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Altun N, Hervello MF, Lombó F, González P. Using staining as reference for spectral imaging: Its application for the development of an analytical method to predict the presence of bacterial biofilms. Talanta 2023; 261:124655. [PMID: 37196402 DOI: 10.1016/j.talanta.2023.124655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
At present, although spectral imaging is known to have a great potential to provide a massive amount of valuable information, the lack of reference methods remains as one of the bottlenecks to access the full capacity of this technique. This work aims to present a staining-based reference method with digital image treatment for spectral imaging, in order to propose a fast, efficient, contactless and non-invasive analytical method to predict the presence of biofilms. Spectral images of Pseudomonasaeruginosa biofilms formed on high density polyethylene coupons were acquired in visible and near infrared (vis-NIR) range between 400 and 1000 nm. Crystal violet staining served as a biofilm indicator, allowing the bacterial cells and the extracellular matrix to be marked on the coupon. Treated digital images of the stained biofilms were used as a reference. The size and pixels of the hyperspectral and digital images were scaled and matched to each other. Intensity color thresholds were used to differentiate the pixels associate to areas containing biofilms from those ones placed in biofilm-free areas. The model facultative Gram-negative bacterium, P. aeruginosa, which can form highly irregularly shaped and heterogeneous biofilm structures, was used to enhance the strength of the method, due to its inherent difficulties. The results showed that the areas with high and low intensities were modeled with good performance, but the moderate intensity areas (with potentially weak or nascent biofilms) were quite challenging. Image processing and artificial neural networks (ANN) methods were performed to overcome the issues resulted from biofilm heterogeneity, as well as to train the spectral data for biofilm predictions.
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Affiliation(s)
- Nazan Altun
- ASINCAR Agrifood Technology Center, Spain; Research Unit "Biotechnology in Nutraceuticals and Bioactive Compounds-BIONUC", Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | | | - Felipe Lombó
- Research Unit "Biotechnology in Nutraceuticals and Bioactive Compounds-BIONUC", Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain; Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
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Wang JL, Xu ZT, Zhan L, Liao M, Xu CJ. Heat-induced antigen retrieval utilizing modified Tris-EDTA buffer for reprobing of Western blots on nitrocellulose paper. Anal Biochem 2023; 672:115179. [PMID: 37150424 DOI: 10.1016/j.ab.2023.115179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
The development of heat-induced antigen retrieval technologies with Tris-EDTA buffer has dramatically improved immunostaining of specific antigens for routine immunohistochemical detection (Krenacs et al., 2010) [1]. However, little evidence exists on whether heat-Induced antigen retrieval utilizing Tris-EDTA buffer can strip western blot (WB) membranes and allow sequential reprobing. Here, we serendipitously discover that ∼95 °C Tris-EDTA buffer with 0.01% Tween 20 could repeatedly strip the Nitrocellulose membranes (NC). After electroblotting, NC blots were soaked into Tris-EDTA stripping buffer (∼95 °C, 10-25min) and we could perform at least five rounds (the following antibodies used: Vinculin, Atg7, Caspase-3, UBA5, JNK and ERK1/2) stripping in sequential chemiluminescent detections. The NC membranes also show clear western signals and background without losing transferred proteins during the reprobing process of WB. Hence, this study report additional new roles of the heat-Induced antigen retrieval Tris-EDTA buffer with 0.01% Tween 20. The method is simpler, more affordable and harmless for the nitrocellulose paper, which will be helpful for effective reprobing in western blotting applications.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China.
| | - Ze-Ting Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China.
| | - Ling Zhan
- School of 1st Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China.
| | - Min Liao
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China.
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China.
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Wang JL, Li MQ, Zhang JJ, Xu CJ. Total protein staining with Congo red as an alternative loading control for western blot analysis. Biotech Histochem 2021; 97:404-414. [PMID: 34903132 DOI: 10.1080/10520295.2021.2008008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
For western blot analysis, a housekeeping protein, such as β-actin or glyceraldehyde-3-phosphate dehydrogenase, is used as loading control with the assumption that these proteins are stable. In practice, these internal loading control proteins vary with different cell states and tissue types. These internal standards are not appropriate for use with serum, extracellular secretion, cerebrospinal fluid analysis or for protein purification. We investigated total protein measurement using Congo red staining and found it to be a superior alternative to routine loading controls. Advantages include lower cost, technical simplicity and improved linear regression. We propose using Congo red staining for total protein immunoblotting to evaluate protein loading in western blots.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Mei-Qi Li
- School of 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Jia-Jia Zhang
- School of 1st Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang, P. R. China
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Xu CJ, Li MQ, Li-Zhao, Chen WG, Wang JL. Short-term high-fat diet favors the appearances of apoptosis and gliosis by activation of ERK1/2/p38MAPK pathways in brain. Aging (Albany NY) 2021; 13:23133-23148. [PMID: 34620734 PMCID: PMC8544319 DOI: 10.18632/aging.203607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/07/2021] [Indexed: 01/26/2023]
Abstract
High-fat diet (HFD) has been associated with neuroinflammation and apoptosis in distinct brain regions. To explore the effect of short-term (7, 14 and 21 days) high-fat overfeeding on apoptosis, inflammatory signaling proteins, APP changes and glial cell activities in cerebral cortex and cerebellum. Mice were fed with HFD for different lengths (up to 21 days) and after each time body weights of mice was tested, then the apoptotic proteins, IL-1β, APP, BACE1and MAPKs, Akt and NF-κB signaling activity were evaluated by western blots. Results demonstrate that short period of high-fat overnutrition significantly promotes apoptosis, APP expression at day 21 of cerebral cortex and at day 7 of cerebellum compared to chow diet. In addition, increased GFAP+astrocytes, Iba-1+microglia and IL-1β 30 were observed in cerebral cortex after 21 days HFD, but no changes for 7 days overfeeding of cerebellum. Serendipitously, ERK1/2 pathway was activated both in cerebral cortex and cerebellum for different time course of HFD. Furthermore, increased phospho-p38 MAPK level was observed in cerebellum only. In consistent with in vivo results, SH-SY5Y cells treatment with cholesterol (50 μM, 100 μM) for 48 h culture in vitro demonstrated that pro-apoptotic proteins were enhanced as well. In brief, short-term HFD consumption increases sensitivity to apoptosis, APP and IL-1β production as well as gliosis in cerebral cortex and cerebellum, which may be related to enhancement of ERK1/2 and p38 MAPK activation.
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Affiliation(s)
- Chao-Jin Xu
- Department of Histology and Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, PR China
| | - Mei-Qi Li
- School of 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, PR China
| | - Li-Zhao
- School of 2nd Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, PR China
| | - Wei-Guang Chen
- Department of Histology and Embryology, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035, PR China
| | - Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, Zhejiang 325000, PR China
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Dabrowska A, Milewska A, Ner-Kluza J, Suder P, Pyrc K. Mass Spectrometry versus Conventional Techniques of Protein Detection: Zika Virus NS3 Protease Activity towards Cellular Proteins. Molecules 2021; 26:molecules26123732. [PMID: 34207340 PMCID: PMC8234618 DOI: 10.3390/molecules26123732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/30/2022] Open
Abstract
Mass spectrometry (MS) used in proteomic approaches is able to detect hundreds of proteins in a single assay. Although undeniable high analytical power of MS, data acquired sometimes lead to confusing results, especially during a search of very selective, unique interactions in complex biological matrices. Here, we would like to show an example of such confusing data, providing an extensive discussion on the observed phenomenon. Our investigations focus on the interaction between the Zika virus NS3 protease, which is essential for virus replication. This enzyme is known for helping to remodel the microenvironment of the infected cells. Several reports show that this protease can process cellular substrates and thereby modify cellular pathways that are important for the virus. Herein, we explored some of the targets of NS3, clearly shown by proteomic techniques, as processed during infection. Unfortunately, we could not confirm the biological relevance of protein targets for viral infections detected by MS. Thus, although mass spectrometry is highly sensitive and useful in many instances, also being able to show directions where cell/virus interaction occurs, we believe that deep recognition of their biological role is essential to receive complete insight into the investigated process.
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Affiliation(s)
- Agnieszka Dabrowska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Aleksandra Milewska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Joanna Ner-Kluza
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland;
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland;
- Correspondence: (P.S.); (K.P.); Tel.: +48-12-617-50-83 (P.S.); +48-12-664-61-21 (K.P.)
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; (A.D.); (A.M.)
- Correspondence: (P.S.); (K.P.); Tel.: +48-12-617-50-83 (P.S.); +48-12-664-61-21 (K.P.)
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Aequorin as a Useful Calcium-Sensing Reporter in Candida albicans. J Fungi (Basel) 2021; 7:jof7040319. [PMID: 33924126 PMCID: PMC8074299 DOI: 10.3390/jof7040319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
In Candida albicans, calcium ions (Ca2+) regulate the activity of several signaling pathways, especially the calcineurin signaling pathway. Ca2+ homeostasis is also important for cell polarization, hyphal extension, and plays a role in contact sensing. It is therefore important to obtain accurate tools with which Ca2+ homeostasis can be addressed in this fungal pathogen. Aequorin from Aequorea victoria has been used in eukaryotic cells for detecting intracellular Ca2+. A codon-adapted aequorin Ca2+-sensing expression system was therefore designed for probing cytosolic Ca2+ flux in C. albicans. The availability of a novel water-soluble formulation of coelenterazine, which is required as a co-factor, made it possible to measure bioluminescence as a readout of intracellular Ca2+ levels in C. albicans. Alkaline stress resulted in an immediate influx of Ca2+ from the extracellular medium. This increase was exacerbated in a mutant lacking the vacuolar Ca2+ transporter VCX1, thus confirming its role in Ca2+ homeostasis. Using mutants in components of a principal Ca2+ channel (MID1, CCH1), the alkaline-dependent Ca2+ spike was greatly reduced, thus highlighting the crucial role of this channel complex in Ca2+ uptake and homeostasis. Exposure to the antiarrhythmic drug amiodarone, known to perturb Ca2+ trafficking, resulted in increased cytoplasmic Ca2+ within seconds that was abrogated by the chelation of Ca2+ in the external medium. Ca2+ import was also dependent on the Cch1/Mid1 Ca2+ channel in amiodarone-exposed cells. In conclusion, the aequorin Ca2+ sensing reporter developed here is an adequate tool with which Ca2+ homeostasis can be investigated in C. albicans.
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Wang JL, Chen WG, Zhang JJ, Xu CJ. Nogo-A-Δ20/EphA4 interaction antagonizes apoptosis of neural stem cells by integrating p38 and JNK MAPK signaling. J Mol Histol 2021; 52:521-537. [PMID: 33555537 DOI: 10.1007/s10735-021-09960-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Nogo-A protein consists of two main extracellular domains: Nogo-66 (rat amino acid [aa] 1019-1083) and Nogo-A-Δ20 (extracellular, active 180 amino acid Nogo-A region), which serve as strong inhibitors of axon regeneration in the adult CNS (Central Nervous System). Although receptors S1PR2 and HSPGs have been identified as Nogo-A-Δ20 binding proteins, it remains at present elusive whether other receptors directly interacting with Nogo-A-Δ20 exist, and decrease cell death. On the other hand, the key roles of EphA4 in the regulation of glioblastoma, axon regeneration and NSCs (Neural Stem Cells) proliferation or differentiation are well understood, but little is known the relationship between EphA4 and Nogo-A-Δ20 in NSCs apoptosis. Thus, we aim to determine whether Nogo-A-Δ20 can bind to EphA4 and affect survival of NSCs. Here, we discover that EphA4, belonging to a member of erythropoietin-producing hepatocellular (Eph) receptors family, could be acting as a high affinity ligand for Nogo-A-Δ20. Trans-membrane protein of EphA4 is needed for Nogo-A-Δ20-triggered inhibition of NSCs apoptosis, which are mediated by balancing p38 inactivation and JNK MAPK pathway activation. Finally, we predict at the atomic level that essential residues Lys-205, Ile-190, Pro-194 in Nogo-A-Δ20 and EphA4 residues Gln-390, Asn-425, Pro-426 might play critical roles in Nogo-A-Δ20/EphA4 binding via molecular docking.
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Affiliation(s)
- Jun-Ling Wang
- Center for Reproductive Medicine, Affiliated Hospital 1 of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wei-Guang Chen
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jia-Jia Zhang
- School of 1St Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Chao-Jin Xu
- Department of Histology & Embryology, School of Basic Medical Science, Wenzhou Medical University, Cha Shan University Town, No.1 Central North Road, Wenzhou, 325035, Zhejiang, People's Republic of China.
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Barkovits K, Pfeiffer K, Eggers B, Marcus K. Protein Quantification Using the "Rapid Western Blot" Approach. Methods Mol Biol 2021; 2228:29-39. [PMID: 33950481 DOI: 10.1007/978-1-0716-1024-4_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For the quantification of certain proteins of interest within a complex sample, Western blot analysis is the most widely used method. It enables detection of a target protein based on the use of specific antibodies. However, the whole procedure is often very time-consuming. Nevertheless, with the development of fast blotting systems and further development of immunostaining methods, a reduction of the processing time can be achieved. Major challenges for the reliable protein quantification by Western blotting are adequate data normalization and stable protein detection. Usually, normalization of the target protein signal is performed based on housekeeping proteins (e.g., glyceraldehyde 3-phosphate dehydrogenase, ß-actin) with the assumption that those proteins are expressed constitutively at the same level across experiments. However, several studies have already shown that this is not always the case making this approach suboptimal. Another strategy uses total protein normalization where the abundance of the target protein is related to the total protein amount in each lane. This approach is independent of a single loading control, and precision of quantification and reliability is increased. For Western blotting several detection methods are available, e.g., colorimetric, chemiluminescent, radioactive, fluorescent detection. Conventional colorimetric staining tends to suffer from low sensitivity, limited dynamic range, and low reproducibility. Chemiluminescence-based methods are straightforward, but the detected signal does not linearly correlate to protein abundance (from protein amounts >5μg) and have a relatively narrow dynamic range. Radioactivity is harmful to health. To overcome these limitations, stain-free methods were developed allowing the combination of fluorescent standards and a stain-free fluorescence-based visualization of total protein in gels and after transfer to the membrane. Here, we present a rapid Western blot protocol, which combines fast blotting using the iBlot system and fast immunostaining utilizing ReadyTector® all-in-one solution with the Smart Protein Layers (SPL) approach.
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Affiliation(s)
- Katalin Barkovits
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for Proteindiagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Kathy Pfeiffer
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for Proteindiagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Britta Eggers
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for Proteindiagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany. .,Medical Proteome Analysis, Center for Proteindiagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.
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