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Charras Q, Rey P, Guillemain D, Dourguin F, Laganier H, Peschoux S, Molinié R, Ismaël M, Caffarri S, Rayon C, Jungas C. An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants. Plant Methods 2024; 20:38. [PMID: 38468328 DOI: 10.1186/s13007-024-01166-7] [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: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND The extraction of thylakoids is an essential step in studying the structure of photosynthetic complexes and several other aspects of the photosynthetic process in plants. Conventional protocols have been developed for selected land plants grown in controlled conditions. Plants accumulate defensive chemical compounds such as polyphenols to cope with environmental stresses. When the polyphenol levels are high, their oxidation and cross-linking properties prevent thylakoid extraction. RESULTS In this study, we developed a method to counteract the hindering effects of polyphenols by modifying the grinding buffer with the addition of both vitamin C (VitC) and polyethylene glycol (PEG4000). This protocol was first applied to the marine plant Posidonia oceanica and then extended to other plants synthesizing substantial amounts of polyphenols, such as Quercus pubescens (oak) and Vitis vinifera (grapevine). Native gel analysis showed that photosynthetic complexes (PSII, PSI, and LHCII) can be extracted from purified membranes and fractionated comparably to those extracted from the model plant Arabidopsis thaliana. Moreover, total protein extraction from frozen P. oceanica leaves was also efficiently carried out using a denaturing buffer containing PEG and VitC. CONCLUSIONS Our work shows that the use of PEG and VitC significantly improves the isolation of native thylakoids, native photosynthetic complexes, and total proteins from plants containing high amounts of polyphenols and thus enables studies on photosynthesis in various plant species grown in natural conditions.
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Affiliation(s)
- Quentin Charras
- CEA, CNRS, BIAM, LGBP Team, Aix-Marseille University, Marseille, France
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, KTH University, Stockholm, Sweden
| | - Pascal Rey
- CEA, CNRS, BIAM, P&E Team, Aix-Marseille University, Saint Paul-Lez-Durance, France
| | - Dorian Guillemain
- CNRS, IRD, IRSTEA, OSU Institut Pythéas, Aix-Marseille University, Marseille, France
| | - Fabian Dourguin
- CEA, CNRS, BIAM, LGBP Team, Aix-Marseille University, Marseille, France
| | - Hugo Laganier
- CEA, CNRS, BIAM, LGBP Team, Aix-Marseille University, Marseille, France
| | - Sacha Peschoux
- UFR Informatique, mathématiques et mathématiques appliquées (IM2AG), Université Grenoble Alpes, Saint Martin d'Heres, France
| | - Roland Molinié
- UMR INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UPJV, Amiens, France
| | - Marwa Ismaël
- UMR INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UPJV, Amiens, France
| | - Stefano Caffarri
- CEA, CNRS, BIAM, LGBP Team, Aix-Marseille University, Marseille, France
| | - Catherine Rayon
- UMR INRAE 1158 Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UPJV, Amiens, France
| | - Colette Jungas
- CEA, CNRS, BIAM, LGBP Team, Aix-Marseille University, Marseille, France.
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Kaur M, Kumar R, Katoch P, Gupta R. Purification and characterization of extracellular lipase from a thermotolerant strain: Bacillus subtilis TTP-06. 3 Biotech 2023; 13:343. [PMID: 37711229 PMCID: PMC10497478 DOI: 10.1007/s13205-023-03717-6] [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: 04/01/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023] Open
Abstract
In current study, lipase from a thermotolerant Bacillus subtilis TTP-06 was purified in a stepwise manner by using ammonium sulfate precipitation and column chromatography. Thenceforth, it was subjected to sodium dodecyl sulfate- and native-polyacrylamide gel electrophoresis to check the homogeneity of the purified enzyme. The ideal substrate concentration, pH, temperature, reaction duration and lipase specificity were identified. With a yield of 11.02%, purified lipase displayed activity of 8.51 U/mg. Thenceforward, the homogeneously purified enzyme was considered to be a homo-dimer of 30 kDa subunits. Enzyme had Km and Vmax value of 9.498 mM and 19.92 mol mg-1 min-1, respectively. Additionally, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method was used to investigate the purified lipase and estimate its 3-D structure, which revealed a catalytic triad of serine, aspartate and histidine.
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Affiliation(s)
- Manpreet Kaur
- Department of Biotechnology, Himachal Pradesh University, SummerHill, Shimla, HP India
| | - Rakesh Kumar
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Poonam Katoch
- Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Reena Gupta
- Department of Biotechnology, Himachal Pradesh University, SummerHill, Shimla, HP India
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Panagiotidou E, Gioran A, Chondrogianni N. In-Plate and In-Gel Assays for the Assessment of Proteasome Activity in Caenorhabditis elegans. Methods Mol Biol 2023; 2602:217-228. [PMID: 36446978 DOI: 10.1007/978-1-0716-2859-1_16] [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: 06/16/2023]
Abstract
This chapter describes two methods for the study of proteasome function in Caenorhabditis elegans (C. elegans). The first method, referred to as "in-plate activities," provides a quantitative measurement of proteasome activities in C. elegans lysates by means of a kinetic reaction in a 96-well plate. The second one, referred to as "in-gel activities," involves the separation of C. elegans protein lysates in a native polyacrylamide gel and the assessment of the activity of each proteasome form. Downstream immunoblotting also allows the semi-quantitative assessment of proteasome assembly. This chapter outlines two detailed protocols along with helpful schematics and representative results that will facilitate researchers to replicate both protocols accurately and reproducibly.
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Affiliation(s)
- Eleni Panagiotidou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Anna Gioran
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
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Kushwaha AS, Kumar M. An effective in-gel assay protocol for the assessment of acid phosphatase (ACPase) isoform expression in the fungus Serendipita indica. 3 Biotech 2022; 12:40. [PMID: 35070630 PMCID: PMC8741913 DOI: 10.1007/s13205-021-03103-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 08/09/2021] [Accepted: 12/27/2021] [Indexed: 02/03/2023] Open
Abstract
The induction of acid phosphatase (ACPase) in the mycorrhizal fungi is an adaptive survival mechanism to cope in a low-phosphate environment. A mycorrhizal fungi Serendipita indica can induce the ACPase enzyme and enhance the phosphate (Pi) level to the host plant through Pi-solubilization mechanism, both intracellular and extracellular (media) levels. The spectrophotometer technique has been widely and commonly used to measure the ACPase enzyme activity in all microorganisms and plants using pNPP as a substrate. However, this technique cannot be useful when studying the involvement of ACPase isoforms in Pi-solubilization. In this article, we developed a single method to identify and express the ACPase isoforms of S. indica that contribute to the Pi-nutrition in the plant. This is native-PAGE electrophoresis with the in-gel assay and staining to detect the isoforms of the ACPase enzyme. The dark red-brown color developed after staining indicates the non-denatured (native) ACPase enzyme. This method utilized a modified minimal media for the de-repression of P-responsive genes such as ACPases with minimum salt contamination in the samples. This method will be helpful for the characterization of secretory and intracellular ACPases in fungi.
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Affiliation(s)
- Aparna Singh Kushwaha
- grid.417638.f0000 0001 2194 5503Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
| | - Manoj Kumar
- grid.417638.f0000 0001 2194 5503Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002 India
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Aso M, Matsumae R, Tanaka A, Tanaka R, Takabayashi A. Unique Peripheral Antennas in the Photosystems of the Streptophyte Alga Mesostigma viride. Plant Cell Physiol 2021; 62:436-446. [PMID: 33416834 DOI: 10.1093/pcp/pcaa172] [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] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Land plants evolved from a single group of streptophyte algae. One of the key factors needed for adaptation to a land environment is the modification in the peripheral antenna systems of photosystems (PSs). Here, the PSs of Mesostigma viride, one of the earliest-branching streptophyte algae, were analyzed to gain insight into their evolution. Isoform sequencing and phylogenetic analyses of light-harvesting complexes (LHCs) revealed that M. viride possesses three algae-specific LHCs, including algae-type LHCA2, LHCA9 and LHCP, while the streptophyte-specific LHCB6 was not identified. These data suggest that the acquisition of LHCB6 and the loss of algae-type LHCs occurred after the M. viride lineage branched off from other streptophytes. Clear-native (CN)-polyacrylamide gel electrophoresis (PAGE) resolved the photosynthetic complexes, including the PSI-PSII megacomplex, PSII-LHCII, two PSI-LHCI-LHCIIs, PSI-LHCI and the LHCII trimer. Results indicated that the higher-molecular weight PSI-LHCI-LHCII likely had more LHCII than the lower-molecular weight one, a unique feature of M. viride PSs. CN-PAGE coupled with mass spectrometry strongly suggested that the LHCP was bound to PSII-LHCII, while the algae-type LHCA2 and LHCA9 were bound to PSI-LHCI, both of which are different from those in land plants. Results of the present study strongly suggest that M. viride PSs possess unique features that were inherited from a common ancestor of streptophyte and chlorophyte algae.
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Affiliation(s)
- Michiki Aso
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-ku, Sapporo, 060-0819 Japan
| | - Renon Matsumae
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-ku, Sapporo, 060-0819 Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-ku, Sapporo, 060-0819 Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-ku, Sapporo, 060-0819 Japan
| | - Atsushi Takabayashi
- Institute of Low Temperature Science, Hokkaido University, N19 W8 Kita-ku, Sapporo, 060-0819 Japan
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Sherman CD, Barnes BJ. Intracellular IRF5 Dimerization Assay. Bio Protoc 2021; 11:e4021. [PMID: 34150928 PMCID: PMC8187113 DOI: 10.21769/bioprotoc.4021] [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: 11/17/2020] [Revised: 02/10/2021] [Accepted: 02/28/2021] [Indexed: 11/02/2022] Open
Abstract
The intracellular interferon regulatory factor 5 (IRF5) dimerization assay is a technique designed to measure molecular interaction(s) with endogenous IRF5. Here, we present two methods that detect endogenous IRF5 homodimerization and interaction of endogenous IR5 with cell penetrating peptide (CPP) inhibitors. Briefly, to detect endogenous IRF5 dimers, THP-1 cells are incubated in the presence or absence of the IRF5-targeted CPP (IRF5-CPP) inhibitor for 30 min then the cells are stimulated with R848 for 1 h. Cell lysates are separated by native-polyacrylamide gel electrophoresis (PAGE) and IRF5 dimers are detected by immunoblotting with IRF5 antibodies. To detect endogenous interactions between IRF5 and FITC-labeled IRF5-CPP, an in-cell fluorescence resonance energy transfer (FRET) assay is used. In this assay, THP-1 cells are left untreated or treated with FITC-IRF5-CPP conjugated inhibitors for 1 h. Next, cells are fixed, permeabilized, and stained with anti-IRF5 and TRITC-conjugated secondary antibodies. Transfer of fluorescence can be measured and calculated as FRET units. These methods provide rapid and accurate assays to detect IRF5 molecular interactions.
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Affiliation(s)
- Cherrie D Sherman
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Betsy J Barnes
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institutes for Medical Research, Manhasset, New York, USA
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7
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Corvest V, Jawhari A. Solubilization and Stabilization of Native Membrane Proteins for Drug Discovery. Methods Mol Biol 2021; 2247:257-267. [PMID: 33301122 DOI: 10.1007/978-1-0716-1126-5_14] [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: 06/12/2023]
Abstract
Membrane proteins (MPs) are stable in their native lipid environment. To enable structural and functional investigations, MPs need to be extracted from the membrane. This is a critical step that represents the main obstacle for MP biochemistry and structural biology. Here we describe detergent solubilization screening of MPs using dot-blot and Western-blot analyses. Good solubilization conditions are ranked for their best capacity to stabilize MPs using thermal shift assay. The protein functionality is evaluated by radioligand binding (for G-protein-coupled receptor) and ATPase activity (ABC Transporter) and finally the aggregation status as well as protein homogeneity are assessed by Native-polyacrylamide gel, chemical cross-linking, and size exclusion chromatography.
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8
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Wang X, Xiang X, Yu H, Liu S, Yin Y, Cui P, Wu Y, Yang J, Jiang C, Yang Q. Monitoring and biochemical characterization of beta-cypermethrin resistance in Spodoptera exigua (Lepidoptera: Noctuidae) in Sichuan Province, China. Pestic Biochem Physiol 2018; 146:71-79. [PMID: 29626995 DOI: 10.1016/j.pestbp.2018.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 02/06/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
The beet armyworm Spodoptera exigua, a major pest affecting numerous cultivated crops in China, has developed a serious resistance to many traditional chemical insecticides. The resistance levels of the field-collected populations from different districts in Sichuan Province, China, to nine insecticides were detected with a diet-incorporation bioassay. Compared to the Lab-ZN strain, five (in 2014) and three (in 2016) field populations displayed either high or extremely high levels of resistance to beta-cypermethrin. All the field populations collected in 2014 were susceptible to emamectin benzoate, hexaflumuron, methoxyfenozide, chlorantraniliprole, cyantraniliprole and indoxacarb but exhibited low or moderate levels of resistance to abamectin. The resistances of field populations collected in 2016 were significantly higher than two years earlier, especial for chlorantraniliprole and cyantraniliprole with RRs rising from 173.4- to 582.6-fold and 175.3- to 287.6-fold, respectively, even though the field populations had retained moderate or low levels of resistance to chlorpyrifos and hexaflumuron. The synergism experiment revealed that the resistance of the LS16 population to beta-cypermethrin may be mainly related to cytochrome P450 monooxygenases (P450s), which was responsible for the highest increase ratio of 37.97-fold, for piperonyl butoxide, rather than either carboxylesterase (CarE) or glutathione S-transferase (GST). The cytochrome P450 ethoxycoumarin O-deethylase activity of the LS16 population was also the strongest among the treatments (P < 0.05). Non-denaturing polyacrylamide gel electrophoresis (native PAGE) indicated that enhanced E11, E13 and E15-E16 bands in the LS16 population likely contribute to the development of resistance to beta-cypermethrin.
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Affiliation(s)
- Xuegui Wang
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xing Xiang
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China
| | - Huiling Yu
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuhua Liu
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Yin
- Plant Protection Station, Agriculture Department of Sichuan, Chengdu 610041, China
| | - Peng Cui
- Agency of Protection and Quarantine, Agriculture Technology and Popularization Center in Central District of Leshan City, Leshan 614000, China
| | - Yaqiong Wu
- Plant Protection Station, Agriculture Department of Sichuan, Chengdu 610041, China
| | - Jing Yang
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Chunxian Jiang
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China
| | - Qunfang Yang
- Biorational Pesticide Research Lab, Sichuan Agricultural University, Chengdu 611130, China
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Abstract
Imidazole-zinc reverse stain (ZN stain) is known for high sensitivity, ease of use, and cost-effective feature. ZN stain is compatible to many experiments of which those are proteomics-related in particular. Here, we describe the ZN staining procedures and the subsequent procedures incorporated in detail, along with the improvements of setup in aspects of visualization and documentation for postprocessing ZN stained gel images.
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Affiliation(s)
- Han-Min Chen
- Department of Life Science, Catholic Fu-Jen University, New Taipei City, Taiwan.
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10
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Carrillo JB, Gomez-Casati DF, Busi MV, Martín M. Development of fast and simple chromogenic methods for glucan phosphatases in-gel activity assays. Anal Biochem 2017; 517:36-39. [PMID: 27836260 DOI: 10.1016/j.ab.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/11/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
Glucan phosphatases are essential for normal starch degradation in plants and glycogen metabolism in mammals. Here we develop two chromogenic methods for the detection of glucan phosphatase activity in situ after non denaturing poliacrylamide gel electrophoresis; one method uses pNPP and the second one applies BCIP/NBT. The assays are sensitive, fast, simple, reliable and cost-effective preventing the use of radioactive or fluorogenic compounds. Taking advantage of an efficient separation method combined with the reported assays it is possible to obtain information about oligomeric state of the active enzymes as well as to simultaneously detect glucan substrate binding and phosphatase activity.
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Affiliation(s)
- Julieta B Carrillo
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Maria V Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, 2000 Rosario, Santa Fe, Argentina.
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Liu Y, Zhang D, Cheng Y, Li Z. Elevated serum immunoinflammation-related protein complexes are associated with psychosis. Psychiatry Res 2015; 230:96-101. [PMID: 26337482 DOI: 10.1016/j.psychres.2015.08.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 07/27/2015] [Accepted: 08/25/2015] [Indexed: 02/09/2023]
Abstract
Emerging evidence suggests an underlying immune and inflammatory response for a variety of psychiatric disorders. Herein, we employed an optimized native-polyacrylamide gel electrophoresis to isolate psychosis-related serum immunoinflammation-related protein complexes (IIRPCs) from 147 patients with schizophrenia (SCH), 158 patients with bipolar disorder (BPD), 132 patients with other psychosis, and 145 normal controls. All participants could be classified into four categories based on serum IIRPCs, which correspond to 290, 215, 70, and 7 serum samples, correspondingly. For each category, significantly enhanced levels of serum IIRPCs in patients with SCH, BPD, and other psychosis groups were observed compared with normal controls. Receiver operating characteristic analysis indicated that serum IIRPCs have excellent diagnostic performance to differentiate SCH, BPD, and other psychosis groups from normal controls, with high sensitivities and specificities of >85%. Total serum amounts of IgG, IgA, and IgM in all patients were significantly decreased compared with normal controls.
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Affiliation(s)
- Yujie Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, PR China
| | - Dan Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, PR China
| | - Yuhang Cheng
- Clinical Examination and Experimental Center, Beijing An Ding Hospital, Capital Medical University, Beijing, PR China.
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, PR China.
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12
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Kesheri M, Kanchan S, Richa, Sinha RP. Isolation and in silico analysis of Fe-superoxide dismutase in the cyanobacterium Nostoc commune. Gene 2014; 553:117-25. [PMID: 25303871 DOI: 10.1016/j.gene.2014.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 05/16/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 12/22/2022]
Abstract
Cyanobacteria are known to endure various stress conditions due to the inbuilt potential for oxidative stress alleviation owing to the presence of an array of antioxidants. The present study shows that Antarctic cyanobacterium Nostoc commune possesses two antioxidative enzymes viz., superoxide dismutase (SOD) and catalase that jointly cope with environmental stresses prevailing at its natural habitat. Native-PAGE analysis illustrates the presence of a single prominent isoform recognized as Fe-SOD and three distinct isoforms of catalase. The protein sequence of Fe-SOD in N. commune retrieved from NCBI protein sequence database was used for in silico analysis. 3D structure of N. commune was predicted by comparative modeling using MODELLER 9v11. Further, this model was validated for its quality by Ramachandran plot, ERRAT, Verify 3D and ProSA-web which revealed good structure quality of the model. Multiple sequence alignment showed high conservation in N and C-terminal domain regions along with all metal binding positions in Fe-SOD which were also found to be highly conserved in all 28 cyanobacterial species under study, including N. commune. In silico prediction of isoelectric point and molecular weight of Fe-SOD was found to be 5.48 and 22,342.98Da respectively. The phylogenetic tree revealed that among 28 cyanobacterial species, Fe-SOD in N. commune was the closest evolutionary homolog of Fe-SOD in Nostoc punctiforme as evident by strong bootstrap value. Thus, N. commune may serve as a good biological model for studies related to survival of life under extreme conditions prevailing at the Antarctic region. Moreover cyanobacteria may be exploited for biochemical and biotechnological applications of enzymatic antioxidants.
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Affiliation(s)
- Minu Kesheri
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Swarna Kanchan
- Department of Biological Science, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, India
| | - Richa
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.
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Abstract
The Santalum peroxidase was extracted from the leaves and precipitated with double volume of chilled acetone. The optimum percent relative activity for the Santalum peroxidase was observed at pH 5.0 and 50 °C temperature. The Santalum peroxidase per cent relative activity was stimulated in the presence of phenolic compounds like ferrulic acid and caffeic acids; however, indole-3-acetic acid (IAA) and protocatechuic acid act as inhibitors. All divalent cations Fe(2+), Mn(2+), Mg(2+), Cu(2+) and Zn(2+) stimulate the relative activity of the Santalum peroxidase at concentration of 2.0 μM. Amino acids like L-alanine and L-valine activate the per cent relative activity, while L-proline and DL-methionine showed moderate inhibition for the Santalum peroxidase. However, a very low a concentration of cysteine acts as a strong inhibitor of Santalum peroxidase at the concentration of 0.4 mM. Native polyacrylamide gel electrophoresis (Native-PAGE) was performed for isoenzyme determination and two bands were observed. Km and Vmax values were calculated from Lineweaver-Burk graph. The apparent Vmax/Km value for O-dianisidine and H2O2 were 400 and 5.0 × 105 Units/min/mL respectively.
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Affiliation(s)
- Pradeep Kumar
- />Central Institute for Subtropical Horticulture, Lucknow, 227107 UP India
| | - Madhu Kamle
- />Central Institute for Subtropical Horticulture, Lucknow, 227107 UP India
| | - Jagtar Singh
- />Department of Biotechnology, Punjab University, Chandigarh, 600 014 India
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