1
|
Calvanese M, D'Angelo C, Lauro C, Tutino ML, Parrilli E. Recombinant protein production in Pseudoalteromonas haloplanktis TAC125 biofilm. Biofilm 2024; 7:100179. [PMID: 38322580 PMCID: PMC10844681 DOI: 10.1016/j.bioflm.2024.100179] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
Biofilms have great potential for producing valuable products, and recent research has been performed on biofilms for the production of compounds with biotechnological and industrial relevance. However, the production of recombinant proteins using this system is still limited. The recombinant protein production in microbial hosts is a well-established technology and a variety of expression systems are available. Nevertheless, the production of some recombinant proteins can result in proteolyzed, insoluble, and non-functional forms, therefore it is necessary to start the exploration of non-conventional production systems that, in the future, could be helpful to produce some "difficult" proteins. Non-conventional production systems can be based on the use of alternative hosts and/or on non-conventional ways to grow recombinant cells. In this paper, the use of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 grown in biofilm conditions was explored to produce two fluorescent proteins, GFP and mScarlet. The best conditions for the production were identified by working on media composition, and induction conditions, and by building a new expression vector suitable for the biofilm conditions. Results reported demonstrated that the optimized system for the recombinant protein production in biofilm, although it takes longer than planktonic production, has the same potentiality as the classical planktonic approach with additional advantages since it needs a lower concentration of the carbon sources and doesn't require antibiotic addition. Moreover, in the case of mScarlet, the production in biofilm outperforms the planktonic system in terms of a better quality of the recombinant product.
Collapse
Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie D’Oro, 305-00136, Roma, Italy
| | - Caterina D'Angelo
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie D’Oro, 305-00136, Roma, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi I.N.B.B, Viale Medaglie D’Oro, 305-00136, Roma, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| |
Collapse
|
2
|
Zhang CJ, Mou H, Yuan J, Wang YH, Sun SN, Wang W, Xu ZH, Yu SJ, Jin K, Jin ZB. Effects of fluorescent protein tdTomato on mouse retina. Exp Eye Res 2024; 243:109910. [PMID: 38663720 DOI: 10.1016/j.exer.2024.109910] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 02/26/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Fluorescent proteins (FPs) have been widely used to investigate cellular and molecular interactions and trace biological events in many applications. Some of the FPs have been demonstrated to cause undesirable cellular damage by light-induced ROS production in vivo or in vitro. However, it remains unknown if one of the most popular FPs, tdTomato, has similar effects in neuronal cells. In this study, we discovered that tdTomato expression led to unexpected retinal dysfunction and ultrastructural defects in the transgenic mouse retina. The retinal dysfunction mainly manifested in the reduced photopic electroretinogram (ERG) responses and decreased contrast sensitivity in visual acuity, caused by mitochondrial damages characterized with cellular redistribution, morphological modifications and molecular profiling alterations. Taken together, our findings for the first time demonstrated the retinal dysfunction and ultrastructural defects in the retinas of tdTomato-transgenic mice, calling for a more careful design and interpretation of experiments involved in FPs.
Collapse
Affiliation(s)
- Chang-Jun Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Hao Mou
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Jing Yuan
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Ya-Han Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Shu-Ning Sun
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Wen Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Ze-Hua Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Si-Jian Yu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China.
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Science Key Laboratory, Beijing, 100730, China.
| |
Collapse
|
3
|
López MG, López CA, Gravisaco MJ, Alfonso V, Taboga O. Comparison between different conditions for the incorporation of foreign proteins into Autographa californica multiple polyhedrovirus polyhedra for biotechnological purposes. Arch Virol 2024; 169:108. [PMID: 38658418 DOI: 10.1007/s00705-024-06015-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/02/2024] [Indexed: 04/26/2024]
Abstract
The occlusion bodies of Autographa californica multiple nucleopolyhedrovirus are proteinaceous formations with significant biotechnological potential owing to their capacity to integrate foreign proteins through fusion with polyhedrin, their primary component. However, the strategy for successful heterologous protein inclusion still requires further refinement. In this study, we conducted a comparative assessment of various conditions to achieve the embedding of recombinant proteins within polyhedra. Two baculoviruses were constructed: AcPHGFP (polh+), with GFP as a fusion to wild type (wt) polyhedrin and AcΔPHGFP (polh+), with GFP fused to a fragment corresponding to amino acids 19 to 110 of polyhedrin. These baculoviruses were evaluated by infecting Sf9 cells and stably transformed Sf9, Sf9POLH, and Sf9POLHE44G cells. The stably transformed cells contributed another copy of wt or a mutant polyhedrin, respectively. Polyhedra of each type were isolated and characterized by classical methods. The fusion PHGFP showed more-efficient incorporation into polyhedra than ΔPHGFP in the three cell lines assayed. However, ΔPHGFP polyhedron yields were higher than those of PHGFP in Sf9 and Sf9POLH cells. Based on an integral analysis of the studied parameters, it can be concluded that, except for the AcΔPHGFP/Sf9POLHE44G combination, deficiencies in one factor can be offset by improved performance by another. The combinations AcPHGFP/Sf9POLHE44G and AcΔPHGFP/Sf9POLH stand out due to their high level of incorporation and the large number of recombinant polyhedra produced, respectively. Consequently, the choice between these approaches becomes dependent on the intended application.
Collapse
Affiliation(s)
- María Gabriela López
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto S/N, B1686IGC, Hurlingham, Buenos Aires, Argentina.
| | - Cinthia Ayelén López
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto S/N, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - María José Gravisaco
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto S/N, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - Victoria Alfonso
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto S/N, B1686IGC, Hurlingham, Buenos Aires, Argentina
| | - Oscar Taboga
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), De los Reseros y N. Repetto S/N, B1686IGC, Hurlingham, Buenos Aires, Argentina.
| |
Collapse
|
4
|
Thiele PJ, Mela-Lopez R, Blandin SA, Klug D. Let it glow: genetically encoded fluorescent reporters in Plasmodium. Malar J 2024; 23:114. [PMID: 38643106 PMCID: PMC11032601 DOI: 10.1186/s12936-024-04936-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/06/2024] [Indexed: 04/22/2024] Open
Abstract
The use of fluorescent proteins (FPs) in Plasmodium parasites has been key to understand the biology of this obligate intracellular protozoon. FPs like the green fluorescent protein (GFP) enabled to explore protein localization, promoter activity as well as dynamic processes like protein export and endocytosis. Furthermore, FP biosensors have provided detailed information on physiological parameters at the subcellular level, and fluorescent reporter lines greatly extended the malariology toolbox. Still, in order to achieve optimal results, it is crucial to know exactly the properties of the FP of choice and the genetic scenario in which it will be used. This review highlights advantages and disadvantages of available landing sites and promoters that have been successfully applied for the ectopic expression of FPs in Plasmodium berghei and Plasmodium falciparum. Furthermore, the properties of newly developed FPs beyond DsRed and EGFP, in the visualization of cells and cellular structures as well as in the sensing of small molecules are discussed.
Collapse
Affiliation(s)
- Pia J Thiele
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Raquel Mela-Lopez
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Stéphanie A Blandin
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Dennis Klug
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France.
- Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps University Marburg, 35037, Marburg, Germany.
| |
Collapse
|
5
|
Valim Parca A, Godoy Pieri NC, Fantinato Neto P, Fernandes Bressan F, Ambrósio CE, Santos Martins DD. Comparative Analysis of Fluorescent Labeling Techniques for Tracking Canine Amniotic Stem Cells. Tissue Eng Part C Methods 2024; 30:183-192. [PMID: 38411508 DOI: 10.1089/ten.tec.2023.0286] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
The utmost aim of regenerative medicine is to promote the regeneration of injured tissues using stem cells. Amniotic mesenchymal stem cells (AmMSCs) have been used in several studies mainly because of their easy isolation from amniotic tissue postpartum and immunomodulatory and angiogenic properties and the low level of rejection. These cells share characteristics of both embryonic/fetal and adult stem cells and are particularly advantageous because they do not trigger tumorigenic activity when injected into immunocompromised animals. The large-scale use of AmMSCs for cellular therapies would greatly benefit from fluorescence labeling studies to validate their tracking in future therapies. This study evaluated the fluorophore positivity, fluorescence intensity, and longevity of canine AmMSCs. For this purpose, canine AmMSCs from the GDTI/USP biobank were submitted to three labeling conditions, two commercial fluorophores [CellTrace CFSE Cell Proliferation kit - CTrace, and CellTracker Green CMFDA - CTracker (CellTracker Green CMFDA, CT, #C2925, Molecular Probes®; Life Technologies)] and green fluorescent protein (GFP) expression after lentiviral transduction, to select the most suitable tracer in terms of adequate persistence and easy handling and analysis that could be used in studies of domestic animals. Fluorescence was detected in all groups; however, the patterns were different. Specifically, CTrace and CTracker fluorescence was detected 6 h after labeling, while GFP was visualized no earlier than 48 h after transduction. Flow cytometry analysis revealed more than 70% of positive cells on day 7 in the CTrace and CTracker groups, while fluorescence decreased significantly to 10% or less on day 20. Variations between repetitions were observed in the GFP group under the present conditions. Our results showed earlier fluorescence detection and more uniform results across repetitions for the commercial fluorophores. In contrast, fluorescence persisted for more extended periods in the GFP group. These results indicate a promising direction for assessing the roles of canine AmMSCs in regenerative medicine without genomic integration.
Collapse
Affiliation(s)
- Andressa Valim Parca
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Naira Caroline Godoy Pieri
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Paulo Fantinato Neto
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Daniele Dos Santos Martins
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| |
Collapse
|
6
|
Tsutsumi E, Tokumoto T. Real-Time Observation of Germinal Vesicle Migration During Oocyte Meiotic Cell Division Using Ovarian Fluorescent Transgenic Zebrafish. Zebrafish 2024; 21:171-176. [PMID: 38621215 DOI: 10.1089/zeb.2023.0048] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
The transgenic (TG) zebrafish allows researchers to bio-image specific biological phenomena in cells and tissues in vivo. We established TG lines to monitor changes in the ovaries of live fish. The original TG line with ovarian fluorescence was occasionally established. Although the cDNA integrated into the line was constructed for the expression of enhanced green fluorescent protein (EGFP) driven by the medaka β-actin promoter, the expression of EGFP is restricted to the oocytes and gills in adult fish. Furthermore, we found that germinal vesicles (GVs) in oocytes of the established line can be observed by relatively strong fluorescence around the GV. In this study, we tried to capture the dynamic processes of germinal vesicle breakdown (GVBD) during meiotic cell division using the GV fluorescent oocytes. As a result, GV migration and GVBD could be monitored in real time. We also succeeded in observing actin filaments involved in the migration of GV to the animal pole. This strain can be used for education in the process of oocyte meiotic cell division.
Collapse
Affiliation(s)
- Eisei Tsutsumi
- Department of Bioscience, Graduate School of Science and Technology, National University Corporation, Shizuoka University, Shizuoka, Japan
| | - Toshinobu Tokumoto
- Department of Bioscience, Graduate School of Science and Technology, National University Corporation, Shizuoka University, Shizuoka, Japan
| |
Collapse
|
7
|
Tomris I, van der Woude R, de Paiva Froes Rocha R, Torrents de la Peña A, Ward AB, de Vries RP. Viral envelope proteins fused to multiple distinct fluorescent reporters to probe receptor binding. Protein Sci 2024; 33:e4974. [PMID: 38533540 DOI: 10.1002/pro.4974] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
Enveloped viruses carry one or multiple proteins with receptor-binding functionalities. Functional receptors can be glycans, proteinaceous, or both; therefore, recombinant protein approaches are instrumental in attaining new insights regarding viral envelope protein receptor-binding properties. Visualizing and measuring receptor binding typically entails antibody detection or direct labeling, whereas direct fluorescent fusions are attractive tools in molecular biology. Here, we report a suite of distinct fluorescent fusions, both N- and C-terminal, for influenza A virus hemagglutinins and SARS-CoV-2 spike RBD. The proteins contained three or six fluorescent protein barrels and were applied directly to cells to assess receptor binding properties.
Collapse
Affiliation(s)
- Ilhan Tomris
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Roosmarijn van der Woude
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Rebeca de Paiva Froes Rocha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Robert P de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| |
Collapse
|
8
|
Sharifi M, Alizadeh AA, Mivehroud MH, Dastmalchi S. Construction of a bacteriophage-derived vector with potential applications in targeted drug delivery and cell imaging. Biotechnol Lett 2024; 46:147-159. [PMID: 38184487 DOI: 10.1007/s10529-023-03455-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 01/08/2024]
Abstract
There is a strong relationship between the dysregulation of epidermal growth factor receptor (EGFR) and the development of epithelial-derived cancers. Therefore, EGFR has usually been considered the desired target for gene therapy. Here, we propose an approach for targeting EGFR-expressing cells by phage particles capable of displaying EGF and GFP as tumor-targeting and reporting elements, respectively. For this purpose, the superfolder GFP-EGF (sfGFP-EGF) coding sequence was inserted at the N-terminus of the pIII gene in the pIT2 phagemid. The capability of the constructed phage to recognize EGFR-overexpressing cells was monitored by fluorescence microscopy, fluorescence-activated cell sorting (FACS), and cell-based ELISA experiments. FACS analysis showed a significant shift in the mean fluorescence intensity (MFI) of the cells treated with phage displaying sfGFP-EGF compared to phage displaying only sfGFP. The binding of phage displaying sfGFP-EGF to A-431 cells, monitored by fluorescence microscopy, indicated the formation of the sfGFP-EGF-EGFR complex on the surface of the treated cells. Cell-based ELISA experiments showed that phages displaying either EGF or sfGFP-EGF can specifically bind EGFR-expressing cells. The vector constructed in the current study has the potential to be engineered for gene delivery purposes as well as cell-based imaging for tumor detection.
Collapse
Affiliation(s)
- Mehdi Sharifi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Medicinal Plants Research Center, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Maryam Hamzeh Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
- Faculty of Pharmacy, Near East University, Po. Box: 99138, Nicosia, North Cyprus, Mersin 10, Turkey.
| |
Collapse
|
9
|
Fuhrmann-Aoyagi MB, Igarashi S, Miura K. Comparative Evaluation of Transient Protein Expression Efficiency in Tissues across Soybean Varieties Using the Tsukuba System. Plants (Basel) 2024; 13:858. [PMID: 38592852 PMCID: PMC10975771 DOI: 10.3390/plants13060858] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/11/2024]
Abstract
Transient protein expression is a versatile tool with diverse applications and can be used in soybeans to study gene function, obtain mutants, and produce proteins for commercial use. However, soybeans are considered recalcitrant for agroinfiltration. Subsequent studies on soybeans have demonstrated a green fluorescent protein (GFP) expression in seedpods, but not in leaves, using syringe agroinfiltration. To evaluate agroinfiltration-based transient protein expression levels in plant cells, we used the transient expression vector pTKB3 harboring the GFP gene. Using Agrobacterium tumefaciens, vacuum agroinfiltration of the leaves and needle agroinfiltration of the seedlings of different soybean varieties were performed. GFP was transiently expressed in all of the samples. However, the Enrei and Williams 82 varieties presented better results than the other varieties in the leaf tissue, with results confirmed by immunoblot analysis, demonstrating that both varieties are good candidates for molecular biological studies. GFP expression in the seedlings was less extensive than that in the leaves, which may be due to the tissue characteristics, with Enrei showing the best results. Based on this observation, we conclude that the Tsukuba system is an effective tool that can be used for different tissues and soybean varieties.
Collapse
Affiliation(s)
| | - Saki Igarashi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8572, Japan; (M.B.F.-A.); (S.I.)
| | - Kenji Miura
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8572, Japan; (M.B.F.-A.); (S.I.)
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan
| |
Collapse
|
10
|
Wang S, Han J, Huang J, Islam K, Shi Y, Zhou Y, Kim D, Zhou J, Lian Z, Liu Y, Huang J. Deep learning-based predictive classification of functional subpopulations of hematopoietic stem cells and multipotent progenitors. Stem Cell Res Ther 2024; 15:74. [PMID: 38475857 PMCID: PMC10935795 DOI: 10.1186/s13287-024-03682-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) play a pivotal role in maintaining lifelong hematopoiesis. The distinction between stem cells and other progenitors, as well as the assessment of their functions, has long been a central focus in stem cell research. In recent years, deep learning has emerged as a powerful tool for cell image analysis and classification/prediction. METHODS In this study, we explored the feasibility of employing deep learning techniques to differentiate murine HSCs and MPPs based solely on their morphology, as observed through light microscopy (DIC) images. RESULTS After rigorous training and validation using extensive image datasets, we successfully developed a three-class classifier, referred to as the LSM model, capable of reliably distinguishing long-term HSCs, short-term HSCs, and MPPs. The LSM model extracts intrinsic morphological features unique to different cell types, irrespective of the methods used for cell identification and isolation, such as surface markers or intracellular GFP markers. Furthermore, employing the same deep learning framework, we created a two-class classifier that effectively discriminates between aged HSCs and young HSCs. This discovery is particularly significant as both cell types share identical surface markers yet serve distinct functions. This classifier holds the potential to offer a novel, rapid, and efficient means of assessing the functional states of HSCs, thus obviating the need for time-consuming transplantation experiments. CONCLUSION Our study represents the pioneering use of deep learning to differentiate HSCs and MPPs under steady-state conditions. This novel and robust deep learning-based platform will provide a basis for the future development of a new generation stem cell identification and separation system. It may also provide new insight into the molecular mechanisms underlying stem cell self-renewal.
Collapse
Affiliation(s)
- Shen Wang
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | - Jianzhong Han
- Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jingru Huang
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences, Shanghai, People's Republic of China
| | - Khayrul Islam
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | - Yuheng Shi
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences, Shanghai, People's Republic of China
| | - Yuyuan Zhou
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Dongwook Kim
- Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jane Zhou
- Health and Human Biology, Brown University, Providence, RI, USA
| | - Zhaorui Lian
- Coriell Institute for Medical Research, Camden, NJ, USA
| | - Yaling Liu
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA.
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA.
| | - Jian Huang
- Coriell Institute for Medical Research, Camden, NJ, USA.
- Cooper Medical School of Rowan University, Camden, NJ, USA.
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
11
|
Clarke DN, Rose NH, De Meulenaere E, Rosental B, Pearse JS, Pearse VB, Deheyn DD. Fluorescent proteins generate a genetic color polymorphism and counteract oxidative stress in intertidal sea anemones. Proc Natl Acad Sci U S A 2024; 121:e2317017121. [PMID: 38457522 PMCID: PMC10945830 DOI: 10.1073/pnas.2317017121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/13/2024] [Indexed: 03/10/2024] Open
Abstract
Fluorescent proteins (FPs) are ubiquitous tools in research, yet their endogenous functions in nature are poorly understood. In this work, we describe a combination of functions for FPs in a clade of intertidal sea anemones whose FPs control a genetic color polymorphism together with the ability to combat oxidative stress. Focusing on the underlying genetics of a fluorescent green "Neon" color morph, we show that allelic differences in a single FP gene generate its strong and vibrant color, by increasing both molecular brightness and FP gene expression level. Natural variation in FP sequences also produces differences in antioxidant capacity. We demonstrate that these FPs are strong antioxidants that can protect live cells against oxidative stress. Finally, based on structural modeling of the responsible amino acids, we propose a model for FP antioxidant function that is driven by molecular surface charge. Together, our findings shed light on the multifaceted functions that can co-occur within a single FP and provide a framework for studying the evolution of fluorescence as it balances spectral and physiological functions in nature.
Collapse
Affiliation(s)
- D. Nathaniel Clarke
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA93950
| | - Noah H. Rose
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA93950
| | - Evelien De Meulenaere
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92037
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva84105, Israel
| | - John S. Pearse
- Department of Ecology and Evolutionary Biology, Joseph M. Long Marine Laboratory, University of California, Santa Cruz, CA95060
| | - Vicki Buchsbaum Pearse
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA93950
- Department of Ecology and Evolutionary Biology, Joseph M. Long Marine Laboratory, University of California, Santa Cruz, CA95060
| | - Dimitri D. Deheyn
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA92037
| |
Collapse
|
12
|
Poding LH, Jägers P, Herlitze S, Huhn M. Diversity and function of fluorescent molecules in marine animals. Biol Rev Camb Philos Soc 2024. [PMID: 38468189 DOI: 10.1111/brv.13072] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.
Collapse
Affiliation(s)
- Lars H Poding
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Peter Jägers
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Mareike Huhn
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| |
Collapse
|
13
|
Mohammad T, Ghogare R, Morton LB, Dhingra A, Potlakayala S, Rudrabhatla S, Dhir SK. Evaluation of Parameters Affecting Agrobacterium-Mediated Transient Gene Expression in Industrial Hemp ( Cannabis sativa L.). Plants (Basel) 2024; 13:664. [PMID: 38475511 DOI: 10.3390/plants13050664] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Industrial hemp Cannabis sativa L. is an economically important crop mostly grown for its fiber, oil, and seeds. Due to its increasing applications in the pharmaceutical industry and a lack of knowledge of gene functions in cannabinoid biosynthesis pathways, developing an efficient transformation platform for the genetic engineering of industrial hemp has become necessary to enable functional genomic and industrial application studies. A critical step in the development of Agrobacterium tumefaciens-mediated transformation in the hemp genus is the establishment of optimal conditions for T-DNA gene delivery into different explants from which whole plantlets can be regenerated. As a first step in the development of a successful Agrobacterium tumefaciens-mediated transformation method for hemp gene editing, the factors influencing the successful T-DNA integration and expression (as measured by transient β-glucuronidase (GUS) and Green Florescent Protein (GFP) expression) were investigated. In this study, the parameters for an agroinfiltration system in hemp, which applies to the stable transformation method, were optimized. In the present study, we tested different explants, such as 1- to 3-week-old leaves, cotyledons, hypocotyls, root segments, nodal parts, and 2- to 3-week-old leaf-derived calli. We observed that the 3-week-old leaves were the best explant for transient gene expression. Fully expanded 2- to 3-week-old leaf explants, in combination with 30 min of immersion time, 60 µM silver nitrate, 0.5 µM calcium chloride, 150 µM natural phenolic compound acetosyringone, and a bacterial density of OD600nm = 0.4 resulted in the highest GUS and GFP expression. The improved method of genetic transformation established in the present study will be useful for the introduction of foreign genes of interest, using the latest technologies such as genome editing, and studying gene functions that regulate secondary metabolites in hemp.
Collapse
Affiliation(s)
- Tasnim Mohammad
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
| | - Rishikesh Ghogare
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Lauren B Morton
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
| | - Amit Dhingra
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Shobha Potlakayala
- The Central Pennsylvania Research and Teaching Laboratory for Biofuels, Penn State Harrisburg, Middletown, PA 17057, USA
| | - Sairam Rudrabhatla
- The Central Pennsylvania Research and Teaching Laboratory for Biofuels, Penn State Harrisburg, Middletown, PA 17057, USA
| | - Sarwan K Dhir
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
| |
Collapse
|
14
|
Seo PW, Kim GJ, Kim JS. A short guide on blue fluorescent proteins: limits and perspectives. Appl Microbiol Biotechnol 2024; 108:208. [PMID: 38353763 PMCID: PMC10866763 DOI: 10.1007/s00253-024-13012-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
The advent of the so-called colorful biology era is in line with the discovery of fluorescent proteins (FPs), which can be widely used to detect the intracellular locations of macromolecules or to determine the abundance of metabolites in organelles. The application of multiple FPs that emit different spectra and colors could be implemented to precisely evaluate cellular events. FPs were initially established with the emergence of the green fluorescent protein (GFP) from jellyfish. Red fluorescent proteins (RFPs) from marine anemones and several corals adopt fluorescent chromophores that are similar to GFP. Chromophores of GFP and GFP-like FPs are formed through the oxidative rearrangement of three chromophore-forming residues, thereby limiting their application to only oxidative environments. Alternatively, some proteins can be fluorescent upon their interaction with cellular prosthetic cofactors and, thus, work in aerobic and anaerobic conditions. The modification of an NADPH-dependent blue fluorescent protein (BFP) also expanded its application to the quantization of NADPH in the cellular environment. However, cofactor-dependent BFPs have an intrinsic weakness of poor photostability with a high fluorescent background. This review explores GFP-derived and NADPH-dependent BFPs with a focus on NADPH-dependent BFPs, which might be technically feasible in the near future upon coupling with two-photon fluorescence microscopy or nucleic acid-mimickers. KEY POINTS: • Oxidation-dependent GFP-like BFPs and redox-free NADPH-dependent BFPs • GFPs of weak photostability and intensity with a high fluorescent background • Real-time imaging using mBFP under two-photon fluorescence microscopy.
Collapse
Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
15
|
Namisy A, Chen SY, Huang JH, Unartngam J, Thanarut C, Chung WH. Histopathology and quantification of green fluorescent protein-tagged Fusarium oxysporum f. sp. luffae isolate in resistant and susceptible Luffa germplasm. Microbiol Spectr 2024; 12:e0312723. [PMID: 38174927 PMCID: PMC10846128 DOI: 10.1128/spectrum.03127-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Fusarium oxysporum f. sp. luffae (Folu) is a severe plant pathogen that causes vascular wilt and root rot in Luffa plants worldwide. A green fluorescent protein (GFP)-tagged isolate of Folu (Fomh16-GFP) was utilized to investigate the infection progress and colonization of Fomh16-GFP in resistant (LA140) and susceptible (LA100) Luffa genotypes. Seven days post-inoculation (dpi), it was observed that Fomh16-GFP had successfully invaded and colonized the vascular bundle of all LA100 parts, including the roots, hypocotyl, and stem. Pathogen colonization continued to increase over time, leading to the complete wilting of plants by 14-17 dpi. In LA140, the Fomh16-GFP isolate colonized the roots and hypocotyl vascular system at 7 dpi. Nevertheless, this colonization was restricted in the hypocotyl and decreased significantly, and no fungal growth was detected in the vascular system at 21 dpi. Thus, the resistant genotype might trigger a robust defense mechanism. In addition, while the pathogen was present in LA140, the inoculated plants did not exhibit any symptoms until 28 dpi. Quantitative PCR was utilized to measure the Fomh16-GFP biomass in various parts of LA100 and LA140 at different time points. The findings indicated a positive correlation between the quantity of Fomh16-GFP DNA and disease development in LA100. Alternatively, a high amount of Fomh16-GFP DNA was identified in the roots of LA140. Nonetheless, no significant correlations were found between DNA amount and disease progression in LA140. Aqueous extracts from LA140 significantly reduced Fomh16-GFP spore germination, while no significant reduction was detected using LA100 extracts.IMPORTANCEFusarium wilt of Luffa, caused by Fusarium oxysporum f. sp. luffae (Folu), causes great losses in Luffa plants worldwide. This study used a green fluorescent protein (GFP)-tagged isolate of Folu (Fomh16-GFP) to investigate the infection progress and colonization dynamics of Fomh16-GFP in the resistant and susceptible Luffa genotypes, which could be important in understanding the resistance mechanism of Folu in Luffa plants. In addition, our work highlights the correlations between DNA amount and disease progression in resistant plants using real-time PCR. We observed a positive correlation between the quantity of Fomh16-GFP DNA and disease progression in LA100, while no significant correlation was found in LA140. These results could be valuable to further investigate the resistance mechanism of Luffa genotypes against Folu. Gaining a better understanding of the interaction between Folu and Luffa plants is crucial for effectively managing Fusarium wilt and enhancing resistance in Luffa rootstock and its varieties.
Collapse
Affiliation(s)
- Ahmed Namisy
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Shu-Yun Chen
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Jin-Hsing Huang
- Plant Pathology Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung, Taiwan
| | - Jintana Unartngam
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Chinnapan Thanarut
- Faculty of Agriculture Production, Division of Pomology Maejo University, Bangkok, Thailand
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung, Taiwan
- Master Program for Plant Medicine and Agricultural Practice, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
16
|
Zarzyńska-Nowak A, Minicka J, Wieczorek P, Hasiów-Jaroszewska B. Development of Stable Infectious cDNA Clones of Tomato Black Ring Virus Tagged with Green Fluorescent Protein. Viruses 2024; 16:125. [PMID: 38257825 PMCID: PMC10819210 DOI: 10.3390/v16010125] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Tomato black ring virus (TBRV) is a member of the Nepovirus genus in the Secoviridae family, which infects a wide range of important crop species worldwide. In this work, we constructed four cDNA infectious clones of the TBRV tagged with the green fluorescent protein (TBRV-GFP), which varied in (i) the length of the sequences flanking the GFP insert, (ii) the position of the GFP insert within the RNA2 polyprotein, and (iii) the addition of a self-cutting 2A protein. The presence of the GFP coding sequence in infected plants was verified by RT-PCR, while the infectivity and stability of the constructs were verified by mechanical inoculation of the host plants. The systemic spread of TBRV-GFP within plants was observed under UV light at a macroscopic level, monitoring GFP-derived fluorescence in leaves, and at a microscopic level using confocal microscopy. The obtained clones are a valuable tool for future studies of TBRV-host interactions, virus biology, and the long-term monitoring of its distribution in infected plants.
Collapse
Affiliation(s)
- Aleksandra Zarzyńska-Nowak
- Department of Virology and Bacteriology, Institute of Plant Protection—National Research Institute, Wladyslawa Wegorka 20, 60-318 Poznan, Poland; (J.M.); (B.H.-J.)
| | - Julia Minicka
- Department of Virology and Bacteriology, Institute of Plant Protection—National Research Institute, Wladyslawa Wegorka 20, 60-318 Poznan, Poland; (J.M.); (B.H.-J.)
| | - Przemysław Wieczorek
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection—National Research Institute, Wladyslawa Wegorka 20, 60-318 Poznan, Poland;
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection—National Research Institute, Wladyslawa Wegorka 20, 60-318 Poznan, Poland; (J.M.); (B.H.-J.)
| |
Collapse
|
17
|
Sparkes I, White RR, Bateman B, Botchway S, Ward A. Using Optical Tweezers Combined with Total Internal Reflection Microscopy to Study Interactions Between the ER and Golgi in Plant Cells. Methods Mol Biol 2024; 2772:179-190. [PMID: 38411814 DOI: 10.1007/978-1-0716-3710-4_13] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Optical tweezers have been used to trap and micro-manipulate several biological specimens ranging from DNA, macromolecules, organelles, to single-celled organisms. Using a combination of the refraction and scattering of laser light from a focused laser beam, refractile objects are physically captured and can be moved within the surrounding media. The technique is routinely used to determine biophysical properties such as the forces exerted by motor proteins. Here, we describe how optical tweezers combined with total internal reflection fluorescence microscopy (TIRF) can be used to assess physical interactions between organelles, more specifically the ER and Golgi bodies in plant cells.
Collapse
Affiliation(s)
- Imogen Sparkes
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | | | - Benji Bateman
- Central Laser Facility, Science and Technology Facilities Council, Oxon, UK
| | - Stanley Botchway
- Central Laser Facility, Science and Technology Facilities Council, Oxon, UK
| | - Andy Ward
- Central Laser Facility, Science and Technology Facilities Council, Oxon, UK
| |
Collapse
|
18
|
Liu X, Gong Y. Determining the Subcellular Localization of Proteins in the Different Membranes of Diatom Secondary Plastid. Methods Mol Biol 2024; 2776:185-196. [PMID: 38502505 DOI: 10.1007/978-1-0716-3726-5_11] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Diatoms such as Phaeodactylum tricornutum arose through a process termed secondary endosymbiosis, in which red alga-derived plastids are surrounded by a complicated membrane system. Subcellular marker proteins provide defined localizations on the compartmental and even sub-compartmental levels in the complex plastids of diatoms. Here we introduce how to use subcellular marker proteins and in vivo co-localization in the diatom P. tricornutum by presenting a step-by-step method allowing the determination of subcellular localization of proteins in different membranes of the secondary plastid. This chapter describes the materials required and the procedures of transformation and microscopic observation.
Collapse
Affiliation(s)
| | - Yangmin Gong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| |
Collapse
|
19
|
Serbus LR. A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging. Methods Mol Biol 2024; 2739:349-373. [PMID: 38006562 DOI: 10.1007/978-1-0716-3553-7_21] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.
Collapse
Affiliation(s)
- Laura Renee Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA.
| |
Collapse
|
20
|
Liu CH, Chen YJ, Wu WC, Lin YH. Magnetic graphene oxide nanoflakes for dual RNA interfering delivery and gene knockdown in prostate and liver cancers. Int J Biol Macromol 2023; 253:127357. [PMID: 37838128 DOI: 10.1016/j.ijbiomac.2023.127357] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/01/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
The development of synthetic carriers for small interfering RNA (siRNA) and plasmids is crucial for effective gene therapy. In this study, we synthesized magnetic graphene oxide nanoflakes as carriers for siRNA delivery, with the goal of knockdown specific genes such as the green fluorescence protein (GFP). Our approach combined magnetically reduced graphene oxide with polyethylenimine (PEI) crosslinked to its surface using carbonyl diimidazole. To evaluate the adsorption capacity of the PEI-modified nanocomposite, we investigated its ability to bind two types of nucleic acids: short-hairpin (sh)RNA plasmids and siRNA targeting GFP. The nanocomposite exhibited significant adsorption, with maximum capacities of 426 ng/μg for shRNA and 71 ng/μg for siRNA, respectively. Simultaneous delivery of siRNA and shRNA using our designed nanocomposites was successfully achieved in human hepatoma and prostate cancer cells. Under magnetic guidance, the knockdown efficiencies reached 73.5 % in hepatoma cells for dual delivery of siRNA and shRNA. Our findings revealed that the nanocomplexes were internalized by the cells through a caveolae-dependent endocytosis mechanism. The demonstrated ability of the nanoflakes to efficiently transport siRNA and shRNA, with high loading capacity, controlled release, and magnetic targeting, resulted in effective GFP knockdown in vitro. These findings highlight the potential of magnetic graphene oxide nanoflakes as promising carriers for siRNA delivery and gene knockdown in therapeutic applications.
Collapse
Affiliation(s)
- Chi-Hsien Liu
- Department of Chemical and Materials Engineering, Chang Gung University, 259, Wen-Hwa First Road, Tao-Yuan, Taiwan; Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 261, Wen-Hwa First Road, Taoyuan, Taiwan; Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, 5, Fu-Hsing Street, Taoyuan, Taiwan.
| | - Yi-Jun Chen
- Department of Chemical and Materials Engineering, Chang Gung University, 259, Wen-Hwa First Road, Tao-Yuan, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou, 5, Fu-Hsing Street, Taoyuan, Taiwan; College of Medicine, Chang Gung University, 259, Wen-Hwa First Road, Taoyuan, Taiwan
| | - Yen-Han Lin
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
21
|
Chakka J, Maniruzzaman M. A Proof-of-Concept Preparation of Lipid-Plasmid DNA Particles Using Novel Extrusion-Based 3D-Printing Technology, SMART. Mol Pharm 2023; 20:6504-6508. [PMID: 37931027 DOI: 10.1021/acs.molpharmaceut.3c00783] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Gene therapy is a promising approach with delivery of mRNA, small interference RNA, and plasmid DNA to elicit a therapeutic action in vitro using cationic or ionizable lipid nanoparticles. In the present study, a novel extrusion-based Sprayed Multi Adsorbed-droplet Reposing Technology (SMART) developed in-house was employed for the preparation, characterization, and transfection abilities of the green fluorescence protein (GFP) plasmid DNA in cancer cells in vitro. The results showed 100% encapsulation of pDNA (GFP) in LNPs of around 150 nm (N/P 5) indicating that the processes developed using SMART technology are consistent and can be utilized for commercial applications.
Collapse
Affiliation(s)
- Jaidev Chakka
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Pharmaceutical Engineering and 3D printing (PharmE3D) Lab, Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Mohammed Maniruzzaman
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Pharmaceutical Engineering and 3D printing (PharmE3D) Lab, Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, Oxford, Mississippi 38677, United States
| |
Collapse
|
22
|
Wagenbach M, Vicente JJ, Wagenbach W, Wordeman L. Production of CRISPR-Cas9 Transgenic Cell Lines for Knocksideways Studies. Curr Protoc 2023; 3:e965. [PMID: 38153181 PMCID: PMC10756642 DOI: 10.1002/cpz1.965] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Protein activity is generally functionally integrated and spatially restricted to key locations within the cell. Knocksideways experiments allow researchers to rapidly move proteins to alternate or ectopic regions of the cell and assess the resultant cellular response. Briefly, individual proteins to be tested using this approach must be modified with moieties that dimerize under treatment with rapamycin to promote the experimental spatial relocalizations. CRISPR technology enables researchers to engineer modified protein directly in cells while preserving proper protein levels because the engineered protein will be expressed from endogenous promoters. Here we provide straightforward instructions to engineer tagged, rapamycin-relocalizable proteins in cells. The protocol is described in the context of our work with the microtubule depolymerizer MCAK/Kif2C, but it is easily adaptable to other genes and alternate tags such as degrons, optogenetic constructs, and other experimentally useful modifications. Off-target effects are minimized by testing for the most efficient target site using a split-GFP construct. This protocol involves no proprietary kits, only plasmids available from repositories (such as addgene.org). Validation, relocalization, and some example novel discoveries obtained working with endogenous protein levels are described. A graduate student with access to a fluorescence microscope should be able to prepare engineered cells with spatially controllable endogenous protein using this protocol. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Choosing a target site for gene modification Basic Protocol 2: Design of gRNA(s) for targeted gene modification Basic Protocol 3: Split-GFP test for target efficiency Basic Protocol 4: Design of the recombination template and analytical primers Support Protocol 1: Design of primers for analytical PCR Basic Protocol 5: Transfection, isolation, and validation of engineered cells Support Protocol 2: Stable transfection of engineered cells with binding partners.
Collapse
Affiliation(s)
- Michael Wagenbach
- Department of Physiology & Biophysics, University of Washington School of Medicine, Seattle, Washington
| | - Juan Jesus Vicente
- Department of Physiology & Biophysics, University of Washington School of Medicine, Seattle, Washington
| | - Wren Wagenbach
- Bieler School of Environment, McGill University, Montreal, Quebec, Canada
| | - Linda Wordeman
- Department of Physiology & Biophysics, University of Washington School of Medicine, Seattle, Washington
| |
Collapse
|
23
|
Pedraz L, Torrents E. An easy method for quantification of anaerobic and microaerobic gene expression with fluorescent reporter proteins. Biotechniques 2023; 75:250-255. [PMID: 37880975 DOI: 10.2144/btn-2023-0064] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
Fluorescent proteins, such as green fluorescent proteins, are invaluable tools for detecting and quantifying gene expression in high-throughput reporter gene assays. However, they introduce significant inaccuracies in studies involving microaerobiosis or anaerobiosis, as oxygen is required for the maturation of these proteins' chromophores. In this study, the authors highlight the errors incurred by using fluorescent proteins under limited oxygenation by comparing standard fluorescence-based reporter gene assays to quantitative real-time PCR data in the study of a complex oxygen-regulated gene network. Furthermore, a solution to perform quantification of anaerobic and microaerobic gene expression with fluorescent reporter proteins using a microplate reader with an oxygen control system and applying pulses of full oxygenation before fluorescence measurements is provided.
Collapse
Affiliation(s)
- Lucas Pedraz
- Bacterial Infections & Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science & Technology (BIST), Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Present address: Department of Microbiology & Immunology, University of British Columbia (UBC), Lower Mall Research Station, Vancouver, BC, V6T 1Z4, Canada
| | - Eduard Torrents
- Bacterial Infections & Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science & Technology (BIST), Baldiri Reixac 15-21, 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology & Statistics, University of Barcelona, 643 Diagonal Avenue, 08028, Barcelona, Spain
| |
Collapse
|
24
|
Rasooly R, Do P, He X, Hernlem B. A Sensitive, Cell-Based Assay for Measuring Low-Level Biological Activity of α-Amanitin. Int J Mol Sci 2023; 24:16402. [PMID: 38003593 PMCID: PMC10671307 DOI: 10.3390/ijms242216402] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
α-Amanitin is one of the primary toxins produced by the poisonous mushroom genus, Amanita. Because it is odorless and tasteless, it is an important cause of death from the consumption of misidentified mushrooms. To study the thermal stability of α-amanitin, novel cell-based assays were developed to measure the toxin's activity, based on the inhibition of RNA polymerase II by α-amanitin. First, an MTT-formazan cell viability assay was used to measure the biological activity of α-amanitin through the inhibition of cellular activity. This method can detect 10 μg/mL of α-amanitin in a time-dependent manner. Second, a more sensitive quantitative PCR approach was developed to examine its inhibition of viral replication. The new RT-qPCR assay enabled the detection of 100 ng/mL. At this level, α-amanitin still significantly reduced adenovirus transcription. Third, a simpler GFP expression-based assay was developed with an equal sensitivity to the RT-qPCR assay. With this assay, aqueous α-amanitin heated at 90 °C for 16 h or treated in the microwave for 3 min retained its biological activity when tested in HEK293 cells, but a slight reduction was observed when tested in Vero cells. Beyond detecting the activity of α-amanitin, the new method has a potential application for detecting the activity of other toxins that are RNA polymerase inhibitors.
Collapse
Affiliation(s)
- Reuven Rasooly
- Foodborne Toxin Detection & Prevention Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA; (P.D.); (X.H.); (B.H.)
| | | | | | | |
Collapse
|
25
|
Wang S, Han J, Huang J, Islam K, Shi Y, Zhou Y, Kim D, Zhou J, Lian Z, Liu Y, Huang J. Deep learning-based predictive classification of functional subpopulations of hematopoietic stem cells and multipotent progenitors. Res Sq 2023:rs.3.rs-3332530. [PMID: 38014055 PMCID: PMC10680918 DOI: 10.21203/rs.3.rs-3332530/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) play a pivotal role in maintaining lifelong hematopoiesis. The distinction between stem cells and other progenitors, as well as the assessment of their functions, has long been a central focus in stem cell research. In recent years, deep learning has emerged as a powerful tool for cell image analysis and classification/prediction. Methods In this study, we explored the feasibility of employing deep learning techniques to differentiate murine HSCs and MPPs based solely on their morphology, as observed through light microscopy (DIC) images. Results After rigorous training and validation using extensive image datasets, we successfully developed a three-class classifier, referred to as the LSM model, capable of reliably distinguishing long-term HSCs (LT-HSCs), short-term HSCs (ST-HSCs), and MPPs. The LSM model extracts intrinsic morphological features unique to different cell types, irrespective of the methods used for cell identification and isolation, such as surface markers or intracellular GFP markers. Furthermore, employing the same deep learning framework, we created a two-class classifier that effectively discriminates between aged HSCs and young HSCs. This discovery is particularly significant as both cell types share identical surface markers yet serve distinct functions. This classifier holds the potential to offer a novel, rapid, and efficient means of assessing the functional states of HSCs, thus obviating the need for time-consuming transplantation experiments. Conclusion Our study represents the pioneering use of deep learning to differentiate HSCs and MPPs under steady-state conditions. With ongoing advancements in model algorithms and their integration into various imaging systems, deep learning stands poised to become an invaluable tool, significantly impacting stem cell research.
Collapse
Affiliation(s)
- Shen Wang
- Lehigh University Department of Mechanical Engineering and Mechanics
| | | | | | - Khayrul Islam
- Lehigh University Department of Mechanical Engineering and Mechanics
| | - Yuheng Shi
- Shanghai Medical College of Fudan University: Fudan University School of Basic Medical Sciences
| | | | | | | | | | | | | |
Collapse
|
26
|
Sun L, Lv S, Song T. Monitoring Autophagy with GFP-LC3 Reporter. Methods Mol Biol 2023. [PMID: 37889422 DOI: 10.1007/7651_2023_501] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Autophagy is a key process that maintains cellular homeostasis. Autophagy contributes to various physiological and pathophysiological processes. Development of methodologies for autophagy detection has greatly facilitated the research on autophagy. Among these methodologies, GFP-LC3 reporter has been popularly used in the literature. In this chapter, we will detail step-by-step the GFP-LC3 reporter protocol we have adapted in our lab. This protocol begins with the generation of lentivirus expressing GFP-LC3. Then, the cells are transduced with titrated virus. After selecting the positive cells, single colonies are isolated, characterized, validated, and used in further study.
Collapse
Affiliation(s)
- Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
27
|
Tchagang CF, Mah TF, Campbell-Valois FX. Anaerobic fluorescent reporters for live imaging of Pseudomonas aeruginosa. Front Microbiol 2023; 14:1245755. [PMID: 37928662 PMCID: PMC10623331 DOI: 10.3389/fmicb.2023.1245755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Pseudomonas aeruginosa thrives in the airways of individuals with cystic fibrosis, in part by forming robust biofilms that are resistant to immune clearance or antibiotic treatment. In the cystic fibrosis lung, the thickened mucus layers create an oxygen gradient, often culminating with the formation of anoxic pockets. In this environment, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa are limited to the GFP and related analogs. However, these reporters require oxygen for the maturation of their chromophore, making them unsuitable for the study of anaerobically grown P. aeruginosa. To overcome this limitation, we evaluated seven alternative fluorescent proteins, including iLOV, phiLOV2.1, evoglow-Bs2, LucY, UnaG, Fluorescence-Activating and Absorption-Shifting Tag (FAST), and iRFP670, which have been reported to emit light under oxygen-limiting conditions. We generated a series of plasmids encoding these proteins and validated their fluorescence using plate reader assays and confocal microscopy. Six of these proteins successfully labeled P. aeruginosa in anoxia. In particular, phiLOV2.1 and FAST provided superior fluorescence stability and enabled dual-color imaging of both planktonic and biofilm cultures. This study provides a set of fluorescent reporters for monitoring P. aeruginosa under low-oxygen conditions. These reporters will facilitate studies of P. aeruginosa in biofilms or other contexts relevant to its pathogenesis, such as those found in cystic fibrosis airways. Due to the broad host range of our expression vector, the phiLOV2.1 and FAST-based reporters may be applicable to the study of other Gram-negative bacteria that inhabit similar low-oxygen niches.
Collapse
Affiliation(s)
- Caetanie F. Tchagang
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
- Host-Microbe Interactions Laboratory, Center for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - François-Xavier Campbell-Valois
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
- Host-Microbe Interactions Laboratory, Center for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
28
|
Hollenstein D, Maurer-Granofszky M, Reiter W, Anrather D, Gossenreiter T, Babic R, Hartl N, Kraft C, Hartl M. Chemical Acetylation of Ligands and Two-Step Digestion Protocol for Reducing Codigestion in Affinity Purification-Mass Spectrometry. J Proteome Res 2023; 22:3383-3391. [PMID: 37712406 PMCID: PMC10563155 DOI: 10.1021/acs.jproteome.3c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 09/16/2023]
Abstract
We present an effective, fast, and user-friendly method to reduce codigestion of bead-bound ligands, such as antibodies or streptavidin, in affinity purification-mass spectrometry experiments. A short preincubation of beads with Sulfo-NHS-Acetate leads to chemical acetylation of lysine residues, making ligands insusceptible to Lys-C-mediated proteolysis. In contrast to similar approaches, our procedure offers the advantage of exclusively using nontoxic chemicals and employing mild chemical reaction conditions. After binding of bait proteins to Sulfo-NHS-Acetate treated beads, we employ a two-step digestion protocol with the sequential use of Lys-C protease for on-bead digestion followed by in-solution digestion of the released proteins with trypsin. The implementation of this protocol results in a strong reduction of contaminating ligand peptides, which allows significantly higher amounts of sample to be subjected to LC-MS analysis, improving sensitivity and quantitative accuracy.
Collapse
Affiliation(s)
- David
M. Hollenstein
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | | | - Wolfgang Reiter
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Dorothea Anrather
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Thomas Gossenreiter
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Riccardo Babic
- Institute
of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
- Faculty
of Biology, University of Freiburg, Freiburg 79104, Germany
- Spemann Graduate
School of Biology and Medicine (SGBM), University
of Freiburg, Freiburg 79104, Germany
| | - Natascha Hartl
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Claudine Kraft
- Institute
of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
- CIBSS
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Markus Hartl
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| |
Collapse
|
29
|
Kanno T, Chiou P, Wu MT, Lin WD, Matzke A, Matzke M. A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs, and coilin function in Arabidopsis thaliana. G3 (Bethesda) 2023; 13:jkad175. [PMID: 37539868 PMCID: PMC10542627 DOI: 10.1093/g3journal/jkad175] [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: 02/25/2023] [Revised: 02/25/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023]
Abstract
Coilin is a scaffold protein essential for the structure of Cajal bodies, which are nucleolar-associated, nonmembranous organelles that coordinate the assembly of nuclear ribonucleoproteins (RNPs) including spliceosomal snRNPs. To study coilin function in plants, we conducted a genetic suppressor screen using a coilin (coi1) mutant in Arabidopsis thaliana and performed an immunoprecipitation-mass spectrometry analysis on coilin protein. The coi1 mutations modify alternative splicing of a GFP reporter gene, resulting in a hyper-GFP phenotype in young coi1 seedlings relative to the intermediate wild-type level. As shown here, this hyper-GFP phenotype is extinguished in older coi1 seedlings by posttranscriptional gene silencing triggered by siRNAs derived from aberrant splice variants of GFP pre-mRNA. In the coi1 suppressor screen, we identified suppressor mutations in WRAP53, a putative coilin-interacting protein; SMU2, a predicted splicing factor; and ZCH1, an incompletely characterized zinc finger protein. These suppressor mutations return the hyper-GFP fluorescence of young coi1 seedlings to the intermediate wild-type level. Additionally, coi1 zch1 mutants display more extensive GFP silencing and elevated levels of GFP siRNAs, suggesting the involvement of wild-type ZCH1 in siRNA biogenesis or stability. The immunoprecipitation-mass spectrometry analysis reinforced the roles of coilin in pre-mRNA splicing, nucleolar chromatin structure, and rRNA processing. The participation of coilin in these processes, at least some of which incorporate small RNAs, supports the hypothesis that coilin provides a chaperone for small RNA trafficking. Our study demonstrates the usefulness of the GFP splicing reporter for investigating alternative splicing, ribosome biogenesis, and siRNA-mediated silencing in the context of coilin function.
Collapse
Affiliation(s)
- Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Phebe Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Ming-Tsung Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
- Genenet Technology (UK) Limited, 128 City Road, London EC1V 2NX, UK
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Antonius Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115201, Taiwan
| |
Collapse
|
30
|
Inubushi S, Kunihisa T, Mizumoto S, Inoue S, Miki M, Suetsugu A, Tanino H, Hoffman RM. Methionine Restriction Increases Exosome Production and Secretion in Breast Cancer Cells. Cancer Genomics Proteomics 2023; 20:412-416. [PMID: 37643781 PMCID: PMC10464940 DOI: 10.21873/cgp.20393] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND/AIM Methionine addiction is the elevated requirement for exogenous methionine for growth and survival of cancer cells, termed the Hoffman effect. Methionine-addicted cancer cells synthesize normal or excess amounts of methionine but still need an external source of methionine. Methionine restriction (MR) by either a methionine-free medium or in vivo by a low-methionine diet or by methioninase, selectively arrests cancer cells in the late S/G2 cell cycle phase, but not normal cells. The present study focuses on the comparison of production and secretion of exosomes by cancer cells under MR and normal conditions. MATERIALS AND METHODS MDA-MB-231 cells (triple-negative breast cancer), containing exosomes labeled with CD63-GFP (CD63-GFP exosomes), were visualized by fluorescence microscopy. MDA-MB-231 cells expressing exosome-specific CD63-GFP were cultured in methionine-containing (MET+) or in methionine-free (MET-) DMEM conditions. Exosomes were isolated from conditioned medium of cultured MDA-MD-231 cells by ultracentrifugation and characterized by nanoparticle tracking analysis (NTA) and Western blotting. RESULTS When MDA-MB-231-CD63-GFP cells were cultured under MR conditions, they arrested their growth and CD63-GFP-expressing exosomes were strongly increased in the cells. MR resulted in approximately a 2-fold increase in exosome production and secretion per cell, even though cell growth was arrested. Methionine restriction thus resulted in elevated exosome production and secretion per surviving cell. CONCLUSION Exosome production and secretion in the cancer cells increased under MR, suggesting a relation between MR and exosome production and secretion.
Collapse
Affiliation(s)
- Sachiko Inubushi
- Division of Breast Surgery, Kobe University Graduate School of Medicine, Hyogo, Japan;
- AntiCancer Inc, San Diego, CA, U.S.A
- Department of Surgery, University of California San Diego, La Jolla, CA, U.S.A
| | - Tomonari Kunihisa
- Division of Breast Surgery, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Sachiko Mizumoto
- Division of Breast Surgery, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Shotaro Inoue
- Division of Breast Surgery, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Mayuko Miki
- Division of Breast Surgery, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Atsushi Suetsugu
- Department of Gastroenterology/Internal Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hirokazu Tanino
- Department of Cardiovascular, Respiratory and Breast Surgery, Wakayama Medical University, Wakayama, Japan
| | - Robert M Hoffman
- AntiCancer Inc, San Diego, CA, U.S.A.;
- Department of Surgery, University of California San Diego, La Jolla, CA, U.S.A
| |
Collapse
|
31
|
Chiem K, Nogales A, Lorenzo M, Morales Vasquez D, Xiang Y, Gupta YK, Blasco R, de la Torre JC, Martínez-Sobrido L. Identification of In Vitro Inhibitors of Monkeypox Replication. Microbiol Spectr 2023; 11:e0474522. [PMID: 37278625 PMCID: PMC10434227 DOI: 10.1128/spectrum.04745-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Monkeypox virus (MPXV) infections in humans have historically been restricted to regions of endemicity in Africa. However, in 2022, an alarming number of MPXV cases were reported globally, with evidence of person-to-person transmission. Because of this, the World Health Organization (WHO) declared the MPXV outbreak a public health emergency of international concern. The supply of MPXV vaccines is limited, and only two antivirals, tecovirimat and brincidofovir, approved by the U.S. Food and Drug Administration (FDA) for the treatment of smallpox, are currently available for the treatment of MPXV infection. Here, we evaluated 19 compounds previously shown to inhibit different RNA viruses for their ability to inhibit orthopoxvirus infections. We first used recombinant vaccinia virus (rVACV) expressing fluorescence (mScarlet or green fluorescent protein [GFP]) and luciferase (Nluc) reporter genes to identify compounds with antiorthopoxvirus activity. Seven compounds from the ReFRAME library (antimycin A, mycophenolic acid, AVN-944, pyrazofurin, mycophenolate mofetil, azaribine, and brequinar) and six compounds from the NPC library (buparvaquone, valinomycin, narasin, monensin, rotenone, and mubritinib) showed inhibitory activity against rVACV. Notably, the anti-VACV activity of some of the compounds in the ReFRAME library (antimycin A, mycophenolic acid, AVN-944, mycophenolate mofetil, and brequinar) and all the compounds from the NPC library (buparvaquone, valinomycin, narasin, monensin, rotenone, and mubritinib) were confirmed with MPXV, demonstrating their inhibitory activity in vitro against two orthopoxviruses. IMPORTANCE Despite the eradication of smallpox, some orthopoxviruses remain important human pathogens, as exemplified by the recent 2022 monkeypox virus (MPXV) outbreak. Although smallpox vaccines are effective against MPXV, access to those vaccines is limited. In addition, current antiviral treatment against MPXV infections is limited to the use of the FDA-approved drugs tecovirimat and brincidofovir. Thus, there is an urgent need to identify novel antivirals for the treatment of MPXV infection and other potentially zoonotic orthopoxvirus infections. Here, we show that 13 compounds, derived from two different libraries, previously found to inhibit several RNA viruses, also inhibit VACV. Notably, 11 compounds also displayed inhibitory activity against MPXV.
Collapse
Affiliation(s)
- Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Aitor Nogales
- Animal Health Research Centre, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Maria Lorenzo
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | | | - Yan Xiang
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yogesh K. Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Rafael Blasco
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | | |
Collapse
|
32
|
Aoki Y, Kobayashi KJ, Varshney N, Kubota Y, Masaki N, Obara K, Wang JD, Tome Y, Bouvet M, Nishida K, Hoffman RM. Precise and Facile Endotracheal Lung-tumor-implantation Mouse Model Visualized by GFP Expression. In Vivo 2023; 37:1477-1481. [PMID: 37369517 DOI: 10.21873/invivo.13231] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND/AIM In osteosarcoma, lung metastasis is a major cause of cancer-related death, as the 5-year survival rate for patients with metastases is approximately only 20-30%. To develop improved therapeutic strategies against lung-metastatic osteosarcoma, an experimental lung-tumor-implantation mouse model is needed for basic research. In the present study, we developed a precise and facile endotracheal lung-tumor-implantation technique. MATERIALS AND METHODS For establishment of the lung-tumor-implantation mouse model of metastatic osteosarcoma, 5 mice were used. A 15-mm longitudinal incision was made in the center of the neck to expose the salivary glands. The salivary glands were then split, exposing the trachea covered by the sternohyoid muscles. The trachea was then clearly exposed by cutting the sternohyoid muscles longitudinally. A 22 G gavage needle was tilted slightly toward the left side of the mouse and inserted from the oral cavity into the bronchus, with confirmation of the position of the tip of the gavage needle visualized through the tracheal wall, followed by injection of 0.5% crystal violet to first confirm the accuracy of endotracheal injection in the lung. A 143B-GFP cell suspension (2.0×106 cells/50 μl PBS) was then injected endotracheally in other mice. RESULTS The procedure, including anesthesia and suturing, took approximately 10 minutes. The left lobe of the lung, in which crystal violet was injected endotracheally, was stained in 3 out of 3 mice (100%). 143B-GFP-osteosarcoma tumors were detected with GFP fluorescence in the left lobe of the lung in 3 out of 4 mice (75%), 5 weeks after endotracheal injection. One mouse died 4 weeks after 143B-GFP-cell implantation. CONCLUSION This novel technique of establishing tumors in the lung via endotracheal injection of cancer cells is precise and facile and can be used widely, since neither a surgical microscope nor X-ray imaging are needed.
Collapse
Affiliation(s)
- Yusuke Aoki
- AntiCancer Inc, San Diego, CA, U.S.A
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Keita J Kobayashi
- School of Biological Science, University of California, San Diego, La Jolla, CA, U.S.A
| | - Nundini Varshney
- School of Biological Science, University of California, San Diego, La Jolla, CA, U.S.A
| | - Yutaro Kubota
- AntiCancer Inc, San Diego, CA, U.S.A
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Noriyuki Masaki
- AntiCancer Inc, San Diego, CA, U.S.A
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Koya Obara
- AntiCancer Inc, San Diego, CA, U.S.A
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Justin D Wang
- School of Medicine, California University of Science and Medicine, Colton, CA, U.S.A
| | - Yasunori Tome
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan;
| | - Michael Bouvet
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| | - Kotaro Nishida
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Robert M Hoffman
- AntiCancer Inc, San Diego, CA, U.S.A.;
- Department of Surgery, University of California, San Diego, La Jolla, CA, U.S.A
| |
Collapse
|
33
|
Hartmann FSF, Weiß T, Kastberg LLB, Workman CT, Seibold GM. Precise and versatile microplate reader-based analyses of biosensor signals from arrayed microbial colonies. Front Microbiol 2023; 14:1187228. [PMID: 37389345 PMCID: PMC10303141 DOI: 10.3389/fmicb.2023.1187228] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in Corynebacterium glutamicum, or promoter activity using GFP as reporter in Saccharomyces cerevisiae, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in Escherichia coli colonies. Applicability of this novel technique was further demonstrated by assessing redox states in C. glutamicum colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
Collapse
|
34
|
Perfilov MM, Zaitseva ER, Baleeva NS, Kublitski VS, Smirnov AY, Bogdanova YA, Krasnova SA, Myasnyanko IN, Mishin AS, Baranov MS. Meta-CF 3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism. Int J Mol Sci 2023; 24:9923. [PMID: 37373071 DOI: 10.3390/ijms24129923] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
Collapse
Affiliation(s)
- Maxim M Perfilov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, Moscow 121205, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Svetlana A Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| |
Collapse
|
35
|
Morsli S, Henriques CM, Ellis PS, Mortiboys H, Baxendale S, Loynes CA, Renshaw SA, Bellantuono I. A p21- GFP zebrafish model of senescence for rapid testing of senolytics in vivo. Aging Cell 2023; 22:e13835. [PMID: 37039087 PMCID: PMC10265157 DOI: 10.1111/acel.13835] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 04/12/2023] Open
Abstract
Senescence drives the onset and severity of multiple ageing-associated diseases and frailty. As a result, there has been an increased interest in mechanistic studies and in the search for compounds targeting senescent cells, known as senolytics. Mammalian models are commonly used to test senolytics and generate functional and toxicity data at the level of organs and systems, yet this is expensive and time consuming. Zebrafish share high homology in genes associated with human ageing and disease. They can be genetically modified relatively easily. In larvae, most organs develop within 5 days of fertilisation and are transparent, which allows tracking of fluorescent cells in vivo in real time, testing drug off-target toxicity and assessment of cellular and phenotypic changes. Here, we have generated a transgenic zebrafish line that expresses green fluorescent protein (GFP) under the promoter of a key senescence marker, p21. We show an increase in p21:GFP+ cells in larvae following exposure to ionising radiation and with natural ageing. p21:GFP+ cells display other markers of senescence, including senescence-associated β-galactosidase and IL6. The observed increase in senescent cells following irradiation is associated with a reduction in the thickness of muscle fibres and mobility, two important ageing phenotypes. We also show that quercetin and dasatinib, two senolytics currently in clinical trials, reduce the number of p21:GFP+ cells, in a rapid 5-day assay. This model provides an important tool to study senescence in a living organism, allowing the rapid selection of senolytics before moving to more expensive and time-consuming mammalian systems.
Collapse
Affiliation(s)
- Samir Morsli
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Oncology and MetabolismUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
- Sheffield Institute for Translational Neuroscience, Department of NeuroscienceUniversity of Sheffield385a Glossop RoadSheffieldS10 2HQUK
- Present address:
Early Cancer InstituteUniversity of CambridgeHutchison BuildingCambridgeCB2 0XZUK
| | - Catarina M. Henriques
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Oncology and MetabolismUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| | - Pamela S. Ellis
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Oncology and MetabolismUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| | - Heather Mortiboys
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Sheffield Institute for Translational Neuroscience, Department of NeuroscienceUniversity of Sheffield385a Glossop RoadSheffieldS10 2HQUK
| | - Sarah Baxendale
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- School of BiosciencesUniversity of SheffieldSheffieldS10 2THUK
| | - Catherine A. Loynes
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Infection, Immunity and Cardiovascular DiseaseUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| | - Stephen A. Renshaw
- The Bateson CentreUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Infection, Immunity and Cardiovascular DiseaseUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| | - Ilaria Bellantuono
- Healthy Lifespan InstituteUniversity of SheffieldWestern BankSheffieldS10 2THUK
- Department of Oncology and MetabolismUniversity of SheffieldBeech Hill RoadSheffieldS10 2RXUK
| |
Collapse
|
36
|
Ronai I. How molecular techniques are developed from natural systems. Genetics 2023:7162666. [PMID: 37184565 DOI: 10.1093/genetics/iyad067] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
A striking characteristic of the molecular techniques of genetics is that they are derived from natural occurring systems. RNA interference, for example, utilizes a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other case studies I highlight are restriction enzymes, DNA sequencing, polymerase chain reaction, gene targeting, fluorescent proteins (such as, green fluorescent protein), induced pluripotent stem cells, and clustered regularly interspaced short palindromic repeats-CRISPR associated 9. The natural systems' strategy for technique development means that biologists utilize the activity of a mechanism's effector (protein or RNA) and exploit biological specificity (protein or nucleic acid can cause precise reactions). I also argue that the developmental trajectory of novel molecular techniques, such as RNA interference, has 4 characteristic phases. The first phase is discovery of a biological phenomenon. The second phase is identification of the biological mechanism's trigger(s): the effector and biological specificity. The third phase is the application of the trigger(s) as a technique. The final phase is the maturation and refinement of the technique. Developing new molecular techniques from nature is crucial for future genetic research.
Collapse
Affiliation(s)
- Isobel Ronai
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
- Department of Organismic and Evolutionary Biology, Harvard University
| |
Collapse
|
37
|
Papp S, Tombor L, Kakuszi B, Réthelyi JM, Bitter I, Czobor P. Electrophysiological underpinnings of dysfunctional inhibitory control in adults with attention-deficit/hyperactivity disorder: evidence for reduced NoGo anteriorization. J Neural Transm (Vienna) 2023:10.1007/s00702-023-02639-0. [PMID: 37131048 DOI: 10.1007/s00702-023-02639-0] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
Our aim was to delineate the electrophysiological basis of dysfunctional inhibitory control of adult ADHD via investigating the anteriorization of the P3 component of the event-related brain response associated with the NoGo task condition (i.e., NoGo anteriorization, NGA). NGA is a neurophysiological measure of brain topography for cognitive response control, which indexes an overall shift of the brain's electrical activity in anterior direction towards the prefrontal areas. While the NoGo P3 received considerable attention in the adult ADHD literature, the brain topography of this component, which reflects the inhibitory process, remains largely unaddressed. EEG recordings were obtained during a Go/NoGo task from 51 subjects (n = 26 adult patients with ADHD, n = 25 healthy controls) using a high-density, 128-channel BioSemi ActiveTwo recording system. ADHD patients had significantly lower P3 NGA response compared to controls. The decrease in NGA was related to impulsivity scores as measured by the Conners' Adult ADHD Rating Scale: patients with higher impulsivity scores had significantly lower NGA. Treatment with stimulant medication, as compared to the lack of such treatment, was associated with a correction of the lower NGA response in ADHD patients. The current study revealed a lower NGA in adult ADHD, a finding which is consistent with the inhibitory control and frontal lobe dysfunctions described in the disorder. Our finding of the inverse relationship between NGA and impulsivity suggests that clinically more severe impulsivity is linked to a more pronounced frontal dysfunction in adult ADHD subjects.
Collapse
Affiliation(s)
- Szilvia Papp
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary.
| | - László Tombor
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary
| | - Brigitta Kakuszi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary
| | - János M Réthelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary
| | - István Bitter
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary
| | - Pál Czobor
- Department of Psychiatry and Psychotherapy, Semmelweis University, Balassa Utca 6., Budapest, 1083, Hungary
| |
Collapse
|
38
|
Krüger G, Kirkpatrick J, Mahieu E, Franzetti B, Gabel F, Carlomagno T. A real-time analysis of GFP unfolding by the AAA+ unfoldase PAN. J Magn Reson 2023; 350:107431. [PMID: 37058954 DOI: 10.1016/j.jmr.2023.107431] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Protein quality control systems are essential to maintain a healthy proteome. They often consist of an unfoldase unit, typically an AAA+ ATPase, coupled with a protease unit. In all kingdoms of life, they function to eliminate misfolded proteins, and thus prevent that their aggregates do harm to the cell, and to rapidly regulate protein levels in the presence of environmental changes. Despite the huge progress made in the past two decades in understanding the mechanism of function of protein degradation systems, the fate of the substrate during the unfolding and proteolytic processes remains poorly understood. Here we exploit an NMR-based approach to monitor GFP processing by the archaeal PAN unfoldase and the PAN-20S degradation system in real time. We find that PAN-dependent unfolding of GFP does not involve the release of partially-folded GFP molecules resulting from futile unfolding attempts. In contrast, once stably engaged with PAN, GFP molecules are efficiently transferred to the proteolytic chamber of the 20S subunit, despite the only weak affinity of PAN for the 20S subunit in the absence of substrate. This is essential to guarantee that unfolded but not proteolyzed proteins are not released into solution, where they would form toxic aggregates. The results of our studies are in good agreement with previous results derived from real-time small-angle-neutron-scattering experiments and have the advantage of allowing the investigation of substrates and products at amino-acid resolution.
Collapse
Affiliation(s)
- Georg Krüger
- Institute of Organic Chemistry and Centre of Biomolecular Drug Design, Leibniz University Hannover, Schneiderberg 38, D-30167 Hannover, Germany
| | - John Kirkpatrick
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom
| | - Emilie Mahieu
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Bruno Franzetti
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Teresa Carlomagno
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom.
| |
Collapse
|
39
|
Tarasenko VI, Tarasenko TA, Gorbenko IV, Konstantinov YM, Koulintchenko MV. [Differential Expression of a Foreign Gene in Arabidopsis Mitochondria In Organelle]. Mol Biol (Mosk) 2023; 57:460-470. [PMID: 37326049 DOI: 10.31857/s002689842303014x, edn: chuecl] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Genetic transformation of higher eukaryote mitochondria in vivo is an unresolved and important problem. For efficient expression of foreign genetic material in mitochondria, it is necessary to select regulatory elements that provide a high level of transcription and transcript stability. This work is aimed at studying the effectiveness of regulatory elements of mitochondrial genes flanking exogenous DNA using the phenomenon of natural competence of plant mitochondria. For this purpose, genetic constructs carrying the GFP gene under the control of the promoter regions of the RRN26 or COX1 genes and one of the two 3'-untranslated regions (3'-UTR) of mitochondrial genes were imported into isolated Arabidopsis mitochondria, followed by transcription in organello. It was shown that the level of GFP expression under the control of promoters of the RRN26 or COX1 genes in organello correlates with the level of transcription of these genes observed in vivo. At the same time, the presence of the tRNA^(Trp) sequence in the 3'-UTR leads to a higher level of the GFP transcript than the presence in this region of the 3'-UTR of the NAD4 gene containing the binding site of the MTSF1 protein. The results we obtained open prospects for creating a system for efficient transformation of the mitochondrial genome.
Collapse
Affiliation(s)
- V I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033 Russia
| | - T A Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033 Russia
| | - I V Gorbenko
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033 Russia
| | - Yu M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033 Russia
| | - M V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk, 664033 Russia
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Center, Russian Academy of Sciences, Kazan, 420111 Russia
| |
Collapse
|
40
|
Bogdanova YA, Zaitseva ER, Smirnov AY, Baleeva NS, Gavrikov AS, Myasnyanko IN, Goncharuk SA, Kot EF, Mineev KS, Mishin AS, Baranov MS. NanoLuc Luciferase as a Fluorogen-Activating Protein for GFP Chromophore Based Fluorogens. Int J Mol Sci 2023; 24:ijms24097958. [PMID: 37175667 PMCID: PMC10178166 DOI: 10.3390/ijms24097958] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In this work, we showed that the well-known NanoLuc luciferase can act as a fluorogen activating protein for various arylidene-imidazolones structurally similar to the Kaede protein chromophore. We showed that such compounds can be used as fluorescent sensors for this protein and can also be used in pairs with it in fluorescent microscopy as a genetically encoded tag.
Collapse
Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Erik F Kot
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| |
Collapse
|
41
|
Wang Y, Wei Z, Fan J, Song X, Xing S. Hyper-expression of GFP-fused active hFGF21 in tobacco chloroplasts. Protein Expr Purif 2023; 208-209:106271. [PMID: 37084839 DOI: 10.1016/j.pep.2023.106271] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/07/2023] [Accepted: 04/09/2023] [Indexed: 04/23/2023]
Abstract
Human fibroblast growth factor 21 (hFGF21) is a promising candidate for metabolic diseases. In this study, a tobacco chloroplast transformation vector, pWYP21406, was constructed that consisted of codon-optimized encoding gene hFGF21 fused with GFP at its 5' terminal; it was driven by the promoter of plastid rRNA operon (Prrn) and terminated by the terminator of plastid rps16 gene (Trps16). Spectinomycin-resistant gene (aadA) was the marker and placed in the same cistron between hFGF21 and the terminator Trps16. Transplastomic plants were generated by the biolistic bombardment method and proven to be homoplastic by Southern blotting analysis. The expression of GFP was detected under ultraviolet light and a laser confocal microscope. The expression of GFP-hFGF21 was confirmed by immunoblotting and quantified by enzyme-linked immunosorbnent assay (ELISA). The accumulation of GFP-hFGF21 was confirmed to be 12.44 ± 0.45% of the total soluble protein (i.e., 1.9232 ± 0.0673 g kg-1 of fresh weight). GFP-hFGF21 promoted the proliferation of hepatoma cell line HepG2, inducing the expression of glucose transporter 1 in hepatoma HepG2 cells and improving glucose uptake. These results suggested that a chloroplast expression is a promising approach for the production of bioactive recombinant hFGF21.
Collapse
Affiliation(s)
- Yunpeng Wang
- Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Zhengyi Wei
- Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China; Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Jieying Fan
- Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xinyuan Song
- Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Shaochen Xing
- Jilin Provincial Crop Transgenic Science and Technology Innovation Center, Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| |
Collapse
|
42
|
Radzevičiūtė-Valčiukė E, Gečaitė J, Želvys A, Zinkevičienė A, Žalnėravičius R, Malyško-Ptašinskė V, Nemeikaitė-Čenienė A, Kašėta V, German N, Novickij J, Ramanavičienė A, Kulbacka J, Novickij V. Improving NonViral Gene Delivery Using MHz Bursts of Nanosecond Pulses and Gold Nanoparticles for Electric Field Amplification. Pharmaceutics 2023; 15:pharmaceutics15041178. [PMID: 37111663 PMCID: PMC10146442 DOI: 10.3390/pharmaceutics15041178] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Gene delivery by the pulsed electric field is a promising alternative technology for nonviral transfection; however, the application of short pulses (i.e., nanosecond) is extremely limited. In this work, we aimed to show the capability to improve gene delivery using MHz frequency bursts of nanosecond pulses and characterize the potential use of gold nanoparticles (AuNPs: 9, 13, 14, and 22 nm) in this context. We have used bursts of MHz pulses 3/5/7 kV/cm × 300 ns × 100 and compared the efficacy of the parametric protocols to conventional microsecond protocols (100 µs × 8, 1 Hz) separately and in combination with nanoparticles. Furthermore, the effects of pulses and AuNPs on the generation of reactive oxygen species (ROS) were analyzed. It was shown that gene delivery using microsecond protocols could be significantly improved with AuNPs; however, the efficacy is strongly dependent on the surface charge of AuNPs and their size. The capability of local field amplification using AuNPs was also confirmed by finite element method simulation. Finally, it was shown that AuNPs are not effective with nanosecond protocols. However, MHz protocols are still competitive in the context of gene delivery, resulting in low ROS generation, preserved viability, and easier procedure to trigger comparable efficacy.
Collapse
Affiliation(s)
- Eivina Radzevičiūtė-Valčiukė
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
- Faculty of Electronics, Vilnius Gediminas Technical University, 10223 Vilnius, Lithuania
| | - Jovita Gečaitė
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Augustinas Želvys
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Auksė Zinkevičienė
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Rokas Žalnėravičius
- State Research Institute Center for Physical Science and Technology, 02300 Vilnius, Lithuania
| | | | - Aušra Nemeikaitė-Čenienė
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Vytautas Kašėta
- Department of Biomodels, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Natalija German
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Jurij Novickij
- Faculty of Electronics, Vilnius Gediminas Technical University, 10223 Vilnius, Lithuania
| | - Almira Ramanavičienė
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Julita Kulbacka
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, 50-367 Wroclaw, Poland
| | - Vitalij Novickij
- Department of Immunology, State Research Institute Centre for Innovative Medicine, 08406 Vilnius, Lithuania
- Faculty of Electronics, Vilnius Gediminas Technical University, 10223 Vilnius, Lithuania
| |
Collapse
|
43
|
Numpadit S, Ito C, Nakaya T, Hagiwara K. Investigation of oncolytic effect of recombinant Newcastle disease virus in primary and metastatic oral melanoma. Med Oncol 2023; 40:138. [PMID: 37022566 PMCID: PMC10079733 DOI: 10.1007/s12032-023-02002-z] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023]
Abstract
Malignant melanoma is aggressive cancer with a high rate of local invasiveness and metastasis. Currently, the treatment options for patients with advanced-stage and metastatic oral melanoma are limited. A promising treatment option is oncolytic viral therapy. This study aimed to evaluate novel therapies for malignant melanoma using a canine model. Oral melanoma, which frequently occurs in dogs is used as a model for human melanoma, was isolated and cultured and used for the evaluation of the tumor lytic effect induced by viral infection. We constructed a recombinant Newcastle disease virus (rNDV) that promotes the extracellular release of IFNγ from the virus-infected melanoma. The expression of oncolytic and apoptosis-related genes, the immune response by lymphocytes, and IFNγ expression were evaluated in virus-infected melanoma cells. The results showed that the rate of rNDV infection varied according to the isolated melanoma cells and the oncolytic effect differed between melanoma cells owing to the infectivity of the virus. The oncolytic effect tended to be greater for the IFNγ-expressing virus than for the GFP-expressing prototype virus. Additionally, lymphocytes co-cultured with the virus showed induced expression of Th1 cytokines. Therefore, recombinant NDV expressing IFNγ is expected to induce cellular immunity and oncolytic activity. This oncolytic treatment shows promise as a therapeutic approach for melanoma treatment once evaluated using clinical samples from humans.
Collapse
Affiliation(s)
- Supaporn Numpadit
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan
| | - Chiaki Ito
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan
| | - Takaaki Nakaya
- Department of Infectious Disease, Kyoto Prefectural University of Medicine, Kamigyo-ku Kajii-cho, Kawaramachi-Hirokoji, Kyoto-shi, 602-8566, Japan
| | - Katsuro Hagiwara
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, 069-8501, Japan.
| |
Collapse
|
44
|
Phillips EK, Cannon JA, Zhou Y, Bonifer KS, Reynolds TB. Conjugation-Mediated Plasmid Transfer Enables Genetic Modification of Diverse Bacillus Species. Microbiol Spectr 2023; 11:e0370022. [PMID: 36975796 PMCID: PMC10101014 DOI: 10.1128/spectrum.03700-22] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Performing genetic manipulations in Bacillus strains is often hindered by difficulty in identifying conditions appropriate for DNA uptake. This shortcoming limits our understanding of the functional diversity within this genus and the practical application of new strains. We have developed a simple method for increasing the genetic tractability of Bacillus spp. through conjugation-mediated plasmid transfer via a diaminopimelic acid (DAP) auxotrophic Escherichia coli donor strain. We observe transfer into representatives of the Bacillus clades subtilis, cereus, galactosidilyticus, and Priestia megaterium and successfully applied this protocol to 9 out of 12 strains attempted. We utilized the BioBrick 2.0 plasmids pECE743 and pECE750, as well as the CRISPR plasmid pJOE9734.1, to generate a xylose-inducible green-fluorescent protein (GFP)-expressing conjugal vector, pEP011. The use of xylose-inducible GFP ensures ease of confirming transconjugants, which enables users to quickly rule out false positives. Additionally, our plasmid backbone offers the flexibility to be used in other contexts, including transcriptional fusions and overexpression, with only a few modifications. IMPORTANCE Bacillus species are widely used to produce proteins and to understand microbial differentiation. Unfortunately, outside a few lab strains, genetic manipulation is difficult and can prevent thorough dissection of useful phenotypes. We developed a protocol that utilizes conjugation (plasmids that initiate their own transfer) to introduce plasmids into a diverse range of Bacillus spp. This will facilitate a deeper study of wild isolates for both industrial and pure research uses.
Collapse
Affiliation(s)
- Elise K. Phillips
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Jordan A. Cannon
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Kyle S. Bonifer
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, USA
| |
Collapse
|
45
|
Primak AL, Orlov NA, Peigneur S, Tytgat J, Ignatova AA, Denisova KR, Yakimov SA, Kirpichnikov MP, Nekrasova OV, Feofanov AV. AgTx2- GFP, Fluorescent Blocker Targeting Pharmacologically Important K v1.x (x = 1, 3, 6) Channels. Toxins (Basel) 2023; 15:toxins15030229. [PMID: 36977120 PMCID: PMC10056440 DOI: 10.3390/toxins15030229] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The growing interest in potassium channels as pharmacological targets has stimulated the development of their fluorescent ligands (including genetically encoded peptide toxins fused with fluorescent proteins) for analytical and imaging applications. We report on the properties of agitoxin 2 C-terminally fused with enhanced GFP (AgTx2-GFP) as one of the most active genetically encoded fluorescent ligands of potassium voltage-gated Kv1.x (x = 1, 3, 6) channels. AgTx2-GFP possesses subnanomolar affinities for hybrid KcsA-Kv1.x (x = 3, 6) channels and a low nanomolar affinity to KcsA-Kv1.1 with moderate dependence on pH in the 7.0-8.0 range. Electrophysiological studies on oocytes showed a pore-blocking activity of AgTx2-GFP at low nanomolar concentrations for Kv1.x (x = 1, 3, 6) channels and at micromolar concentrations for Kv1.2. AgTx2-GFP bound to Kv1.3 at the membranes of mammalian cells with a dissociation constant of 3.4 ± 0.8 nM, providing fluorescent imaging of the channel membranous distribution, and this binding depended weakly on the channel state (open or closed). AgTx2-GFP can be used in combination with hybrid KcsA-Kv1.x (x = 1, 3, 6) channels on the membranes of E. coli spheroplasts or with Kv1.3 channels on the membranes of mammalian cells for the search and study of nonlabeled peptide pore blockers, including measurement of their affinity.
Collapse
Affiliation(s)
- Alexandra L Primak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikita A Orlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Steve Peigneur
- Toxicology and Pharmacology, Campus Gasthuisberg O&N2, University of Leuven (KU Leuven), Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, Campus Gasthuisberg O&N2, University of Leuven (KU Leuven), Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium
| | - Anastasia A Ignatova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Kristina R Denisova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sergey A Yakimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Oksana V Nekrasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexey V Feofanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| |
Collapse
|
46
|
Nuñez S, Barra M, Garrido D. Developing a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli. Biosensors (Basel) 2023; 13:bios13030388. [PMID: 36979599 PMCID: PMC10046853 DOI: 10.3390/bios13030388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 05/28/2023]
Abstract
L-Fucose is a monosaccharide abundant in mammalian glycoconjugates. In humans, fucose can be found in human milk oligosaccharides (HMOs), mucins, and glycoproteins in the intestinal epithelium. The bacterial consumption of fucose and fucosylated HMOs is critical in the gut microbiome assembly of infants, dominated by Bifidobacterium. Fucose metabolism is important for the production of short-chain fatty acids and is involved in cross-feeding microbial interactions. Methods for assessing fucose concentrations in complex media are lacking. Here we designed and developed a molecular quantification method of free fucose using fluorescent Escherichia coli. For this, low- and high-copy plasmids were evaluated with and without the transcription factor fucR and its respective fucose-inducible promoter controlling the reporter gene sfGFP. E. coli BL21 transformed with a high copy plasmid containing pFuc and fucR displayed a high resolution across increasing fucose concentrations and high fluorescence/OD values after 18 h. The molecular circuit was specific against other monosaccharides and showed a linear response in the 0-45 mM range. Adjusting data to the Hill equation suggested non-cooperative, simple regulation of FucR to its promoter. Finally, the biosensor was tested on different concentrations of free fucose and the supernatant of Bifidobacterium bifidum JCM 1254 supplemented with 2-fucosyl lactose, indicating the applicability of the method in detecting free fucose. In conclusion, a bacterial biosensor of fucose was validated with good sensitivity and precision. A biological method for quantifying fucose could be useful for nutraceutical and microbiological applications, as well as molecular diagnostics.
Collapse
|
47
|
Sorenson AE, Schaeffer PM. Real-Time Temperature Sensing Using a Ratiometric Dual Fluorescent Protein Biosensor. Biosensors (Basel) 2023; 13:338. [PMID: 36979550 PMCID: PMC10046200 DOI: 10.3390/bios13030338] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Accurate temperature control within biological and chemical reaction samples and instrument calibration are essential to the diagnostic, pharmaceutical and chemical industries. This is particularly challenging for microlitre-scale reactions typically used in real-time PCR applications and differential scanning fluorometry. Here, we describe the development of a simple, inexpensive ratiometric dual fluorescent protein temperature biosensor (DFPTB). A combination of cycle three green fluorescent protein and a monomeric red fluorescent protein enabled the quantification of relative temperature changes and the identification of temperature discrepancies across a wide temperature range of 4-70 °C. The maximal sensitivity of 6.7% °C-1 and precision of 0.1 °C were achieved in a biologically relevant temperature range of 25-42 °C in standard phosphate-buffered saline conditions at a pH of 7.2. Good temperature sensitivity was achieved in a variety of biological buffers and pH ranging from 4.8 to 9.1. The DFPTB can be used in either purified or mixed bacteria-encapsulated formats, paving the way for in vitro and in vivo applications for topologically precise temperature measurements.
Collapse
|
48
|
Tavares M, Sousa-Filho JC, Machado IA, Gonçales RA, Antunes D, Mendes-Frias A, Silvestre R, Carvalho A, Torrado E, Cunha C, Rodrigues F. Development of a Versatile Toolbox for Genetic Manipulation of Sporothrix brasiliensis. Microbiol Spectr 2023; 11:e0456422. [PMID: 36847570 PMCID: PMC10101026 DOI: 10.1128/spectrum.04564-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Sporothrix brasiliensis has emerged as the most virulent species in the Sporothrix schenckii complex, accounting for sporotrichosis. Albeit the new insights into the understanding of host-pathogen interactions and comparative genomics of this fungi, the lack of genetic tools has hindered significant advances in this field of research. Here, we established an Agrobacterium tumefaciens-mediated transformation (ATMT) system to transform different strains of S. brasiliensis. We report parameters that account for a transformation efficiency of 3,179 ± 1,171 transformants/co-cultivation, which include the use of A. tumefaciens AGL-1 in a 2:1 ratio (bacteria:fungi) during 72 h at 26°C. Our data show that a single-copy transgene is transferred to S. brasiliensis that is mitotically stable in 99% of cells after 10 generations without selective pressure. In addition, we created a plasmid toolkit that allows the establishment of fusion proteins of any S. brasiliensis gene of interest with sGFP or mCherry under the control of the GAPDH or H2A endogenous promoters. These modules allow different levels of expression of the desired fusion. Moreover, we successfully targeted these fluorescent proteins to the nucleus and used fluorescence-tagged strains to assess phagocytosis. Overall, our data show that the ATMT system is an easy-to-use and efficient genetic toolbox for studies on recombinant expression and gene function in S. brasiliensis. IMPORTANCE Sporotrichosis is the most prevalent subcutaneous mycosis worldwide and has recently become a public health concern. Although immunocompetent hosts are also prone to sporotrichosis, immunodeficient hosts often develop a more severe and disseminated form of disease. To date, the Rio de Janeiro state in Brazil is the most significant feline zoonotic transmission epicenter in the world, with more than 4,000 human and feline diagnosed cases. Cats play an essential role in the S. brasiliensis infection due to their high susceptibility and transmissibility to other felines and humans. S. brasiliensis is the most virulent etiological agent of sporotrichosis, causing the most severe clinical manifestations. Despite the increasing incidence of sporotrichosis, the identification of virulence traits important for disease establishment, development, and severity has been lacking. In this work, we established an efficient genetic toolbox to manipulate S. brasiliensis that will guide future studies to define new virulence mechanisms and a better understanding of host-pathogen interactions from a molecular perspective.
Collapse
Affiliation(s)
- Matheus Tavares
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Jorge Carlos Sousa-Filho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ian Alves Machado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Relber Aguiar Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Daniela Antunes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ana Mendes-Frias
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| |
Collapse
|
49
|
Kenri T. Genetic Manipulation of Mycoplasma pneumoniae. Methods Mol Biol 2023; 2646:347-57. [PMID: 36842129 DOI: 10.1007/978-1-0716-3060-0_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Mycoplasma pneumoniae is a small cell wall-lacking bacterium that is a common cause of bronchitis and pneumonia in humans. In addition to its clinical importance, M. pneumoniae has recently been considered a promising model organism for synthetic biology because of its small genome size and unique cell structure. At one cell pole, M. pneumoniae forms the attachment organelle that is responsible for adherence to host cells and gliding motility. The attachment organelle is a membrane protrusion and is composed of number of molecules, including adhesin and cytoskeletal proteins. Genetic manipulation techniques are key research approaches for understanding the structure and the function of this unique molecular machinery. In this chapter, standard genetic engineering methods for this species using the Tn4001 transposon vector are described.
Collapse
|
50
|
Ilina A, Linkova N. A Transgenic 5xFAD-M Line of Mice for Dendritic Spine Morphology Analysis in Alzheimer's Disease. Brain Sci 2023; 13. [PMID: 36831849 DOI: 10.3390/brainsci13020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Cognitive impairments are closely related to synaptic loss in Alzheimer's disease (AD). Functional changes in synaptic contacts are reflected in dendritic spine morphology. Visualization of neurons for morphological studies in vivo is complicated by the fixed brain slice staining or expensive adeno-associated virus injections. We created a transgenic 5xFAD-M line of mice with AD-associated mutations and expressed GFP protein in single neurons of the brain. This mouse model of AD is a useful tool for the simplified visualization of the hippocampal neurons' morphology in vivo without additional staining manipulations. The progressive elimination of mushroom spines was demonstrated in 5xFAD-M mice between 4 and 5 months of age. Five-month-old 5xFAD-M male and female mice showed change both in the total density and the mushroom spines number compared to sex-matched control. We conclude 5xFAD-M mice can be a useful AD model for studying the mechanisms of synaptic pathology under neurodegenerative conditions and evaluating the effects of potential therapeutic agents on spine morphology as crucial aspect of memory loss in AD.
Collapse
|