1
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Ozadam H, Tonn T, Han CM, Segura A, Hoskins I, Rao S, Ghatpande V, Tran D, Catoe D, Salit M, Cenik C. Single-cell quantification of ribosome occupancy in early mouse development. Nature 2023:10.1038/s41586-023-06228-9. [PMID: 37344592 DOI: 10.1038/s41586-023-06228-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/16/2023] [Indexed: 06/23/2023]
Abstract
Translation regulation is critical for early mammalian embryonic development1. However, previous studies had been restricted to bulk measurements2, precluding precise determination of translation regulation including allele-specific analyses. Here, to address this challenge, we developed a novel microfluidic isotachophoresis (ITP) approach, named RIBOsome profiling via ITP (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key mechanism regulating genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high-coverage measurements enabled, to our knowledge, the first analysis of allele-specific ribosome engagement in early development. These led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts exhibiting allele-biased expression. By integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle-stage oocytes is the predominant determinant of protein abundance in the zygote. The Ribo-ITP approach will enable numerous applications by providing high-coverage and high-resolution ribosome occupancy measurements from ultra-low input samples including single cells.
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Affiliation(s)
- Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Tori Tonn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Crystal M Han
- Department of Mechanical Engineering, San Jose State University, San Jose, CA, USA
| | - Alia Segura
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Vighnesh Ghatpande
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Duc Tran
- Department of Chemical and Materials Engineering, San Jose State University, San Jose, CA, USA
| | - David Catoe
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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2
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Zambrana W, Catoe D, Coffman MM, Kim S, Anand A, Solis D, Sahoo MK, Pinsky BA, Bhatt AS, Boehm AB, Wolfe MK. SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level. ACS ES T Water 2022; 2:2025-2033. [PMID: 37552722 PMCID: PMC9128006 DOI: 10.1021/acsestwater.2c00050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 05/30/2023]
Abstract
Monitoring wastewater for SARS-CoV-2 from populations smaller than those served by wastewater treatment plants may help identify small spatial areas (subsewersheds) where COVID-19 infections are present. We sampled wastewater from three nested locations with different sized populations within the same sewer network at a university campus and quantified SARS-CoV-2 RNA using reverse transcriptase droplet digital polymerase chain reaction (PCR). SARS-CoV-2 RNA concentrations and/or concentrations normalized by PMMoV were positively associated with laboratory-confirmed COVID-19 cases for both the sewershed level and the subsewershed level. We also used an antigen-based assay to detect the nucleocapsid (N) antigen from SARS-CoV-2 in wastewater samples at the sewershed level. The N antigen was regularly detected at the sewershed level, but the results were not associated with either laboratory-confirmed COVID-19 cases or SARS-CoV-2 RNA concentrations. The results of this study indicate that wastewater monitoring based on quantification of SARS-CoV-2 RNA using PCR-based methods is associated with COVID-19 cases at multiple geographic scales within the subsewershed level and can serve to aid the public health response.
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Affiliation(s)
- Winnie Zambrana
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - David Catoe
- Joint Initiative for Metrology in Biology,
SLAC National Accelerator Laboratory, 2575 Sand Hill Road,
Menlo Park, California 94025, United States
| | - Mhara M. Coffman
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Archana Anand
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Daniel Solis
- Department of Pathology, Stanford
University School of Medicine, Stanford, California 94305, United
States
| | - Malaya K. Sahoo
- Department of Pathology, Stanford
University School of Medicine, Stanford, California 94305, United
States
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford
University School of Medicine, Stanford, California 94305, United
States
- Department of Medicine, Division of Infectious
Diseases and Geographic Medicine, Stanford University School of
Medicine, Stanford, California 94305, United
States
| | - Ami S. Bhatt
- Department of Medicine (Hematology) and Department of
Genetics, Stanford University, Stanford, California 94305,
United States
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Marlene K. Wolfe
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
- Gangarosa Department of Environmental Health, Rollins School
of Public Health, Emory University, Atlanta, Georgia 30322,
United States
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3
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Sivaganesan M, Willis JR, Karim M, Babatola A, Catoe D, Boehm AB, Wilder M, Green H, Lobos A, Harwood VJ, Hertel S, Klepikow R, Howard MF, Laksanalamai P, Roundtree A, Mattioli M, Eytcheson S, Molina M, Lane M, Rediske R, Ronan A, D'Souza N, Rose JB, Shrestha A, Hoar C, Silverman AI, Faulkner W, Wickman K, Kralj JG, Servetas SL, Hunter ME, Jackson SA, Shanks OC. Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917. Water Res 2022; 225:119162. [PMID: 36191524 PMCID: PMC9932931 DOI: 10.1016/j.watres.2022.119162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Mohammad Karim
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - Akin Babatola
- Environmental Services Laboratory, City of Santa Cruz, Santa Cruz, CA, USA
| | - David Catoe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Maxwell Wilder
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Hyatt Green
- Department of Environmental Biology, SUNY-ESF, Syracuse, NY, USA
| | - Aldo Lobos
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Stephanie Hertel
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Regina Klepikow
- U.S. Environmental Protection Agency, Region 7 Laboratory, Kansas City, KS, USA
| | | | | | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mia Mattioli
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie Eytcheson
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Marirosa Molina
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Molly Lane
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Richard Rediske
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, USA
| | - Amanda Ronan
- U.S. Environmental Protection Agency, Region 2 Laboratory, Edison, NJ, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Abhilasha Shrestha
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Catherine Hoar
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, New York University Tandon School of Engineering, Brooklyn, NY, USA
| | | | | | - Jason G Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Monique E Hunter
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Scott A Jackson
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
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4
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Wolfe MK, Archana A, Catoe D, Coffman MM, Dorevich S, Graham KE, Kim S, Grijalva LM, Roldan-Hernandez L, Silverman AI, Sinnott-Armstrong N, Vugia DJ, Yu AT, Zambrana W, Wigginton KR, Boehm AB. Scaling of SARS-CoV-2 RNA in Settled Solids from Multiple Wastewater Treatment Plants to Compare Incidence Rates of Laboratory-Confirmed COVID-19 in Their Sewersheds. Environ Sci Technol Lett 2021; 8:398-404. [PMID: 37566351 PMCID: PMC8056949 DOI: 10.1021/acs.estlett.1c00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 05/19/2023]
Abstract
Published and unpublished reports show that SARS-CoV-2 RNA in publicly owned treatment work (POTW) wastewater influent and solids is associated with new COVID-19 cases or incidence in associated sewersheds, but methods for comparing data collected from diverse POTWs to infer information about the relative incidence of laboratory-confirmed COVID-19 cases, and scaling to allow such comparisons, have not been previously established. Here, we show that SARS-CoV-2 N1 and N2 concentrations in solids normalized by concentrations of PMMoV RNA in solids can be used to compare incidence of laboratory confirmed new COVID-19 cases across POTWs. Using data collected at seven POTWs along the United States West Coast, Midwest, and East Coast serving ∼3% of the U.S. population (9 million people), we show that a 1 log change in N gene/PMMoV is associated with a 0.24 (range 0.19 to 0.29) log10 change in incidence of laboratory confirmed COVID-19. Scaling of N1 and N2 by PMMoV is consistent, conceptually, with a mass balance model relating SARS-CoV-2 RNA to the number of infected individuals shedding virus in their stool. This information should support the application of wastewater-based epidemiology to inform the response to the COVID-19 pandemic and potentially future viral pandemics.
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Affiliation(s)
- Marlene K. Wolfe
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Anand Archana
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - David Catoe
- Joint Initiative for Metrology in Biology,
SLAC National Accelerator Laboratory, Stanford, California
94305, United States
| | - Mhara M. Coffman
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Samuel Dorevich
- Division of Environmental and Occupational Health
Sciences, School of Public Health, University of Illinois,
Chicago, Illinois 60612, United States
| | - Katherine E. Graham
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Lorelay Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Laura Roldan-Hernandez
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Andrea I. Silverman
- Department of Civil and Urban Engineering, Tandon
School of Engineering, New York University, Brooklyn, New York
11201, United States
- School of Global Public Health, New York
University, New York, New York 10003, United
States
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University
School of Medicine, Stanford, California 94305, United
States
| | - Duc J. Vugia
- Infectious Diseases Branch, California
Department of Public Health, Richmond, California 94804, United
States
| | - Alexander T. Yu
- Infectious Diseases Branch, California
Department of Public Health, Richmond, California 94804, United
States
| | - Winnie Zambrana
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering,
University of Michigan,Ann Arbor, Michigan 48109,
United States
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford, California
94305, United States
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5
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Graham KE, Loeb SK, Wolfe MK, Catoe D, Sinnott-Armstrong N, Kim S, Yamahara KM, Sassoubre LM, Mendoza Grijalva LM, Roldan-Hernandez L, Langenfeld K, Wigginton KR, Boehm AB. SARS-CoV-2 RNA in Wastewater Settled Solids Is Associated with COVID-19 Cases in a Large Urban Sewershed. Environ Sci Technol 2021; 55:488-498. [PMID: 33283515 PMCID: PMC7737534 DOI: 10.1021/acs.est.0c06191] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 05/11/2023]
Abstract
Wastewater-based epidemiology may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the preanalytical and analytical approaches and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise, SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlated positively and significantly with COVID-19 clinically confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARS-CoV-2 in influent.
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Affiliation(s)
- Katherine E. Graham
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Stephanie K. Loeb
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Marlene K. Wolfe
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - David Catoe
- Joint Initiative for Metrology in Biology,
SLAC National Accelerator Laboratory, Stanford 94305,
California, United States
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University
School of Medicine, Stanford 94305, California, United
States
- Emmett Interdisciplinary Program in Environment and
Resources, Stanford University, Stanford 94305, California,
United States
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Kevan M. Yamahara
- Monterey Bay Aquarium Research
Institute, Moss Landing 95039, California, United
States
| | - Lauren M. Sassoubre
- Department of Engineering, University of San
Francisco, San Francisco 94117, California, United
States
| | - Lorelay M. Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Laura Roldan-Hernandez
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Kathryn Langenfeld
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor 48109, Michigan,
United States
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor 48109, Michigan,
United States
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
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6
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Scanlan LD, Coskun SH, Jaruga P, Hanna SK, Sims CM, Almeida JL, Catoe D, Coskun E, Golan R, Dizdaroglu M, Nelson BC. Measurement of Oxidatively Induced DNA Damage in Caenorhabditis elegans with High-Salt DNA Extraction and Isotope-Dilution Mass Spectrometry. Anal Chem 2019; 91:12149-12155. [PMID: 31454479 PMCID: PMC6996937 DOI: 10.1021/acs.analchem.9b01503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Caenorhabditis elegans is used extensively as a medical and toxicological model organism. However, little is known about background levels of oxidatively induced DNA damage in the nematode or how culturing methods affect DNA damage levels. The tough C. elegans cuticle makes it challenging to extract genomic DNA without harsh procedures that can artifactually increase DNA damage. Therefore, a mild extraction protocol based on enzymatic digestion of the C. elegans cuticle with high-salt phase-separation of DNA has been developed and optimized. This method allows for efficient extraction of >50 μg DNA using a minimum of 250000 nematodes grown in liquid culture. The extracted DNA exhibited acceptable RNA levels (<10% contamination), functionality in polymerase chain reaction assays, and reproducible DNA fragmentation. Gas chromatography/tandem mass spectrometry (GC-MS/MS) with isotope-dilution measured lower lesion levels in high-salt extracts than in phenol extracts. Phenolic extraction produced a statistically significant increase in 8-hydroxyguanine, a known artifact, and additional artifactual increases in 2,6-diamino-4-hydroxy-5-formamidopyrimidine, 4,6-diamino-5-formamidopyrimidine, and 8-hydroxyadenine. The high-salt DNA extraction procedure utilizes green solvents and reagents and minimizes artifactual DNA damage, making it more suitable for molecular and toxicological studies in C. elegans. This is, to our knowledge, the first use of GC-MS/MS to measure multiple 8,5'-cyclopurine-2'-deoxynucleosides in a toxicologically important terrestrial organism.
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Affiliation(s)
- Leona D. Scanlan
- Material Measurement Laboratory – Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sanem Hosbas Coskun
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Gazi University, Faculty of Pharmacy, Ankara, 06330, Turkey
| | - Pawel Jaruga
- Material Measurement Laboratory – Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Shannon K. Hanna
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Christopher M. Sims
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jamie L. Almeida
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - David Catoe
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Erdem Coskun
- Material Measurement Laboratory – Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Rachel Golan
- Material Measurement Laboratory – Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Miral Dizdaroglu
- Material Measurement Laboratory – Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Bryant C. Nelson
- Material Measurement Laboratory – Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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7
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Han CM, Catoe D, Munro SA, Khnouf R, Snyder MP, Santiago JG, Salit ML, Cenik C. Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer. Lab Chip 2019; 19:2741-2749. [PMID: 31328753 PMCID: PMC7272188 DOI: 10.1039/c9lc00311h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We present an on-chip method for the extraction of RNA within a specific size range from low-abundance samples. We use isotachophoresis (ITP) with an ionic spacer and a sieving matrix to enable size-selection with a high yield of RNA in the target size range. The spacer zone separates two concentrated ITP peaks, the first containing unwanted single nucleotides and the second focusing RNA of the target size range (2-35 nt). Our ITP method excludes >90% of single nucleotides and >65% of longer RNAs (>35 nt). Compared to size selection using gel electrophoresis, ITP-based size-selection yields a 2.2-fold increase in the amount of extracted RNAs within the target size range. We also demonstrate compatibility of the ITP-based size-selection with downstream next generation sequencing. On-chip ITP-prepared samples reveal higher reproducibility of transcript-specific measurements compared to samples size-selected by gel electrophoresis. Our method offers an attractive alternative to conventional sample preparation for sequencing with shorter assay time, higher extraction efficiency and reproducibility. Potential applications of ITP-based size-selection include sequencing-based analyses of small RNAs from low-abundance samples such as rare cell types, samples from fluorescence activated cell sorting (FACS), or limited clinical samples.
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Affiliation(s)
- Crystal M Han
- Department of Mechanical Engineering, San Jose State University, San Jose, CA 95192, USA and Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, USA.
| | - David Catoe
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, USA.
| | - Sarah A Munro
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, USA. and Minnesota Supercomputing Institute, University of Minnesota, MN 55455, USA
| | - Ruba Khnouf
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, Jordan and Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Marc L Salit
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford, CA, USA.
| | - Can Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA.
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8
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Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data 2016; 3:160025. [PMID: 27271295 PMCID: PMC4896128 DOI: 10.1038/sdata.2016.25] [Citation(s) in RCA: 385] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 03/15/2016] [Indexed: 02/01/2023] Open
Abstract
The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.
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Affiliation(s)
- Justin M. Zook
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - David Catoe
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Jennifer McDaniel
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Lindsay Vang
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Noah Spies
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Stanford University, Stanford, California 94305, USA
| | - Arend Sidow
- Stanford University, Stanford, California 94305, USA
| | - Ziming Weng
- Stanford University, Stanford, California 94305, USA
| | - Yuling Liu
- Stanford University, Stanford, California 94305, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA
| | - Elizabeth Henaff
- Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA
| | - Alexa B.R. McIntyre
- Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA
| | - Dhruva Chandramohan
- Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University, New York, New York 10065, USA
| | - Feng Chen
- Illumina Mission Bay, San Francisco, California 94158, USA
| | - Erich Jaeger
- Illumina Mission Bay, San Francisco, California 94158, USA
| | - Ali Moshrefi
- Illumina Mission Bay, San Francisco, California 94158, USA
| | - Khoa Pham
- BioNano Genomics, San Diego, California 92121, USA
| | | | | | | | | | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | - Han Cao
- BioNano Genomics, San Diego, California 92121, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | | | | | - Natali Gulbahce
- Complete Genomics Inc., Mountain View, California 94043, USA
| | - Keyan Zhao
- Thermo Fisher Scientific, South San Francisco, California 94080, USA
| | - Srinka Ghosh
- Thermo Fisher Scientific, South San Francisco, California 94080, USA
| | - Fiona Hyland
- Thermo Fisher Scientific, South San Francisco, California 94080, USA
| | - Yutao Fu
- Thermo Fisher Scientific, South San Francisco, California 94080, USA
| | - Mark Chaisson
- Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, Maryland 20892, USA
| | - Jonathan Trow
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, Maryland 20892, USA
| | - Stephen T. Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, Maryland 20892, USA
| | | | | | - Jason Bobe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- PersonalGenomes.org, Boston, Massachusetts 02115, USA
| | - Preston Estep
- PersonalGenomes.org, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - George M. Church
- PersonalGenomes.org, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Kirkeveien 166, Bygg 25, Oslo 0450, Norway
| | | | - Marc Salit
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Stanford University, Stanford, California 94305, USA
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