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Mautner L, Baillie CK, Herold HM, Volkwein W, Guertler P, Eberle U, Ackermann N, Sing A, Pavlovic M, Goerlich O, Busch U, Wassill L, Huber I, Baiker A. Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Virol J 2020; 17:160. [PMID: 33087160 PMCID: PMC7576985 DOI: 10.1186/s12985-020-01435-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Background Fast, reliable and easy to handle methods are required to facilitate urgently needed point-of-care testing (POCT) in the current coronavirus pandemic. Life-threatening severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world, infecting more than 33,500,000 people and killing over 1 million of them as of October 2020. Infected individuals without any symptoms might still transfer the virus to others underlining the extraordinary transmissibility of this new coronavirus. In order to identify early infections effectively, treat patients on time and control disease spreading, rapid, accurate and onsite testing methods are urgently required. Results Here we report the development of a loop-mediated isothermal amplification (LAMP) based method to detect SARS-CoV-2 genes ORF8 and N directly from pharyngeal swab samples. The established reverse transcription LAMP (RT-LAMP) assay detects SARS-CoV-2 directly from pharyngeal swab samples without previous time-consuming and laborious RNA extraction. The assay is sensitive and highly specific for SARS-CoV-2 detection, showing no cross reactivity when tested on 20 other respiratory pathogens. The assay is 12 times faster and 10 times cheaper than routine reverse transcription real-time polymerase chain reaction, depending on the assay used.
Conclusion The fast and easy to handle RT-LAMP assay amplifying specifically the genomic regions ORF8 and N of SARS-CoV-2 is ideally suited for POCT at e.g. railway stations, airports or hospitals. Given the current pandemic situation, rapid, cost efficient and onsite methods like the here presented RT-LAMP assay are urgently needed to contain the viral spread.
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Affiliation(s)
- Lena Mautner
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Christin-Kirsty Baillie
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Heike Marie Herold
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Wolfram Volkwein
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Patrick Guertler
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ute Eberle
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Nikolaus Ackermann
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Melanie Pavlovic
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ottmar Goerlich
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Lars Wassill
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Armin Baiker
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany.
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Dier M, Meinen R, Erbs M, Kollhorst L, Baillie CK, Kaufholdt D, Kücke M, Weigel HJ, Zörb C, Hänsch R, Manderscheid R. Effects of free air carbon dioxide enrichment (FACE) on nitrogen assimilation and growth of winter wheat under nitrate and ammonium fertilization. Glob Chang Biol 2018; 24:e40-e54. [PMID: 28715112 DOI: 10.1111/gcb.13819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/21/2017] [Indexed: 05/27/2023]
Abstract
A 2-year Free Air CO2 Enrichment (FACE) experiment was conducted with winter wheat. It was investigated whether elevated atmospheric CO2 concentration (e[CO2 ]) inhibit nitrate assimilation and whether better growth and nitrogen acquisition under e[CO2 ] can be achieved with an ammonium-based fertilization as it was observed in hydroponic culture with wheat. Under e[CO2 ] a decrease in nitrate assimilation has been discussed as the cause for observed declines in protein concentration in C3 cereals. Wheat was grown under ambient [CO2 ] and e[CO2 ] (600 ppm) with three levels (deficiency, optimal, and excessive) of nitrate-based fertilization (calcium ammonium nitrate; CAN) or with optimal ammonium-based fertilization. Ammonium fertilization was applied via injection of an ammonium solution into the soil in the 1st year and by surface application of urea combined with nitrification inhibitors (UNI) in the 2nd year. Results showed that ammonium-based fertilization was successfully achieved in the 2nd year with respect to nitrification control, as soil ammonium concentration was considerably higher over the growing season for UNI fertilized plots compared to optimal CAN plots. Also, stem nitrate concentration, flag leaf nitrate reductase activity, and transcript levels were lower in UNI fertilized plants compared to optimal CAN. Regarding the e[CO2 ] effect on nitrate reductase activity and transcript levels, no alteration could be observed for any nitrogen fertilizer treatment. Flag leaf growth was stimulated under e[CO2 ] leading to an enhanced nitrate reductase activity referred to m2 ground area at late flowering being in line with a higher nitrogen acquisition under e[CO2 ]. Moreover, nitrogen acquisition was considerably higher in nitrate fertilized plants compared to ammonium fertilized plants under e[CO2 ]. Our results obtained under field conditions show that a change from nitrate- to ammonium-based fertilization will not lead to a better growth and nitrogen acquisition of winter wheat under future e[CO2 ].
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Affiliation(s)
- Markus Dier
- Thünen Institute of Biodiversity, Braunschweig, Germany
- Institute of Crop Science, Quality of Plant Products, University of Hohenheim, Stuttgart, Germany
| | - Rieke Meinen
- Institute of Plant Biology, Technische Universität, Braunschweig, Germany
| | - Martin Erbs
- Deutsche Agrarforschungsallianz (DAFA) German Agricultural Research Alliance, c/o Thünen Institute, Braunschweig, Germany
| | | | | | - David Kaufholdt
- Institute of Plant Biology, Technische Universität, Braunschweig, Germany
| | - Martin Kücke
- Julius Kühn Institute, Institute of Crop & Soil Science, Braunschweig, Germany
| | | | - Christian Zörb
- Institute of Crop Science, Quality of Plant Products, University of Hohenheim, Stuttgart, Germany
| | - Robert Hänsch
- Institute of Plant Biology, Technische Universität, Braunschweig, Germany
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Kaufholdt D, Baillie CK, Meinen R, Mendel RR, Hänsch R. The Molybdenum Cofactor Biosynthesis Network: In vivo Protein-Protein Interactions of an Actin Associated Multi-Protein Complex. Front Plant Sci 2017; 8:1946. [PMID: 29184564 PMCID: PMC5694649 DOI: 10.3389/fpls.2017.01946] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/30/2017] [Indexed: 05/09/2023]
Abstract
Survival of plants and nearly all organisms depends on the pterin based molybdenum cofactor (Moco) as well as its effective biosynthesis and insertion into apo-enzymes. To this end, both the central Moco biosynthesis enzymes are characterized and the conserved four-step reaction pathway for Moco biosynthesis is well-understood. However, protection mechanisms to prevent degradation during biosynthesis as well as transfer of the highly oxygen sensitive Moco and its intermediates are not fully enlightened. The formation of protein complexes involving transient protein-protein interactions is an efficient strategy for protected metabolic channelling of sensitive molecules. In this review, Moco biosynthesis and allocation network is presented and discussed. This network was intensively studied based on two in vivo interaction methods: bimolecular fluorescence complementation (BiFC) and split-luciferase. Whereas BiFC allows localisation of interacting partners, split-luciferase assay determines interaction strengths in vivo. Results demonstrate (i) interaction of Cnx2 and Cnx3 within the mitochondria and (ii) assembly of a biosynthesis complex including the cytosolic enzymes Cnx5, Cnx6, Cnx7, and Cnx1, which enables a protected transfer of intermediates. The whole complex is associated with actin filaments via Cnx1 as anchor protein. After biosynthesis, Moco needs to be handed over to the specific apo-enzymes. A potential pathway was discovered. Molybdenum-containing enzymes of the sulphite oxidase family interact directly with Cnx1. In contrast, the xanthine oxidoreductase family acquires Moco indirectly via a Moco binding protein (MoBP2) and Moco sulphurase ABA3. In summary, the uncovered interaction matrix enables an efficient transfer for intermediate and product protection via micro-compartmentation.
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Kaufholdt D, Baillie CK, Meyer MH, Schwich OD, Timmerer UL, Tobias L, van Thiel D, Hänsch R, Mendel RR. Identification of a protein-protein interaction network downstream of molybdenum cofactor biosynthesis in Arabidopsis thaliana. J Plant Physiol 2016; 207:42-50. [PMID: 27792900 DOI: 10.1016/j.jplph.2016.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 05/24/2023]
Abstract
The molybdenum cofactor (Moco) is ubiquitously present in all kingdoms of life and vitally important for survival. Among animals, loss of the Moco-containing enzyme (Mo-enzyme) sulphite oxidase is lethal, while for plants the loss of nitrate reductase prohibits nitrogen assimilation. Moco is highly oxygen-sensitive, which obviates a freely diffusible pool and necessitates protein-mediated distribution. During the highly conserved Moco biosynthesis pathway, intermediates are channelled through a multi-protein complex facilitating protected transport. However, the mechanism by which Moco is subsequently transferred to apo-enzymes is still unclear. Moco user enzymes can be divided into two families: the sulphite oxidase (SO) and the xanthine oxidoreductase (XOR) family. The latter requires a final sulphurisation of Moco catalysed via ABA3. To examine Moco transfer towards apo-Mo-enzymes, two different and independent protein-protein interaction assays were performed in vivo: bimolecular fluorescence complementation and split luciferase. The results revealed a direct contact between Moco producer molybdenum insertase CNX1, which represents the last biosynthesis step, and members of the SO family. However, no protein contact was observed between Moco producer CNX1 and apo-enzymes of the XOR family or between CNX1 and the Moco sulphurase ABA3. Instead, the Moco-binding protein MOBP2 was identified as a mediator between CNX1 and ABA3. This interaction was followed by contact between ABA3 and enzymes of the XOR family. These results allow to describe an interaction matrix of proteins beyond Moco biosynthesis and to demonstrate the complexity of transferring a prosthetic group after biosynthesis.
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Affiliation(s)
- David Kaufholdt
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Christin-Kirsty Baillie
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Martin H Meyer
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Oliver D Schwich
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Ulrike L Timmerer
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Lydia Tobias
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Daniela van Thiel
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Robert Hänsch
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
| | - Ralf R Mendel
- Department of Plant Biology, Technical University of Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany.
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Kaufholdt D, Baillie CK, Bikker R, Burkart V, Dudek CA, von Pein L, Rothkegel M, Mendel RR, Hänsch R. The molybdenum cofactor biosynthesis complex interacts with actin filaments via molybdenum insertase Cnx1 as anchor protein in Arabidopsis thaliana. Plant Sci 2016; 244:8-18. [PMID: 26810449 DOI: 10.1016/j.plantsci.2015.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/16/2015] [Accepted: 12/24/2015] [Indexed: 05/24/2023]
Abstract
The pterin based molybdenum cofactor (Moco) plays an essential role in almost all organisms. Its biosynthesis is catalysed by six enzymes in a conserved four step reaction pathway. The last three steps are located in the cytoplasm, where a multimeric protein complex is formed to protect the intermediates from degradation. Bimolecular fluorescence complementation was used to test for cytoskeleton association of the Moco biosynthesis enzymes with actin filaments and microtubules using known cytoskeleton associated proteins, thus permitting non-invasive in vivo studies. Coding sequences of binding proteins were cloned via the GATEWAY system. No Moco biosynthesis enzyme showed any interaction with microtubules. However, alone the two domain protein Cnx1 exhibited interaction with actin filaments mediated by both domains with the Cnx1G domain displaying a stronger interaction. Cnx6 showed actin association only if unlabelled Cnx1 was co-expressed in comparable amounts. So Cnx1 is likely to be the anchor protein for the whole biosynthesis complex on actin filaments. A stabilization of the whole Moco biosynthesis complex on the cytoskeleton might be crucial. In addition a micro-compartmentation might either allow a localisation near the mitochondrial ATM3 exporter providing the first Moco intermediate or near one of the three molybdate transporters enabling efficient molybdate incorporation.
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Affiliation(s)
- David Kaufholdt
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Christin-Kirsty Baillie
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Rolf Bikker
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Valentin Burkart
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Christian-Alexander Dudek
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Linn von Pein
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Martin Rothkegel
- Institut für Zoologie, Spielmannstrasse 7, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Ralf R Mendel
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
| | - Robert Hänsch
- Institut für Pflanzenbiologie, Humboldtstrasse 1, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
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