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Prado NO, Marin AM, Lalli LA, Sanchuki HBS, Wosniaki DK, Nardin JM, Morales HMP, Blanes L, Zanette DL, Aoki MN. Development and evaluation of a lyophilization protocol for colorimetric RT-LAMP diagnostic assay for COVID-19. Sci Rep 2024; 14:10612. [PMID: 38719936 PMCID: PMC11078981 DOI: 10.1038/s41598-024-61163-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular diagnostics involving nucleic acids (DNA and RNA) are regarded as extremely functional tools. During the 2020 global health crisis, efforts intensified to optimize the production and delivery of molecular diagnostic kits for detecting SARS-CoV-2. During this period, RT-LAMP emerged as a significant focus. However, the thermolability of the reagents used in this technique necessitates special low-temperature infrastructure for transport, storage, and conservation. These requirements limit distribution capacity and necessitate cost-increasing adaptations. Consequently, this report details the development of a lyophilization protocol for reagents in a colorimetric RT-LAMP diagnostic kit to detect SARS-CoV-2, facilitating room-temperature transport and storage. We conducted tests to identify the ideal excipients that maintain the molecular integrity of the reagents and ensure their stability during room-temperature storage and transport. The optimal condition identified involved adding 5% PEG 8000 and 75 mM trehalose to the RT-LAMP reaction, which enabled stability at room temperature for up to 28 days and yielded an analytical and diagnostic sensitivity and specificity of 83.33% and 90%, respectively, for detecting SARS-CoV-2. This study presents the results of a lyophilized colorimetric RT-LAMP COVID-19 detection assay with diagnostic sensitivity and specificity comparable to RT-qPCR, particularly in samples with high viral load.
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Affiliation(s)
- Nayra Oliveira Prado
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Anelis Maria Marin
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Larissa Araujo Lalli
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Denise Kusma Wosniaki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Jeanine Marie Nardin
- Erasto Gaertner Hospital, Dr. Ovande Do Amaral 201 Street, Curitiba, Paraná, 81520-060, Brazil
| | - Hugo Manoel Paz Morales
- Erasto Gaertner Hospital, Dr. Ovande Do Amaral 201 Street, Curitiba, Paraná, 81520-060, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Prof. Algacyr Munhoz Mader 3775 Street, Curitiba, 81350-010, Brazil.
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Salman AA, Goldring JPD. Expression and copper binding studies of a Plasmodium falciparum protein with Cox19 copper binding motifs. Exp Parasitol 2023:108572. [PMID: 37348640 DOI: 10.1016/j.exppara.2023.108572] [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: 01/26/2023] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Copper can exist in an oxidized and a reduced form, which enables the metal to play essential roles as a catalytic co-factor in redox reactions in many organisms. Copper confers redox activity to the terminal electron transport chain cytochrome c oxidase protein. Cytochrome c oxidase in yeast obtains copper for the CuB site in the Cox1 subunit from Cox11 in association with Cox19. When copper is chelated in growth medium, Plasmodium falciparum parasite development in infected red blood cells is inhibited and excess copper is toxic for the parasite. The gene of a 26 kDa Plasmodium falciparum PfCox19 protein with two Cx9C Cox19 copper binding motifs, was cloned and expressed as a 66 kDa fusion protein with maltose binding protein and affinity purified (rMBP-PfCox19). rMBP-PfCox19 bound copper measured by: a bicinchoninic acid release assay; an in vivo bacterial host growth inhibition assay; ascorbate oxidation inhibition and differential scanning fluorimetry. The native protein was detected by antibodies raised against rMBP-PfCox19. PfCox19 binds copper and is predicted to associate with PfCox11 in the insertion of copper into the CuB site of Plasmodium cytochrome c oxidase. Characterisation of the proteins involved in Plasmodium spp. copper metabolism will help us understand the role of cytochrome c oxidase and this essential metal in Plasmodium homeostasis.
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Affiliation(s)
| | - J P Dean Goldring
- Biochemistry, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa.
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Salman AA, Goldring JPD. Expression and copper binding characteristics of Plasmodium falciparum cytochrome c oxidase assembly factor 11, Cox11. Malar J 2022; 21:173. [PMID: 35672733 PMCID: PMC9172173 DOI: 10.1186/s12936-022-04188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background Copper is an essential metal for living organisms as a catalytic co-factor for important enzymes, like cytochrome c oxidase the final enzyme in the electron transport chain. Plasmodium falciparum parasites in infected red blood cells are killed by excess copper and development in erythrocytes is inhibited by copper chelators. Cytochrome c oxidase in yeast obtains copper for the CuB site in the Cox1 subunit from Cox11. Methods A 162 amino acid carboxy-terminal domain of the P. falciparum Cox11 ortholog (PfCox11Ct) was recombinantly expressed and the rMBPPfCox11Ct affinity purified. Copper binding was measured in vitro and in Escherichia coli host cells. Site directed mutagenesis was used to identify key copper binding cysteines. Antibodies confirmed the expression of the native protein. Results rMBPPfCox11Ct was expressed as a 62 kDa protein fused with the maltose binding protein and affinity purified. rMBPPfCox11Ct bound copper measured by: a bicinchoninic acid release assay; atomic absorption spectroscopy; a bacterial host growth inhibition assay; ascorbate oxidation inhibition and in a thermal shift assay. The cysteine 157 amino acid was shown to be important for in vitro copper binding by PfCox11whilst Cys 60 was not. The native protein was detected by antibodies against rMBPPfCox11Ct. Conclusions Plasmodium spp. express the PfCox11 protein which shares structural features and copper binding motifs with Cox11 from other species. PfCox11 binds copper and is, therefore, predicted to transfer copper to the CuB site of Plasmodium cytochrome c oxidase. Characterization of Plasmodium spp. proteins involved in copper metabolism will help sceintists understand the role of cytochrome c oxidase and this essential metal in Plasmodium homeostasis.
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Tang L, Wu Z, Wang J, Zhang X. Formaldehyde Derivatization: An Unexpected Side Reaction During Filter-Aided Sample Preparation. Anal Chem 2020; 92:12120-12125. [PMID: 32786431 DOI: 10.1021/acs.analchem.0c01981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The filter-aided sample preparation (FASP) method has been commonly used for proteomic sample preparation due to its high efficiency in removing impurities. Herein, we report an overlooked +12 Da side modification during FASP method using Microcon spin filters. We confirmed that the side modification is caused by formaldehyde released from the spin filter and found that the side modification leads to 10.5% and 9.5% loss in proteome-level peptide and protein identification, respectively. We evaluated different pretreatment procedures to reduce the side reaction. Furthermore, on the basis of the evaluation results of different brands of spin filters, we recommend Nanosep spin filters for different proteomic studies, especially for amine-labeling proteomic studies. Our results would benefit researchers employing the spin filters to improve their results and also help spin filter manufacturers to improve the product quality. Data are available via ProteomeXchange with identifier PXD018737.
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Affiliation(s)
- Langlang Tang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Wang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
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Chen T, Tong T, Yang L, Liao F, Yang X. [Resonance light scattering spectroscopy can directly characterize protein solubility]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:843-849. [PMID: 32895202 DOI: 10.12122/j.issn.1673-4254.2020.06.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To develop a fast, sensitive and cost-effective method based on resonance light scattering (RLS) for characterization of protein solubility to facilitate detection of changes in solubility of mutant proteins. METHODS We examined the response curve of RLS intensities to the protein concentrations in synchronous scanning mode. The curve intersection points were searched to predict the maximal concentrations of the protein in dispersion state, which defined the solubility of the protein in this given state. Bovine serum albumin (BSA, 0-50 g/L) was used as the model to investigate the influences of pH values (6.5, 7.0, and 7.4) and salt concentrations (0.05, 0.10, 0.15, and 0.20 mol/L) on the determined solubility. The solubility of glutathione S-transferase isoenzymes alpha (GSTA, 0-27.0 g/L) and Mμ (GSTM, 0-20.0 g/L) were estimated for comparison. The RLS-based method was used to determine the solubility of uricase (MGU, 0-0.4 g/L) to provide assistance in improving the solubility of its mutants. RESULTS We identified two intersection points in the RLS response curves of the tested proteins, among which the lower one represented an approximation of the maximal concentration (or the solubility of the protein) in single molecular dispersion, and the higher one the saturated concentration of the protein in multiple molecular aggregation. In HEPES buffer, the two intersection points of BSA (isoelectric point 4.6) both increased with the increase of pH (6.5-7.4), and their values were ~1.2 g/L and ~33 g/L at pH 7.4, respectively; the latter concentration approached the solubility of commercial BSA in the same buffer at the same pH. The addition of NaCl reduced the values of the two intersection points, and increasing salt ion concentration decreased the values of the lower intersection points. Further characterizations of GSTA and GSTM showed that the low concentration intersection points of the two proteins were ~0.7 g/L and ~0.8 g/L, and their high concentration intersection points were ~10 g/L and ~11 g/L, respectively, both lower than those of BSA, indicating the feasibility of the direct characterization of protein solubility by RLS. The two concentration intersection points of MGU were 0.24 g/L and 0.30 g/L, respectively, and the low concentration intersection point of its selected mutant was increased by 2 times. CONCLUSIONS RLS allows direct characterization of the solubility of macromolecular proteins. This method, which is simple and sensitive and needs only a small amount of proteins, has a unique advantage for rapid comparison of solubility of low-abundance protein mutants.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Ministry of Education of China, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tingting Tong
- Key Laboratory of Medical Laboratory Diagnostics of the Ministry of Education of China, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Linyu Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Ministry of Education of China, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Fei Liao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 401135, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Ministry of Education of China, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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Larsen JM, Bang-Berthelsen CH, Qvortrup K, Sancho AI, Hansen AH, Andersen KIH, Thacker SSN, Eiwegger T, Upton J, Bøgh KL. Production of allergen-specific immunotherapeutic agents for the treatment of food allergy. Crit Rev Biotechnol 2020; 40:881-894. [PMID: 32515236 DOI: 10.1080/07388551.2020.1772194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Allergen-specific immunotherapy (IT) is emerging as a viable avenue for the treatment of food allergies. Clinical trials currently investigate raw or slightly processed foods as therapeutic agents, as trials using food-grade agents can be performed without the strict regulations to which conventional drugs are subjected. However, this limits the ability of standardization and may affect clinical trial outcomes and reproducibility. Herein, we provide an overview of methods used in the production of immunotherapeutic agents for the treatment of food allergies, including processed foods, allergen extracts, recombinant allergens, and synthetic peptides, as well as the physical and chemical processes for the reduction of protein allergenicity. Commercial interests currently favor producing standardized drug-grade allergen extracts for therapeutic use, and clinical trials are ongoing. In the near future, recombinant production could replace purification strategies since it allows the manufacturing of pure, native allergens or sequence-modified allergens with reduced allergenicity. A recurring issue within this field is the inadequate reporting of production procedures, quality control, product physicochemical characteristics, allergenicity, and immunological properties. This information is of vital importance in assessing therapeutic standardization and clinical safety profile, which are central parameters for the development of future therapeutic agents.
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Affiliation(s)
- Jeppe Madura Larsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ana Isabel Sancho
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | | | - Thomas Eiwegger
- Division of Immunology and Allergy, Food Allergy and Anaphylaxis Program, The Department of Pediatrics, The Hospital for Sick Children, Toronto, Canada.,Research Institute, The Hospital for Sick Children, Translational Medicine Program, Toronto, Canada.,Department of Immunology, The University of Toronto, Toronto, Canada
| | - Julia Upton
- Division of Immunology and Allergy, Food Allergy and Anaphylaxis Program, The Department of Pediatrics, The Hospital for Sick Children, Toronto, Canada
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Krause RGE, Dean Goldring JP. Continuous Elution SDS-PAGE with a Modified Standard Gel Apparatus to Separate and Isolate an Array of Proteins from Complex Mixtures. Methods Mol Biol 2019; 1855:467-478. [PMID: 30426440 DOI: 10.1007/978-1-4939-8793-1_39] [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] [Indexed: 06/09/2023]
Abstract
Sodium dodecyl sulfate polyacrylamide gel electrophoresis is a powerful tool to separate proteins according to their relative sizes. The technique provides information about both the size of a number of proteins and potentially the comparative amounts of each protein. To confirm the identity of proteins, proteins can be eluted from the gel and transferred electrophoretically to nitrocellulose for antibody-based detection. During electrophoresis, if the current is not stopped, proteins continue to pass down the gel and elute from the bottom of the gel. The standard electrophoresis gel apparatus can be employed with the addition of some tubing and alterations to the separating gel to collect proteins separated by size as they elute from the base of the gel as described in this chapter. Complex protein mixtures can be separated into multiple fractions containing single proteins in a few hours. Small amounts (<500 μg of protein) of protein sample can be fractionated.
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Affiliation(s)
- Robert G E Krause
- Biochemistry, University of KwaZulu-Natal, Scottsville, South Africa
| | - J P Dean Goldring
- Biochemistry, University of KwaZulu-Natal, Scottsville, South Africa.
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Mazzucchelli G, Holzhauser T, Cirkovic Velickovic T, Diaz‐Perales A, Molina E, Roncada P, Rodrigues P, Verhoeckx K, Hoffmann‐Sommergruber K. Current (Food) Allergenic Risk Assessment: Is It Fit for Novel Foods? Status Quo and Identification of Gaps. Mol Nutr Food Res 2018; 62:1700278. [PMID: 28925060 PMCID: PMC5814866 DOI: 10.1002/mnfr.201700278] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/28/2017] [Indexed: 01/08/2023]
Abstract
Food allergies are recognized as a global health concern. In order to protect allergic consumers from severe symptoms, allergenic risk assessment for well-known foods and foods containing genetically modified ingredients is installed. However, population is steadily growing and there is a rising need to provide adequate protein-based foods, including novel sources, not yet used for human consumption. In this context safety issues such as a potential increased allergenic risk need to be assessed before marketing novel food sources. Therefore, the established allergenic risk assessment for genetically modified organisms needs to be re-evaluated for its applicability for risk assessment of novel food proteins. Two different scenarios of allergic sensitization have to be assessed. The first scenario is the presence of already known allergenic structures in novel foods. For this, a comparative assessment can be performed and the range of cross-reactivity can be explored, while in the second scenario allergic reactions are observed toward so far novel allergenic structures and no reference material is available. This review summarizes the current analytical methods for allergenic risk assessment, highlighting the strengths and limitations of each method and discussing the gaps in this assessment that need to be addressed in the near future.
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Affiliation(s)
- Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry – MolSysDepartment of ChemistryUniversity of LiegeLiegeBelgium
| | | | - Tanja Cirkovic Velickovic
- Center of Excellence for Molecular Food SciencesUniversity of Belgrade – Faculty of ChemistryBelgradeSerbia
- Ghent University Global CampusYeonsu‐guIncheonSouth Korea
| | | | | | - Paola Roncada
- Istituto Sperimentale Italiano Lazzaro SpallanzaniMilanoItaly
| | - Pedro Rodrigues
- CCMARCenter of Marine ScienceUniversity of AlgarveFaroPortugal
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Abstract
SIGNIFICANCE Secreted proteins are important both as signaling molecules and potential biomarkers. Recent Advances: Protein can undergo different types of oxidation, both in physiological conditions or under oxidative stress. Several redox proteomics techniques have been successfully applied to the identification of glutathionylated proteins, an oxidative post-translational modification consisting in the formation of a mixed disulfide between a protein cysteine and glutathione. Redox proteomics has also been used to study other forms of protein oxidation. CRITICAL ISSUES Because of the highest proportion of free cysteines in the cytosol, redox proteomics of protein thiols has focused, so far, on intracellular proteins. However, plasma proteins, such as transthyretin and albumin, have been described as glutathionylated or cysteinylated. The present review discusses the redox state of protein cysteines in relation to their cellular distribution. We describe the various approaches used to detect secreted glutathionylated proteins, the only thiol modification studied so far in secreted proteins, and the specific problems presented in the study of the secretome. FUTURE DIRECTIONS This review focusses on glutathionylated proteins secreted under inflammatory conditions and that may act as soluble mediators (cytokines). Future studies on the redox secretome (including other forms of oxidation) might identify new soluble mediators and biomarkers of oxidative stress. Antioxid. Redox Signal. 26, 299-312.
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Affiliation(s)
- Pietro Ghezzi
- 1 Brighton & Sussex Medical School , Brighton, United Kingdom
| | - Philippe Chan
- 2 PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen , Rouen, France
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