle, J. F. Bell, B. L. Ehlmann, Y. Liu, J. N. Maki, M. E. Schmidt, A. C. Allwood, H. E. F. Amundsen, R. Bhartia, T. Bosak, A. J. Brown, B. C. Clark, A. Cousin, O. Forni, T. S. J. Gabriel, Y. Goreva, S. Gupta, S. -E. Hamran, C. D. K. Herd, K. Hickman-Lewis, J. R. Johnson, L. C. Kah, P. B. Kelemen, K. B. Kinch, L. Mandon, N. Mangold, C. Quantin-Nataf, M. S. Rice, P. S. Russell, S. Sharma, S. Siljestrom, A. Steele, R. Sullivan, M. Wadhwa, B. P. Weiss, A. J. Williams, B. V. Wogsland, P. A. Willis, T. A. Acosta-Maeda, P. Beck, K. Benzerara, S. Bernard, A. S. Burton, E. L. Cardarelli, B. Chide, E. Clave, E. A. Cloutis, B. A. Cohen, A. D. Czaja, V. Debaille, E. Dehouck, A. G. Fairen, D. T. Flannery, S. Z. Fleron, T. Fouchet, J. Frydenvang, B. J. Garczynski, E. F. Gibbons, E. M. Hausrath, A. G. Hayes, J. Henneke, J. L. Jorgensen, E. M. Kelly, J. Lasue, S. Le Mouelic, J. M. Madariaga, S. Maurice, M. Merusi, P. -Y. Meslin, S. M. Milkovich, C. C. Million, R. C. Moeller, J. I. Nunez, A. M. Ollila, G. Paar, D. A. Paige, D. A. K. Pedersen, P. Pilleri, C. Pilorget, P. C. Pinet, J. W. Rice, C. Royer, V. Sautter, M. Schulte, M. A. Sephton, S. K. Sharma, S. F. Sholes, N. Spanovich, M. St. Clair, C. D. Tate, K. Uckert, S. J. VanBommel, A. G. Yanchilina, M. -P. Zorzano
Summary: The Perseverance rover has discovered water-altered igneous rocks in the Jezero crater on Mars and found evidence of brine evaporation in the core samples. These samples may be brought back to Earth for further research.
Review
Astronomy & Astrophysics
Marc D. Fries, Carina Lee, Rohit Bhartia, Joseph Razzell Hollis, Luther W. Beegle, Kyle Uckert, Trevor G. Graff, William Abbey, Zachary Bailey, Eve L. Berger, Aaron S. Burton, Michael J. Callaway, Emily L. Cardarellis, Kristine N. Davis, Lauren DeFloress, Kenneth S. Edgete, Allison C. Fox, Daniel H. Garrison, Nikole C. Haney, Roger S. Harrington, Ryan S. Jakubek, Megan R. Kennedy, Keyron Hickman-Lewis, Francis M. McCubbin, Ed Millers, Brian Monacelli, Randy Pollocks, Richard Rhodes, Sandra Siljestrom, Sunanda Sharman, Caroline L. Smith, Andrew Steele, Margarite Sylvia, Vinh D. Tran, Ryan H. Weiner, Anastasia G. Yanchilina, R. Aileen Yingst
Summary: The SHERLOC instrument on NASA's Perseverance rover is used to study geological materials on Mars. In order to ensure data accuracy, the instrument requires calibration, with calibration targets located at the front of the rover and including various types of targets for calibration purposes.
SPACE SCIENCE REVIEWS
(2022)
Article
Biology
Allison C. Fox, Jason D. Boettger, Eve L. Berger, Aaron S. Burton
Summary: The salt-induced peptide formation (SIPF) reaction is a plausible mechanism for the polymerization of amino acids into peptides on early Earth. Previous studies suggested that the distortion of the CuCl active complex could amplify the chiral differences between l- and d-amino acids, leading to stereoselectivity. However, this study found that the geometry of the active complex is not the primary driver of stereoselectivity in the SIPF reaction.