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Romano P, Simonetti S, Gambi MC, Luckenbach T, Zupo V, Corsi I. Preliminary investigation on the potential involvement of an ABC-like gene in Halomicronema metazoicum (Cyanobacteria) tolerance to low seawater pH in an ocean acidification scenario. MARINE POLLUTION BULLETIN 2024; 205:116584. [PMID: 38878421 DOI: 10.1016/j.marpolbul.2024.116584] [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: 12/05/2023] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 07/24/2024]
Abstract
Decreasing ocean surface pH, called ocean acidification (OA), is among the major risks for marine ecosystems due to human-driven atmospheric pCO2 increase. Understanding the molecular mechanisms of adaptation enabling marine species to tolerate a lowered seawater pH could support predictions of consequences of future OA scenarios for marine life. This study examined whether the ATP-binding cassette (ABC)-like gene slr2019 confers tolerance to the marine cyanobacterium Halomicronema metazoicum to low seawater pH conditions (7.7, 7.2, 6.5) in short- and long-term exposures (7 and 30 d). Photosynthetic pigment content indicated that the species can tolerate all three lowered-pH conditions. At day 7, slr2019 was up-regulated at pH 7.7 while no changes were observed at lower pH. After 30-d exposure, a significant decrease in slr2019 transcript levels was observed in all low-pH treatments. These first results indicate an effect of low pH on the examined transporter expression in H. metazoicum.
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Affiliation(s)
- Patrizia Romano
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Department of BEOM, Napoli, Italy.
| | - Silvia Simonetti
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Integrative Marine Ecology Department, Napoli, Italy.
| | | | - Till Luckenbach
- Department Ecotoxicology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Valerio Zupo
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Integrative Marine Ecology Department, Napoli, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, via Mattioli, 4, 53100 Siena, Italy
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2
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Chaffin JD, Barker KB, Bickman SR, Bratton JF, Bridgeman TB, Bhatia M, Buchholz SD, Bullerjahn GS, Johengen TH, Kang DW, Lewis GG, Lochhead MJ, Macdonald BM, Petrou CL, Platz M, Purcell H, Roser J, Seo Y, Siddiquee M, Snyder B, Taylor AT, Verhamme EM, Westrick JA. An assessment of a biosensor system for the quantification of microcystins in freshwater cyanobacterial blooms. Anal Biochem 2024; 687:115429. [PMID: 38113981 DOI: 10.1016/j.ab.2023.115429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Microcystin-producing cyanobacterial blooms are a global issue threatening drinking water supplies and recreation on lakes and beaches. Direct measurement of microcystins is the only way to ensure waters have concentrations below guideline concentrations; however, analyzing water for microcystins takes several hours to days to obtain data. We tested LightDeck Diagnostics' bead beater cell lysis and two versions of the quantification system designed to give microcystin concentrations within 20 min and compared it to the standard freeze-thaw cycle lysis method and ELISA quantification. The bead beater lyser was only 30 % effective at extracting microcystins compared to freeze-thaw. When considering freeze-thaw samples analyzed in 2021, there was good agreement between ELISA and LightDeck version 2 (n = 152; R2 = 0.868), but the LightDeck slightly underestimated microcystins (slope of 0.862). However, we found poor relationships between LightDeck version 2 and ELISA in 2022 (n = 49, slopes 0.60 to 1.6; R2 < 0.6) and LightDeck version 1 (slope = 1.77 but also a high number of less than quantifiable concentrations). After the quantification issues are resolved, combining the LightDeck system with an already-proven rapid lysis method (such as microwaving) will allow beach managers and water treatment operators to make quicker, well-informed decisions.
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Affiliation(s)
- Justin D Chaffin
- F.T. Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put in Bay, Ohio 43456, USA; Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | | | - Sarah R Bickman
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - John F Bratton
- LimnoTech, Inc. 501 Avis Dr., Ann Arbor Michigan 48108, USA
| | | | - Mudit Bhatia
- Department of Civil and Environmental Engineering, University of Toledo, 3006 Nitschke Hall, Toledo, Ohio 43606, USA
| | - Seth D Buchholz
- Bowling Green State University, Bowling Green, Ohio 43403, USA
| | | | - Thomas H Johengen
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dae-Wook Kang
- Department of Civil and Environmental Engineering, University of Toledo, 3006 Nitschke Hall, Toledo, Ohio 43606, USA
| | - Gregory G Lewis
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - Michael J Lochhead
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - Brooks M Macdonald
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - Cassandra L Petrou
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - Michelle Platz
- LimnoTech, Inc. 501 Avis Dr., Ann Arbor Michigan 48108, USA
| | - Heidi Purcell
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jack Roser
- LightDeck Diagnostics, Inc., 5603 Arapahoe Ave, Boulder, Colorado 80303, USA
| | - Youngwoo Seo
- Department of Civil and Environmental Engineering, University of Toledo, 3006 Nitschke Hall, Toledo, Ohio 43606, USA; Department of Chemical Engineering, University of Toledo, 3048 Nitschke Hall, Toledo, Ohio 43606, USA
| | - Mashuk Siddiquee
- Department of Civil and Environmental Engineering, University of Toledo, 3006 Nitschke Hall, Toledo, Ohio 43606, USA
| | - Brenda Snyder
- Lake Erie Center, The University of Toledo, Oregon, Ohio 43616, USA
| | - Autumn T Taylor
- F.T. Stone Laboratory and Ohio Sea Grant, The Ohio State University, Put in Bay, Ohio 43456, USA
| | | | - Judy A Westrick
- Lumigen Instrument Center, Wayne State University, 5101Cass Ave., Detroit, Michigan 48202, USA
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3
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:microorganisms11040851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME COMMUNICATIONS 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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5
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Sandwich Hybridization Assay for In Situ Real-Time Cyanobacterial Detection and Monitoring: A Review. BIOSENSORS 2022; 12:bios12080640. [PMID: 36005037 PMCID: PMC9405892 DOI: 10.3390/bios12080640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
As cyanobacterial harmful algal bloom (cHAB) events increase in scale, severity, frequency, and duration around the world, rapid and accurate monitoring and characterization tools have become critically essential for regulatory and management decision-making. The composition of cHAB-forming cyanobacteria community can change significantly over time and space and be altered by sample preservation and transportation, making in situ monitoring necessary to obtain real-time and localized information. Sandwich hybridization assay (SHA) utilizes capture oligonucleotide probes for sensitive detection of target-specific nucleic acid sequences. As an amplification-free molecular biology technology, SHA can be adapted for in-situ, real-time or near real-time detection and qualitatively or semi-quantitatively monitoring of cHAB-forming cyanobacteria, owing to its characteristics such as being rapid, portable, inexpensive, and amenable to automation, high sensitivity, specificity and robustness, and multiplexing (i.e., detecting multiple targets simultaneously). Despite its successful application in the monitoring of marine and freshwater phytoplankton, there is still room for improvement. The ability to identify a cHAB community rapidly would decrease delays in cyanotoxin analyses, reduce costs, and increase sample throughput, allowing for timely actions to improve environmental and human health and the understanding of short- and long-term bloom dynamics. Real-time detection and quantitation of HAB-forming cyanobacteria is essential for improving environmental and public health and reducing associated costs. We review and propose to apply SHA for in situ cHABs monitoring.
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Kim Tiam S, Comte K, Dalle C, Delagrange M, Djediat C, Ducos B, Duval C, Feilke K, Hamlaoui S, Le Manach S, Setif P, Yéprémian C, Marie B, Kirilovsky D, Gugger M, Bernard C. The success of the bloom-forming cyanobacteria Planktothrix: Genotypes variability supports variable responses to light and temperature stress. HARMFUL ALGAE 2022; 117:102285. [PMID: 35944963 DOI: 10.1016/j.hal.2022.102285] [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: 02/01/2022] [Revised: 05/05/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Cyanobacterial blooms can modify the dynamic of aquatic ecosystems and have harmful consequences for human activities. Moreover, cyanobacteria can produce a variety of cyanotoxins, including microcystins, but little is known about the role of environmental factors on the prevalence of microcystin producers in the cyanobacterial bloom dynamics. This study aimed to better understand the success of Planktothrix in various environments by unveiling the variety of strategies governing cell responses to sudden changes in light intensity and temperature. The cellular responses (photosynthesis, photoprotection, heat shock response and metabolites synthesis) of four Planktothrix strains to high-light or high-temperature were studied, focusing on how distinct ecotypes (red- or green-pigmented) and microcystin production capability affect cyanobacteria's ability to cope with such abiotic stimuli. Our results showed that high-light and high-temperature impact different cellular processes and that Planktothrix responses are heterogeneous, specific to each strain and thus, to genotype. The ability of cyanobacteria to cope with sudden increase in light intensity and temperature was not related to red- or green-pigmented ecotype or microcystin production capability. According to our results, microcystin producers do not cope better to high-light or high-temperature and microcystin content does not increase in response to such stresses.
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Affiliation(s)
- Sandra Kim Tiam
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France.
| | - Katia Comte
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Caroline Dalle
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris, F-75015, France
| | - Marine Delagrange
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris-Cité, Sorbonne Université UPMC Paris 06, CNRS, High Throughput qPCR Core Facility of the ENS, IBENS, 46 rue d'Ulm, Paris,, 75005 France
| | - Chakib Djediat
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Bertrand Ducos
- Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris-Cité, Sorbonne Université UPMC Paris 06, CNRS, High Throughput qPCR Core Facility of the ENS, IBENS, 46 rue d'Ulm, Paris,, 75005 France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Kathleen Feilke
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, 91198, France
| | - Sahima Hamlaoui
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Séverine Le Manach
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Pierre Setif
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, 91198, France
| | - Claude Yéprémian
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Benjamin Marie
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, 91198, France
| | - Muriel Gugger
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, Paris, F-75015, France.
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 39, 57 rue Cuvier, Paris, 75005, France.
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7
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Leibrock LB, Hofmann DM, Fuchs B, Birt A, Reinholz M, Guertler A, Frank K, Giunta RE, Egaña JT, Nickelsen J, Schenck TL, Moellhoff N. In vitro and in vivo detection of microbial gene expression in bioactivated scaffolds seeded with cyanobacteria. Lett Appl Microbiol 2022; 75:401-409. [PMID: 35587396 DOI: 10.1111/lam.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 11/30/2022]
Abstract
Dermal replacement materials bioactivated with cyanobacteria have shown promising potential for wound regeneration. To date, extraction of cyanobacteria RNA from seeded scaffolds has not been described. Aim of this study was to develop a method to isolate total RNA from bioactivated scaffolds and to propose a new approach in determining living bacteria based on real-time PCR. Transgenic synechococcus sp. PCC 7002 (tSyn7002) were seeded in liquid cultures or in scaffolds for dermal regeneration in vitro and in vivo for 7 days. RNA was extracted with a 260/280 ratio of ≥ 2. The small subunit of the 30S ribosome in prokaryotes (16S) and RNAse P protein (rnpA) were validated as reference transcripts for PCR analysis. Gene expression patterns differed in vitro and in vivo. Expression of 16S was significantly upregulated in scaffolds in vitro, as compared to liquid cultures, while rnpA expression was comparable. In vivo, both 16S and rnpA showed reduced expression compared to in vitro (16S: in vivo Ct value 13.21±0.32, in vitro 12.44±0.42; rnpA in vivo Ct value 19.87±0.41, in vitro 17.75±1.41). Overall, the results demonstrate rnpA and 16S expression after 7 days of implantation in vitro and in vivo, proving presence of living bacteria embedded in scaffolds using qPCR.
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Affiliation(s)
- Lars B Leibrock
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - Daniel M Hofmann
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - Benedikt Fuchs
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - Alexandra Birt
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - Markus Reinholz
- Department of Dermatology and Allergy, University Hospital of Munich, LMU, Germany
| | - Anne Guertler
- Department of Dermatology and Allergy, University Hospital of Munich, LMU, Germany
| | - Konstantin Frank
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - Riccardo E Giunta
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
| | - José T Egaña
- Institute for Biological and Medical Engineering, Schools of Engineering, Biological Sciences and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Joerg Nickelsen
- Molecular Plant Science, Department Biology I, LMU Munich, Munich, Germany
| | - Thilo L Schenck
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany.,Frauenklinik Dr. Geisenhofer GmbH, 80538, Munich, Germany
| | - Nicholas Moellhoff
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Germany
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8
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Alafeef M, Moitra P, Dighe K, Pan D. RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19. Nat Protoc 2021; 16:3141-3162. [PMID: 33931780 DOI: 10.1038/s41596-021-00546-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19) highlights the shortcomings of the current testing paradigm for viral disease diagnostics. Here, we report a stepwise protocol for an RNA-extraction-free nano-amplified colorimetric test for rapid and naked-eye molecular diagnosis of COVID-19. The test employs a unique dual-prong approach that integrates nucleic acid (NA) amplification and plasmonic sensing for point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a sample-to-assay response time of <1 h. The RNA-extraction-free nano-amplified colorimetric test utilizes plasmonic gold nanoparticles capped with antisense oligonucleotides (ASOs) as a colorimetric reporter to detect the amplified nucleic acid from the COVID-19 causative virus, SARS-CoV-2. The ASOs are specific for the SARS-CoV-2 N-gene, and binding of the ASOs to their target sequence results in the aggregation of the plasmonic gold nanoparticles. This highly specific agglomeration step leads to a change in the plasmonic response of the nanoparticles. Furthermore, when tested using clinical samples, the accuracy, sensitivity and specificity of the test were found to be >98.4%, >96.6% and 100%, respectively, with a detection limit of 10 copies/μL. The test can easily be adapted to diagnose other viral infections with a simple modification of the ASOs and primer sequences. It also provides a low-cost, rapid approach requiring minimal instrumentation that can be used as a screening tool for the diagnosis of COVID-19 at point-of-care settings in resource-poor situations. The colorimetric readout of the test can even be monitored using a handheld optical reader to obtain a quantitative response. Therefore, we anticipate that this protocol will be widely useful for the development of biosensors for the molecular diagnostics of COVID-19 and other infectious diseases.
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Affiliation(s)
- Maha Alafeef
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Biomedical Engineering Department, Jordan University of Science and Technology, Irbid, Jordan.,Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA.,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Parikshit Moitra
- Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Ketan Dighe
- Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA.,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Dipanjan Pan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA. .,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA.
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9
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Hamilton A, Harper SJ, Critzer F. Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces. Microorganisms 2020; 8:microorganisms8101480. [PMID: 32993184 PMCID: PMC7601045 DOI: 10.3390/microorganisms8101480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.:+1-509-786-9209
| | - Scott J. Harper
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Faith Critzer
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
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