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Adnane M, de Almeida AM, Chapwanya A. Unveiling the power of proteomics in advancing tropical animal health and production. Trop Anim Health Prod 2024; 56:182. [PMID: 38825622 DOI: 10.1007/s11250-024-04037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.
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Affiliation(s)
- Mounir Adnane
- Department of Biomedicine, Institute of Veterinary Sciences, University of Tiaret, Tiaret, 14000, Algeria.
| | - André M de Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349-017, Portugal
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, 00265, Saint Kitts and Nevis
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2
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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3
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Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules. Molecules 2022; 27:molecules27196367. [PMID: 36234904 PMCID: PMC9573451 DOI: 10.3390/molecules27196367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.
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4
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Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
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Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
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5
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Carreño A, Gacitúa M, Solis-Céspedes E, Páez-Hernández D, Swords WB, Meyer GJ, Preite MD, Chávez I, Vega A, Fuentes JA. New Cationic fac-[Re(CO) 3(deeb)B2] + Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE. Front Chem 2021; 9:647816. [PMID: 33842435 PMCID: PMC8027506 DOI: 10.3389/fchem.2021.647816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) can be used to separate proteins based mainly on their size such as in denaturing gels. Different staining methods have been reported to observe proteins in the gel matrix, where the most used dyes are generally anionic. Anionic dyes allow for interactions with protonated amino acids, retaining the dye in the proteins. Fluorescent staining is an alternative technique considered to be sensitive, safe, and versatile. Some anionic complexes based on d6 transition metals have been used for this purpose, where cationic dyes have been less explored in this context. In this work, we synthesized and characterized a new monocationic rhenium complex fac-[Re(CO)3(deeb)B2]+ (where deeb is 4,4′-bis(ethoxycarbonyl)-2,2′-bpy and B2 is 2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol). We carried out a structural characterization of this complex by MS+, FTIR, 1H NMR, D2O exchange, and HHCOSY. Moreover, we carried out UV-Vis, luminescence, and cyclic voltammetry experiments to understand the effect of ligands on the complex’s electronic structure. We also performed relativistic theoretical calculations using the B3LYP/TZ2P level of theory and R-TDDFT within a dielectric continuum model (COSMO) to better understand electronic transitions and optical properties. We finally assessed the potential of fac-[Re(CO)3(deeb)B2]+ (as well as the precursor fac-Re(CO)3(deeb)Br and the free ligand B2) to stain proteins separated by SDS-PAGE. We found that only fac-[Re(CO)3(deeb)B2]+ proved viable to be directly used as a luminescent dye for proteins, presumably due to its interaction with negatively charged residues in proteins and by weak interactions provided by B2. In addition, fac-[Re(CO)3(deeb)B2]+ seems to interact preferentially with proteins and not with the gel matrix despite the presence of sodium dodecyl sulfate (SDS). In future applications, these alternative cationic complexes might be used alone or in combination with more traditional anionic compounds to generate counterion dye stains to improve the process.
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Affiliation(s)
- Alexander Carreño
- Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | | | - Eduardo Solis-Céspedes
- Escuela de Bioingeniería Médica, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile.,Laboratorio de Bioinformática y Química Computacional, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Dayán Páez-Hernández
- Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | - Wesley B Swords
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gerald J Meyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marcelo D Preite
- Departamento de Química Orgánica, Facultad de Química y Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ivonne Chávez
- Departamento de Química Inorgánica, Facultad de Química y Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés Vega
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Viña del Mar, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología Cedenna, Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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6
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Coombs KM. Update on Proteomic approaches to uncovering virus-induced protein alterations and virus -host protein interactions during the progression of viral infection. Expert Rev Proteomics 2020; 17:513-532. [PMID: 32910682 DOI: 10.1080/14789450.2020.1821656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Viruses induce profound changes in the cells they infect. Understanding these perturbations will assist in designing better therapeutics to combat viral infection. System-based proteomic assays now provide unprecedented opportunity to monitor large numbers of cellular proteins. AREAS COVERED This review will describe various quantitative and functional mass spectrometry-based methods, and complementary non-mass spectrometry-based methods, such as aptamer profiling and proximity extension assays, and examples of how each are used to delineate how viruses affect host cells, identify which viral proteins interact with which cellular proteins, and how these change during the course of a viral infection. PubMed was searched multiple times prior to manuscript submissions and revisions, using virus, viral, proteomics; in combination with each keyword. The most recent examples of published works from each search were then analyzed. EXPERT OPINION There has been exponential growth in numbers and types of proteomic analyses in recent years. Continued development of reagents that allow increased multiplexing and deeper proteomic probing of the cell, at quantitative and functional levels, enhancements that target more important protein modifications, and improved bioinformatics software tools and pathway prediction algorithms will accelerate this growth and usher in a new era of host proteome understanding.
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Affiliation(s)
- Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba , Winnipeg, Manitoba, Canada.,Manitoba Centre for Proteomics and Systems Biology , Winnipeg, Manitoba, Canada.,Manitoba Institute of Child Health , Winnipeg, Manitoba, Canada
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7
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Turk N, Raza A, Wuytens P, Demol H, Daele MV, Detavernier C, Skirtach A, Gevaert K, Baets R. Waveguide-based surface-enhanced Raman spectroscopy detection of protease activity using non-natural aromatic amino acids. BIOMEDICAL OPTICS EXPRESS 2020; 11:4800-4816. [PMID: 32923079 PMCID: PMC7449744 DOI: 10.1364/boe.398038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 05/08/2023]
Abstract
Surface enhanced Raman spectroscopy (SERS) is a selective and sensitive technique, which allows for the detection of protease activity by monitoring the cleavage of peptide substrates. Commonly used free-space based SERS substrates, however, require the use of bulky and expensive instrumentation, limiting their use to laboratory environments. An integrated photonics approach aims to implement various free-space optical components to a reliable, mass-reproducible and cheap photonic chip. We here demonstrate integrated SERS detection of trypsin activity using a nanoplasmonic slot waveguide as a waveguide-based SERS substrate. Despite the continuously improving SERS performance of the waveguide-based SERS substrates, they currently still do not reach the SERS enhancements of free-space substrates. To mitigate this, we developed an improved peptide substrate in which we incorporated the non-natural aromatic amino acid 4-cyano-phenylalanine, which provides a high intrinsic SERS signal. The use of non-natural aromatics is expected to extend the possibilities for multiplexing measurements, where the activity of several proteases can be detected simultaneously.
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Affiliation(s)
- Nina Turk
- Photonics Research Group, Ghent University – IMEC, Technologiepark 126, 9052 Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent, Belgium
| | - Ali Raza
- Photonics Research Group, Ghent University – IMEC, Technologiepark 126, 9052 Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent, Belgium
- Currently with Microsoft, Keilalahdentie 2-4, 02150 Espoo, Finland
| | - Pieter Wuytens
- Photonics Research Group, Ghent University – IMEC, Technologiepark 126, 9052 Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent, Belgium
- Currently with IMEC, Kapeldreef 75, 3001 Heverlee, Belgium
| | - Hans Demol
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Michiel Van Daele
- Department of Solid State Sciences, CoCooN Research Group, Ghent University, Belgium
| | | | - Andre Skirtach
- Center for Nano- and Biophotonics, Ghent, Belgium
- Department of Biotechnology, Ghent University, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Roel Baets
- Photonics Research Group, Ghent University – IMEC, Technologiepark 126, 9052 Ghent, Belgium
- Center for Nano- and Biophotonics, Ghent, Belgium
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8
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Petry R, Saboia VM, Franqui LS, Holanda CDA, Garcia TR, de Farias MA, de Souza Filho AG, Ferreira OP, Martinez DS, Paula AJ. On the formation of protein corona on colloidal nanoparticles stabilized by depletant polymers. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 105:110080. [DOI: 10.1016/j.msec.2019.110080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 01/09/2023]
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9
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Counterion Dye Staining of Proteins in One- and Two-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Tryptic Gel Digestion of Stained Protein for Mass Spectrometry. Methods Mol Biol 2019. [PMID: 30097930 DOI: 10.1007/978-1-4939-8745-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
A fast and matrix-assisted laser desorption/ionization-mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet to form an ion-pair complex. The protocol including fixing, staining, and quick washing steps can be completed in 1-1.5 h depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.
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10
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Lau BYC, Othman A, Ramli US. Application of Proteomics Technologies in Oil Palm Research. Protein J 2018; 37:473-499. [DOI: 10.1007/s10930-018-9802-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Zhou Y, Xiao L, Tang S. Annexin A2 and FTH1 are potential biomarkers for lupus nephritis. Exp Ther Med 2018; 16:3766-3776. [PMID: 30344652 PMCID: PMC6176168 DOI: 10.3892/etm.2018.6686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022] Open
Abstract
Lupus nephritis (LN) occurs in ~50% of patients with systemic lupus erythematosus and is a major cause of morbidity and mortality of the affected individuals. Therefore, identification of novel and predictive biomarkers for the early diagnosis and progression of LN is required. The present study included 10 patients with LN whose diagnoses were confirmed by renal biopsy and 5 healthy participants as control subjects. Sera were collected both from patients with LN and healthy controls. Subsequently, mesangial cells were treated with these sera for 24 h. Differential proteins between groups were detected by two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry analysis. 2D-DIGE maps of cellar proteins were obtained for LN and normal control groups. A total of 45 proteins were characterized, and 2 low-abundance proteins were identified. Compared with the normal human sera group, expression level of Annexin A2 was elevated in patients with LN, while the expression of the ferritin heavy chain (FTH1) decreased in the LN group; the analysis was carried out by DeCyder version 7.0 automatically. The results of the present study suggest that Annexin A2 and FTH1 contributed to the progression of LN and could serve as potential biomarkers for this disease.
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Affiliation(s)
- Yanni Zhou
- Division of Nephrology, Xiamen Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Xiamen, Fujian 361000, P.R. China.,Division of Nephrology, First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Liangxiang Xiao
- Division of Nephrology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Shuifu Tang
- Division of Nephrology, First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
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12
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Abdallah AO, Coleman H, Kamel M, Davis R, Landrum T, Spencer H, Mackintosh S, Mahmoud FA, Milojkovic N, Wicker C, Arnaoutakis K, Nakagawa M. A novel prostate cancer immunotherapy using prostate-specific antigen peptides and Candida skin test reagent as an adjuvant. SAGE Open Med 2018; 6:2050312118800202. [PMID: 30245818 PMCID: PMC6144584 DOI: 10.1177/2050312118800202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/21/2018] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Our group developed the use of the Candida skin test reagent as an adjuvant of cell-mediated immunity in designing a human papillomavirus therapeutic vaccine. Here, this technology is being applied for designing a prostate cancer immunotherapy. METHODS Peptides based on the prostate-specific antigen amino acid sequences were selected, synthesized, and evaluated in terms of their (1) solubility, (2) maturation effects on Langerhans cells by fluorescence-activated cell sorter analysis, and (3) recognition by peripheral immune cells from prostate cancer patients using interferon-γ enzyme-linked immunospot assay. RESULTS The peptides were soluble in 10 mM succinate at pH of 5 with 5% glycine, and they demonstrated no maturation effects on Langerhans cells from healthy donors. On the other hand, peripheral immune cells from 4 of 10 prostate cancer patients examined had positive responses in enzyme-linked immunospot assay to one or more prostate-specific antigen peptides. CONCLUSION In summary, a design and a formulation of a novel prostate cancer immunotherapy are described. The immunogenicity of prostate-specific antigen peptides in some prostate cancer patients supports further development of this immunotherapy.
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Affiliation(s)
- Al-Ola Abdallah
- Department of Internal Medicine, College
of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Hematologic Malignancies and
Cellular Therapeutics, Department of Internal Medicine, School of Medicine, Kansas
University Medical Center, Kansas City, KS, USA
| | - Hannah Coleman
- Department of Pathology, College of
Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mohamed Kamel
- Department of Urology, College of
Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Urology, Ain Shams
University, Cairo, Egypt
| | - Rodney Davis
- Department of Urology, College of
Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Teri Landrum
- Division of Hematology and Oncology,
Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical
Sciences, Little Rock, AR, USA
| | - Horace Spencer
- Department of Biostatistics, College of
Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sam Mackintosh
- Department of Biochemistry and Molecular
Biology, College of Medicine, University of Arkansas for Medical Sciences, Little
Rock, AR, USA
| | - Fade A Mahmoud
- Department of Internal Medicine, College
of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Natasa Milojkovic
- Department of Internal Medicine, College
of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Chester Wicker
- Division of Hematology and Oncology,
Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical
Sciences, Little Rock, AR, USA
| | - Konstantinos Arnaoutakis
- Department of Internal Medicine, College
of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mayumi Nakagawa
- Department of Pathology, College of
Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Abstract
In-depth analysis of molecular regulatory networks in cancer holds the promise of improved knowledge of the pathophysiology of tumor cells so that it will become possible to design a detailed molecular tumor taxonomy. This knowledge will also offer new opportunities for the identification and validation of key molecular tumor targets to be exploited for novel therapeutic approaches. Some signaling proteins have already been identified as such, e.g. c-Myc, Cyclin D1, Bcl-XL, kinases and some nuclear receptors. This has led to the successful development of a few function-modulatory drugs (Glivec, SERM, Iressa), providing proof-of-principle of the validity of this approach. Further developments are likely to derive from “-omic” approaches, aimed at the understanding of signaling networks and of the mechanism of action of newfound lead molecules. High-throughput screening of small drug-like molecules from combinatorial chemical libraries or from microbial extracts will identify novel, “intelligent” drug candidates. An additional medicinal chemistry strategy (via 40–50 unit rosary-bead chains) has the potential to be much more effective than small molecules in interfering with protein-protein interactions. This may lead to considerably higher selectivity and effectiveness compared with historical approaches in drug discovery.
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Affiliation(s)
- S Alberti
- Laboratory of Experimental Oncology, Department of Cell Biology and Oncology, Mario Negri Institute-Consorzio Mario Negri Sud, Santa Maria Imbaro (CH), Italy.
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14
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Abstract
Staining of proteins separated on gels provides the basis for determination of the critical properties of these biopolymers, such as their molecular weight and/or charge. Detection of proteins on gels and blots require stains. These stains vary in sensitivity, ease of use, color, stability, versatility, and specificity. This review discusses different stains and applications with details on how to use the stains, and advantages and disadvantages of each stain. It also compiles some important points to be considered in imaging and evaluation. Commonly used colorimetric and fluorescent dyes for general protein staining, and stains that detect posttranslational modification-specific detection methods are also discussed.
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Affiliation(s)
- Pazhani Sundaram
- Recombinant Technologies LLC, 1090 Meriden Waterbury Turnpike, Suite 1, Cheshire, CT 06410, USA.
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15
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Amanullah A, Upadhyay A, Joshi V, Mishra R, Jana NR, Mishra A. Progressing neurobiological strategies against proteostasis failure: Challenges in neurodegeneration. Prog Neurobiol 2017; 159:1-38. [DOI: 10.1016/j.pneurobio.2017.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/01/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023]
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16
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Vikram Singh A, Gharat T, Batuwangala M, Park B, Endlein T, Sitti M. Three‐dimensional patterning in biomedicine: Importance and applications in neuropharmacology. J Biomed Mater Res B Appl Biomater 2017; 106:1369-1382. [DOI: 10.1002/jbm.b.33922] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 04/19/2017] [Accepted: 04/22/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Ajay Vikram Singh
- Department of Physical IntelligenceMax Planck Institute for Intelligent Systems, Heisenbergstr 370569Stuttgart Germany
| | - Tanmay Gharat
- Department of Chemical and Biological EngineeringRensselaer Polytechnic InstituteNew York New York12180
| | - Madu Batuwangala
- Department of Physical IntelligenceMax Planck Institute for Intelligent Systems, Heisenbergstr 370569Stuttgart Germany
| | - Byung‐Wook Park
- Department of Physical IntelligenceMax Planck Institute for Intelligent Systems, Heisenbergstr 370569Stuttgart Germany
| | - Thomas Endlein
- Department of Physical IntelligenceMax Planck Institute for Intelligent Systems, Heisenbergstr 370569Stuttgart Germany
| | - Metin Sitti
- Department of Physical IntelligenceMax Planck Institute for Intelligent Systems, Heisenbergstr 370569Stuttgart Germany
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17
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Zhang Y, Yu D, Dai J, Wang X, Zhu Z, Huang Y, Sun J, Chen Z, Jin L, Wang Y. A method for rapid and sensitive negative staining of proteins in SDS-PAGE using 2′,7′-dichlorofluorescein. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yuan Zhang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Dongdong Yu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jiangbo Dai
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Xu Wang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Zhongxin Zhu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yewei Huang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jia Sun
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Zhiwei Chen
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Litai Jin
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yang Wang
- Institute of neuroscience, Department of histology and embryology; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
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18
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Naryzhny S. Towards the Full Realization of 2DE Power. Proteomes 2016; 4:proteomes4040033. [PMID: 28248243 PMCID: PMC5260966 DOI: 10.3390/proteomes4040033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 01/29/2023] Open
Abstract
Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow 119121, Russia.
- B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute", Leningrad region, Gatchina 188300, Russia.
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Murphy S, Dowling P, Ohlendieck K. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis. Proteomes 2016; 4:proteomes4030027. [PMID: 28248237 PMCID: PMC5217355 DOI: 10.3390/proteomes4030027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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20
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Abstract
In-gel digestion coupled with mass spectrometric analysis (GeLC-MS/MS) is a cornerstone for protein identification and characterization. Here I review this versatile approach which combines classical and modern biochemistry strategies and allows for targeted and proteome-wide analyses. Starting with any protein sample, reduced and alkylated proteins are precipitated prior to fractionation by SDS-PAGE. Proteins are in-gel digested and the resulting peptides are extracted and desalted for downstream LC-MS/MS analysis. GeLC-MS/MS leverages the advantages of both traditional SDS-PAGE visualization and protein fractionation with the robust protein and post-translational modification identification and quantitation capabilities of state-of-the-art mass spectrometry-based technology. As such, this strategy allows for the visible assessment of protein amount and quality, prior to analysis via virtually any mass spectrometry platform. Moreover, gel extracted peptides may be derived from any sample type—e.g., from cell culture, tissue, body fluid, or recombinantly-expressed protein—and are fully compatible with isobaric tagging. GeLC-MS/MS is an invaluable technique for proteomic analyses.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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21
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Krappmann M, de Boer AR, Kool DRW, Irth H, Letzel T. Mass spectrometric real-time monitoring of an enzymatic phosphorylation assay using internal standards and data-handling freeware. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1019-1030. [PMID: 27003039 DOI: 10.1002/rcm.7529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Continuous-flow reaction detection systems (monitoring enzymatic reactions with mass spectrometry (MS)) lack quantitative values so far. Therefore, two independent internal standards (IS) are implemented in a way that the online system stability can be observed, quantitative conversion values for substrate and product can be obtained and they can be used as mass calibration standards for high MS accuracy. METHODS An application previously developed for the MS detection of peptide phosphorylation by cAMP-dependent protein kinase A (PKA) (De Boer et al., Anal. Bioanal. Chem. 2005, 381, 647-655) was transferred to a continuous-flow reaction detection system. This enzymatic reaction, involving enzyme activation as well as the transfer of a phosphate group from ATP to a peptide substrate, was used to prove the compatibility of a quantitative enzymatic assay in a continuous-flow real-time system (connected to MS). RESULTS Moreover (using internal standards), the critical parameter reaction temperature (including solution density variations depending on temperature) was studied in the continuous-flow mixing system. Furthermore, two substrates (malantide and kemptide), two enzyme types (catalytic subunit of PKA and complete PKA) and one inhibitor were tested to determine system robustness and long-term availability. Even spraying solutions that contained significant amount of MS contaminants (e.g. the polluted catalytic subunit) resulted in quantifiable MS signal intensities. Subsequent recalculations using the internal standards led to results representing the power of this application. CONCLUSIONS The presented methodology and the data evaluation with available Achroma freeware enable the direct coupling of biochemical assays with quantitative MS detection. Monitoring changes such as temperature, reaction time, inhibition, or compound concentrations can be observed quantitatively and thus enzymatic activity can be calculated.
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Affiliation(s)
- Michael Krappmann
- Zentrum für Forschung und Weiterbildung, Weihenstephan-Triesdorf - University of Applied Science, Am Staudengarten 7, D-85354, Freising-Weihenstephan, Germany
| | - Arjen R de Boer
- Faculty of Sciences, Division of Chemistry, Department of Analytical Chemistry and Applied Spectroscopy, Free University of Amsterdam, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
| | - Daniël R W Kool
- Faculty of Sciences, Division of Chemistry, Department of Analytical Chemistry and Applied Spectroscopy, Free University of Amsterdam, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
| | - Hubertus Irth
- Faculty of Sciences, Division of Chemistry, Department of Analytical Chemistry and Applied Spectroscopy, Free University of Amsterdam, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
| | - Thomas Letzel
- Faculty of Sciences, Division of Chemistry, Department of Analytical Chemistry and Applied Spectroscopy, Free University of Amsterdam, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands
- Analytical Research Group, Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 8, D-85748, Garching, Germany
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22
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Charter NW, Horecka J, Loh CY, Doan A, Wehrman T, Olson KR. Rapid, Antibody-Free Detection of Recombinant Proteins on Blots Using Enzyme Fragment Complementation. Methods Mol Biol 2016; 1314:51-61. [PMID: 26139254 DOI: 10.1007/978-1-4939-2718-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Alternative, antibody-free techniques to western analysis of protein blots can offer reduced assay times for routine analysis of expression of recombinant proteins. We have adapted the commercially available enzyme fragment complementation technology to provide a rapid protein detection method for protein blots based on significantly reducing the number of incubation and washing steps used in traditional approaches, and eliminating the requirement for antibodies. In this chapter, we highlight the use of this assay for measuring recombinant protein expressed in mammalian cells for a range of applications, including dot blot screening of large numbers of different cell samples, assessment of protein integrity through detection of degradation bands, and characterization of posttranslational protein modifications such as glycosylation.
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Affiliation(s)
- Neil W Charter
- DiscoveRx Corporation, 42501 Albrae St., Fremont, CA, 94538, USA,
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23
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Lv Y, Wu J, Wu P, Chen YZ, Tan Y, Tan C, Jiang Y. A sensitive polymeric dark quencher-based sensing platform for fluorescence “turn on” detection of proteins. RSC Adv 2016. [DOI: 10.1039/c6ra07310g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A sensing platform consisting of polymeric dark quenchers and oppositely charged probes was constructed for detection of proteins.
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Affiliation(s)
- Ying Lv
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Jiatao Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Pan Wu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yu Zong Chen
- Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics
- Shenzhen Kivita Innovative Drug Discovery Institute
- Shenzhen 518055
- P. R. China
| | - Ying Tan
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
| | - Chunyan Tan
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- P. R. China
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
| | - Yuyang Jiang
- The Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology
- Graduate School at Shenzhen
- Tsinghua University
- Shenzhen 518055
- P. R. China
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24
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Abstract
Compared to genomics or transcriptomics, proteomics is often regarded as an "emerging technology," i.e., as not having reached the same level of maturity. While the successful implementation of proteomics workflows and technology still requires significant levels of expertise and specialization, great strides have been made to make the technology more powerful, streamlined and accessible. In 2014, two landmark studies published the first draft versions of the human proteome.We aim to provide an introduction specifically into the background of mass spectrometry (MS)-based proteomics. Within the field, mass spectrometry has emerged as a core technology. Coupled to increasingly powerful separations and data processing and bioinformatics solution, it allows the quantitative analysis of whole proteomes within a matter of days, a timescale that has made global comparative proteome studies feasible at last. We present and discuss the basic concepts behind proteomics mass spectrometry and the accompanying topic of protein and peptide separations, with a focus on the properties of datasets emerging from such studies.
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25
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Lin TE, Cortés-Salazar F, Lesch A, Qiao L, Bondarenko A, Girault HH. Multiple scanning electrochemical microscopy mapping of tyrosinase in micro-contact printed fruit samples on polyvinylidene fluoride membrane. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.03.224] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Tabarés G, Hoesel W, Jung K. Two-Dimensional Electrophoresis in Prostate Cancer Research and Diagnostics. Lab Med 2015. [DOI: 10.1309/9tmwpme1q1mk3n39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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27
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Chiu CW, Chen HM, Wu TT, Shih YC, Huang KK, Tsai YF, Hsu YL, Chen SF. Differential proteomics of monosodium urate crystals-induced inflammatory response in dissected murine air pouch membranes by iTRAQ technology. Proteomics 2015. [PMID: 26205848 DOI: 10.1002/pmic.201400626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The precipitation of monosodium urate crystals within joints triggers an acute inflammatory reaction that is the root cause of gout. The inflammation induced by the injection of MSU crystals into the murine air pouch for 1, 3, and 5 h was examined by iTRAQ-based proteomic profiling. The iTRAQ-labeled peptides were fractionated by SCX, basic-RP or solution-IEF, followed by LC-MS/MS analysis. A total of 951 proteins were quantified from the total combined fractions. Among them, 317 proteins exhibited a differential expression, compared to that of the controls at one time point or more. The majority of the differentially expressed proteins were found in the sample after a 5-h MSU treatment. Western blot revealed that the expression levels of cathelin-related antimicrobial peptide and S100A9 were positively correlated with the time-course treated with MSU. Further analysis of GeneGO pathway demonstrated that these differentially expressed proteins are primarily related to the immune-related complement system and the tricarboxylic acid cycle. Moreover, seven genes from the TCA cycle were found to be significantly downregulated at the transcriptional level and its correlation with gout and possible therapeutic applications are worth further investigation. Last, we found that pyruvate carboxylation could be potential targets for antigout treatment.
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Affiliation(s)
- Chih-Wei Chiu
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
| | - Han-Min Chen
- Department of Life Science, Fu-Jen Catholic University, Taipei, Taiwan
| | - Tzong-Ta Wu
- Department of Life Science, Fu-Jen Catholic University, Taipei, Taiwan
| | - Ying-Chu Shih
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Kuo-Kuei Huang
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Ying-Fei Tsai
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Yi-Ling Hsu
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei 116, Taiwan
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28
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Morrison JM, John GH. Non-classical azoreductase secretion in Clostridium perfringens in response to sulfonated azo dye exposure. Anaerobe 2015; 34:34-43. [PMID: 25881497 DOI: 10.1016/j.anaerobe.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/27/2015] [Accepted: 04/12/2015] [Indexed: 01/06/2023]
Abstract
Clostridium perfringens, a strictly anaerobic microorganism and inhabitant of the human intestine, has been shown to produce an azoreductase enzyme (AzoC), an NADH-dependent flavin oxidoreductase. This enzyme reduces azo dyes into aromatic amines, which can be carcinogenic. A significant amount of work has been completed on the activity of AzoC. Despite this, much is still unknown, including whether azoreduction of these dyes occurs intracellularly or extracellulary. A physiological study of C. perfringens involving the effect of azo dye exposure was completed to answer this question. Through exposure studies, azo dyes were found to cause cytoplasmic protein release, including AzoC, from C. perfringens in dividing and non-dividing cells. Sulfonation (negative charge) of azo dyes proved to be the key to facilitating protein release of AzoC and was found to be azo-dye-concentration-dependent. Additionally, AzoC was found to localize to the Gram-positive periplasmic region. Using a ΔazoC knockout mutant, the presence of additional azoreductases in C. perfringens was suggested. These results support the notion that the azoreduction of these dyes may occur extracellularly for the commensal C. perfringens in the intestine.
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Affiliation(s)
- Jessica M Morrison
- Oklahoma State University, Department of Microbiology and Molecular Genetics, 307 Life Science East, Stillwater, OK 74078, USA.
| | - Gilbert H John
- Oklahoma State University, Department of Microbiology and Molecular Genetics, 307 Life Science East, Stillwater, OK 74078, USA
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29
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Hattan SJ, Du J, Parker KC. Bifunctional Glass Membrane Designed to Interface SDS-PAGE Separations of Proteins with the Detection of Peptides by Mass Spectrometry. Anal Chem 2015; 87:3685-93. [DOI: 10.1021/ac503980x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen J. Hattan
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
| | - Jie Du
- Toxikon Corporation, 15 Wiggins Avenue, Bedford, Massachusetts 01730, United States
| | - Kenneth C. Parker
- SimulTOF Systems, 60 Union Avenue, Sudbury, Massachusetts 01776, United States
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30
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Kumari S, Panda C, Mazumdar S, Sen Gupta S. A molecular Fe-complex as a catalyst probe for in-gel visual detection of proteins via signal amplification. Chem Commun (Camb) 2015; 51:15257-60. [DOI: 10.1039/c5cc04399a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the use of a molecular peroxidase mimic biuret FeTAML for chemoselective labeling of proteins and the subsequent visual detection (<0.1 pmoles) of the conjugate in a polyacrylamide gel by catalytic signal amplification.
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Affiliation(s)
- Sushma Kumari
- CReST Chemical Engineering Division
- CSIR-National Chemical Laboratory
- Pune-411008
- India
| | - Chakadola Panda
- CReST Chemical Engineering Division
- CSIR-National Chemical Laboratory
- Pune-411008
- India
| | - Shyamalava Mazumdar
- Division of Chemical Sciences
- Tata Institute of Fundamental Research
- Colaba
- India
| | - Sayam Sen Gupta
- CReST Chemical Engineering Division
- CSIR-National Chemical Laboratory
- Pune-411008
- India
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31
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OWEN CHRISTOPHERB, HUGHES DAVIDJ, BAQUERO-PEREZ BELINDA, BERNDT ANJA, SCHUMANN SOPHIE, JACKSON BRIANR, WHITEHOUSE ADRIAN. Utilising proteomic approaches to understand oncogenic human herpesviruses (Review). Mol Clin Oncol 2014; 2:891-903. [PMID: 25279171 PMCID: PMC4179824 DOI: 10.3892/mco.2014.341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/10/2014] [Indexed: 12/16/2022] Open
Abstract
The γ-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are successful pathogens, each infecting a large proportion of the human population. These viruses persist for the life of the host and may each contribute to a number of malignancies, for which there are currently no cures. Large-scale proteomic-based approaches provide an excellent means of increasing the collective understanding of the proteomes of these complex viruses and elucidating their numerous interactions within the infected host cell. These large-scale studies are important for the identification of the intricacies of viral infection and the development of novel therapeutics against these two important pathogens.
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Affiliation(s)
- CHRISTOPHER B. OWEN
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - DAVID J. HUGHES
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - BELINDA BAQUERO-PEREZ
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - ANJA BERNDT
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - SOPHIE SCHUMANN
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - BRIAN R. JACKSON
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - ADRIAN WHITEHOUSE
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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32
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Rocha AS, Santos FM, Monteiro JP, Castro-de-Sousa JP, Queiroz JA, Tomaz CT, Passarinha LA. Trends in proteomic analysis of human vitreous humor samples. Electrophoresis 2014; 35:2495-508. [DOI: 10.1002/elps.201400049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/02/2014] [Accepted: 05/02/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Ana S. Rocha
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Fátima M. Santos
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - João P. Monteiro
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| | - João P. Castro-de-Sousa
- Medical Sciences Department; Faculty of Health sciences; University of Beira Interior; Covilhã Portugal
- Ophthalmology Service; Leiria-Pombal Hospital Center; Pombal Portugal
| | - João A. Queiroz
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Cândida T. Tomaz
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Luís A. Passarinha
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Medical Sciences Department; Faculty of Health sciences; University of Beira Interior; Covilhã Portugal
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33
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Ahmed FE. Mining the oncoproteome and studying molecular interactions for biomarker development by 2DE, ChIP and SPR technologies. Expert Rev Proteomics 2014; 5:469-96. [DOI: 10.1586/14789450.5.3.469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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34
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Abstract
A major aim of present-day proteomics is to study changes in protein expression levels at a global level, ideally monitoring all proteins present in cells or tissue. Mass spectrometry is a well-respected technology in proteomics that is widely used for the identification of proteins. More recently, methodologies have been introduced showing that mass spectrometry can also be used for protein quantification. This article reviews various mass spectrometry-based technologies in quantitative proteomics, highlighting several interesting applications in areas ranging from cell biology to clinical applications.
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Affiliation(s)
- Albert J R Heck
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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Govender P, Baugh JA, Pennington SR, Dunn MJ, Donnelly SC. Role of proteomics in the investigation of pulmonary fibrosis. Expert Rev Proteomics 2014; 4:379-88. [PMID: 17552922 DOI: 10.1586/14789450.4.3.379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pulmonary fibrosis arises as a consequence of aberrant remodeling and defective repair mechanisms within the lung. This destructive process is the cause of much of the morbidity and mortality in many pulmonary disorders. Unfortunately, therapeutic options are limited. A significant advancement in the management of patients with pulmonary fibrosis would be the identification of biomarkers for diagnosis, prognosis and prediction of patient response to therapy. Bronchoalveolar lavage is an ideal tissue target for the discovery of these potential biomarkers in pulmonary fibrosis. Integrative approaches using both gel- and mass spectrometry-based proteomic workflows will allow full coverage of this complex proteome, thereby unlocking this potential information as a clinical tool to aid diagnosis and guide treatment for individual patients with pulmonary fibrosis.
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Affiliation(s)
- Praveen Govender
- University College Dublin, School of Medicine & Medical Science, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
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Panfoli I, Calzia D, Santucci L, Ravera S, Bruschi M, Candiano G. A blue dive: from ‘blue fingers’ to ‘blue silver’. A comparative overview of staining methods for in-gel proteomics. Expert Rev Proteomics 2014; 9:627-34. [DOI: 10.1586/epr.12.63] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Abstract
The scope of the current paper is to review existing and potential applications of proteomic analysis to aging research. The focus will lie on the unique opportunities of high-throughput studies for uncovering specific alterations in protein expression, protein complexes or protein modifications caused by biological aging. The result of such studies will outline aging phenotypes and potentially indicate pathways involved in the pathogenesis of age-associated disfunctions. Specific attention is paid to the illustrations of successful applications of proteomic technologies and potential applications of new proteomic concepts to biogerontological studies.
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Affiliation(s)
- Victor S Sharov
- University of Kansas, Pharmaceutical Chemistry Department, Lawrence, KS 66047, USA.
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Cieniewski-Bernard C, Dupont E, Deracinois B, Lambert M, Bastide B. Multiplexed Detection of O-GlcNAcome, Phosphoproteome, and Whole Proteome within the Same Gel. Front Endocrinol (Lausanne) 2014; 5:184. [PMID: 25389416 PMCID: PMC4211549 DOI: 10.3389/fendo.2014.00184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/11/2014] [Indexed: 11/18/2022] Open
Abstract
The cellular diversity of proteins results in part from their post-translational modifications. Among all of them, the O-GlcNAcylation is an atypical glycosylation, more similar to phosphorylation than classical glycosylations. Highly dynamic, reversible, and exclusively localized on cytosolic, nuclear, and mitochondrial proteins, O-GlcNAcylation is known to regulate almost all if not all cellular processes. Fundamental for the cell life, O-GlcNAcylation abnormalities are involved in the etiology of several inherited diseases. Assessing to O-GlcNAcylation pattern will permit to get relevant data about the role of O-GlcNAcylation in cell physiology. To get understanding about the role of O-GlcNAcylation, as also considering its interplay with phosphorylation, the O-GlcNAc profiling remains a real challenge for the community of proteomists/glycoproteomists. The development of multiplexed proteomics based on fluorescent detection of proteins permits to go further in the understanding of the proteome complexity. We propose herein a multiplexed proteomic strategy to detect O-GlcNAcylated proteins, phosphoproteins, and the whole proteome within the same bidimensional gel. In particular, we investigated the phosphoproteome through the ProQ Diamond staining, while the whole proteome was visualized through Sypro Ruby staining, or after the labeling of proteins with a T-Dye fluorophore. The O-GlcNAcome was revealed by the way of the Click chemistry and the azide-alkyne cycloaddition of a fluorophore on GlcNAc moieties. This method permits, after sequential image acquisition, the direct in-gel detection of O-GlcNAcome, phosphoproteome, and whole proteome.
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Affiliation(s)
- Caroline Cieniewski-Bernard
- Université Lille Nord de France, Lille, France
- EA4488, APMS (Physical activity muscle and health), URePSSS, Université de Lille 1, Villeneuve d’Ascq, France
- *Correspondence: Caroline Cieniewski-Bernard, EA4488 Laboratoire Activité Physique, Muscle et Santé, IFR114, Biology Department, Université de Lille 1, Villeneuve d’Ascq 59655, France e-mail:
| | - Erwan Dupont
- Université Lille Nord de France, Lille, France
- EA4488, APMS (Physical activity muscle and health), URePSSS, Université de Lille 1, Villeneuve d’Ascq, France
| | - Barbara Deracinois
- Université Lille Nord de France, Lille, France
- EA4488, APMS (Physical activity muscle and health), URePSSS, Université de Lille 1, Villeneuve d’Ascq, France
| | - Matthias Lambert
- Université Lille Nord de France, Lille, France
- EA4488, APMS (Physical activity muscle and health), URePSSS, Université de Lille 1, Villeneuve d’Ascq, France
| | - Bruno Bastide
- Université Lille Nord de France, Lille, France
- EA4488, APMS (Physical activity muscle and health), URePSSS, Université de Lille 1, Villeneuve d’Ascq, France
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Ni MW, Ye WJ, Cong WT, Hong GY, Zhu ZX, Duan YM, Zhou X, Jin LT. Fluorescent staining of protein in sodium dodecyl sulfate polyacrylamide gels by salicylaldehyde azine. Electrophoresis 2013; 34:3171-9. [PMID: 24105885 DOI: 10.1002/elps.201300241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 11/07/2022]
Abstract
As a non-covalent fluorescence probe, in this study, salicylaldehyde azine (SA) was introduced as a sensitive fluorescence-based dye for detecting proteins both in 1-D and 2-D polyacrylamide electrophoresis gels. Down to 0.2 ng of single protein band could be detected within 1 h, which similars to that of glutaraldehyde (GA)-silver stain, but approximately four times higher than that of SYPRO Ruby fluorescent stain. Furthermore, comparative analysis of the MS compatibility of SA stain with SYPRO Ruby stain indicated that SA stain is compatible with the downstream of protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Additionally, the probable mechanism of the SA stain was investigated by molecular docking. The results demonstrated that the interaction between SA and protein was mainly contributed by hydrogen bonding and hydrophobic forces.
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Affiliation(s)
- Mao-Wei Ni
- Zhejiang Provincial Key Laboratory of Biopharmaceuticals, Wenzhou Medical College, Wenzhou, Zhejiang, P. R. China
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Identification of cellular proteome using two-dimensional difference gel electrophoresis in ST cells infected with transmissible gastroenteritis coronavirus. Proteome Sci 2013; 11:31. [PMID: 23855489 PMCID: PMC3734006 DOI: 10.1186/1477-5956-11-31] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/23/2013] [Indexed: 01/05/2023] Open
Abstract
Background Transmissible gastroenteritis coronavirus (TGEV) is an enteropathogenic coronavirus that causes diarrhea in pigs, which is correlated with high morbidity and mortality in suckling piglets. Information remains limited about the comparative protein expression of host cells in response to TGEV infection. In this study, cellular protein response to TGEV infection in swine testes (ST) cells was analyzed, using the proteomic method of two-dimensional difference gel electrophoresis (2D DIGE) coupled with MALDI-TOF-TOF/MS identification. Results 33 differentially expressed protein spots, of which 23 were up-regulated and 10 were down-regulated were identified. All the protein spots were successfully identified. The identified proteins were involved in the regulation of essential processes such as cellular structure and integrity, RNA processing, protein biosynthesis and modification, vesicle transport, signal transduction, and the mitochondrial pathway. Western blot analysis was used to validate the changes of alpha tubulin, keratin 19, and prohibitin during TGEV infection. Conclusions To our knowledge, we have performed the first analysis of the proteomic changes in host cell during TGEV infection. 17 altered cellular proteins that differentially expressed in TGEV infection were identified. The present study provides protein-related information that should be useful for understanding the host cell response to TGEV infection and the underlying mechanism of TGEV replication and pathogenicity.
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Drews O. High-resolution separation of cardiovascular proteomes: two-dimensional electrophoresis and liquid chromatography. ACTA ACUST UNITED AC 2013; 5:592. [PMID: 23074339 DOI: 10.1161/circgenetics.110.958637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Oliver Drews
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany.
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2D gels still have a niche in proteomics. J Proteomics 2013; 88:4-13. [PMID: 23353020 DOI: 10.1016/j.jprot.2013.01.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 01/26/2023]
Abstract
With the rapid advance of MS-based proteomics one might think that 2D gel-based proteomics is dead. This is far from the truth. Current research has shown that there are still a number of places in the field of protein and molecular biology where 2D gels still play a leading role. The aim of this review is to highlight some of these applications. Examples from our own research as well as from other published works are used to illustrate the 2D gel driven research in the areas of: 1) de novo sequencing and protein identification from organisms with no or incomplete genome sequences available; 2) alternative detection methods for modification specific proteomics; 3) identification of protein isoforms and modified proteins. With an example of the glycoprotein TIMP-1 protein we illustrate the unique properties of 2D gels for the separation and characterisation of multiply modified proteins. We also show that careful analysis of experimental and theoretical protein mass and pI can lead to the identification of unanticipated protein variants modified by for example proteolytic cleavage. Together this shows that there is an important niche for 2D gel-based proteomics, which compliments traditional LC-MS techniques for specific protein research purposes.
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Maron BA, Tang SS, Loscalzo J. S-nitrosothiols and the S-nitrosoproteome of the cardiovascular system. Antioxid Redox Signal 2013; 18:270-87. [PMID: 22770551 PMCID: PMC3518544 DOI: 10.1089/ars.2012.4744] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 06/26/2012] [Accepted: 07/08/2012] [Indexed: 12/13/2022]
Abstract
SIGNIFICANCE Since their discovery in the early 1990's, S-nitrosylated proteins have been increasingly recognized as important determinants of many biochemical processes. Specifically, S-nitrosothiols in the cardiovascular system exert many actions, including promoting vasodilation, inhibiting platelet aggregation, and regulating Ca(2+) channel function that influences myocyte contractility and electrophysiologic stability. RECENT ADVANCES Contemporary developments in liquid chromatography-mass spectrometry methods, the development of biotin- and His-tag switch assays, and the availability of cyanide dye-labeling for S-nitrosothiol detection in vitro have increased significantly the identification of a number of cardiovascular protein targets of S-nitrosylation in vivo. CRITICAL ISSUES Recent analyses using modern S-nitrosothiol detection techniques have revealed the mechanistic significance of S-nitrosylation to the pathophysiology of numerous cardiovascular diseases, including essential hypertension, pulmonary hypertension, ischemic heart disease, stroke, and congestive heart failure, among others. FUTURE DIRECTIONS Despite enhanced insight into S-nitrosothiol biochemistry, translating these advances into beneficial pharmacotherapies for patients with cardiovascular diseases remains a primary as-yet unmet goal for investigators within the field.
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Affiliation(s)
- Bradley A Maron
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Menckhoff L, Mielke-Ehret N, Buck F, Vuletić M, Lüthje S. Plasma membrane-associated malate dehydrogenase of maize (Zea mays L.) roots: native versus recombinant protein. J Proteomics 2013; 80:66-77. [PMID: 23313174 DOI: 10.1016/j.jprot.2012.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/21/2012] [Accepted: 12/29/2012] [Indexed: 11/28/2022]
Abstract
Malate dehydrogenase (MDH, EC 1.1.1.37) is involved in several cellular processes including plant development, nutrient uptake and oxidative stress. Evidence for a plasma membrane-associated MDH has been presented for maize (Zea mays L.) roots. In the present study isoenzymes of MDH were purified from highly enriched plasma membrane preparations of maize and compared with soluble isoenzymes (Km, pH optima, pI and molecular masses). Modified SDS-PAGE analyses revealed monomers of 41 kDa for membrane-associated MDH, whereas monomers (35 kDa) and dimers (70 kDa) were detected for soluble isoenzymes. Membrane-associated MDH of cauliflower (Brassica oleracea L.) inflorescences and spinach (Spinacia oleracea L.) leaves showed molecular masses similar to the membrane-associated MDH of maize. The specific maize MDH involved was identified by mass spectrometry (ESI-QTOF-MS/MS, MALDI-TOF-MS). The corresponding gene was cloned and the protein was characterised after heterologous expression in Escherichia coli. Enzyme kinetics and properties of the recombinant and native proteins were compared. The function of thiol groups and the presence of disulphide bonds were analysed by the effect of N-ethylmaleimide, diagonal electrophoresis and labelling. Semiquantitative reverse transcription polymerase chain reaction of maize root transcripts demonstrated a constitutive expression of the gene encoding plasma membrane-associated MDH.
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Affiliation(s)
- Ljiljana Menckhoff
- University of Hamburg, Biocentre Klein Flottbek and Botanical Garden, Plant Physiology, Ohnhorststraße 18, D-22609 Hamburg, Germany
| | - Nicole Mielke-Ehret
- University of Hamburg, Biocentre Klein Flottbek and Botanical Garden, Plant Physiology, Ohnhorststraße 18, D-22609 Hamburg, Germany
| | - Friedrich Buck
- University Hospital Eppendorf, Institute of Clinical Chemistry, Campus Science, Martinistrasse 52, D-20246 Hamburg, Germany
| | - Mirjana Vuletić
- Maize Research Institute, Zemun Polje, Slobodana Bajića 1, 11185 Belgrade, Serbia
| | - Sabine Lüthje
- University of Hamburg, Biocentre Klein Flottbek and Botanical Garden, Plant Physiology, Ohnhorststraße 18, D-22609 Hamburg, Germany.
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D'Amici GM, Timperio AM, Rinalducci S, Zolla L. Combinatorial peptide ligand libraries to discover liver disease biomarkers in plasma samples. Methods Mol Biol 2012; 909:311-9. [PMID: 22903724 DOI: 10.1007/978-1-61779-959-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
High-abundance proteins present in blood plasma make the detection of low-abundance proteins extremely difficult by proteomics technology. Hexapeptide combinatorial ligand libraries can be used to investigate the hidden proteome in depth. Here we describe how liver disease biomarkers can be successfully discovered in blood plasma by two main steps: preparative methods that reduce the dynamic range of protein concentration, and analytic methods that allow resolution of proteins. Thus, blood plasma from hepatitis B virus infected patients were treated with ProteoMiner™ enrichment kit and analyzed by two dimensional gel electrophoresis and mass spectrometry. This approach allowed us to identify plasma gelsolin as possible candidate biomarker for hepatitis B-associated liver cirrhosis.
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Affiliation(s)
- Gian Maria D'Amici
- Department of Environmental Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, Italy
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Hines HB. Microbial proteomics using mass spectrometry. Methods Mol Biol 2012; 881:159-86. [PMID: 22639214 DOI: 10.1007/978-1-61779-827-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteomic analyses involve a series of intricate, interdependent steps involving approaches and technical issues that must be fully coordinated to obtain the optimal amount of required information about the test subject. Fortunately, many of these steps are common to most test subjects, requiring only modifications to or, in some cases, substitution of some of the steps to ensure they are relevant to the desired objective of a study. This fortunate occurrence creates an essential core of proteomic approaches and techniques that are consistently available for most studies, regardless of test subject. In this chapter, an overview of some of these core approaches, techniques, and mass spectrometric instrumentation is given, while indicating how such steps are useful for and applied to bacterial investigations. To exemplify how such proteomic concepts and techniques are applicable to bacterial investigations, a practical, quantitative method useful for bacterial proteomic analysis is presented with a discussion of possibilities, pitfalls, and some emerging technology to provide a compilation of information from the diverse literature that is intermingled with experimental experience.
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Affiliation(s)
- Harry B Hines
- Integrated Toxicology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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Sandu ICA, Schäfer S, Magrini D, Bracci S, Roque CA. Cross-section and staining-based techniques for investigating organic materials in painted and polychrome works of art: a review. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2012; 18:860-875. [PMID: 22849802 DOI: 10.1017/s1431927612000554] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The article presents a review of the use of cross-section and staining techniques for investigating natural organic materials (mainly proteinaceous and oil-based binders/varnishes) in painted and polychrome artworks, considering the requirements of conservation practice and routine diagnostics. The reviewed literature calls attention to the importance of using cross sections to prepare samples for optical microscopy and to different properties of embedding resins; the most appropriate instrumental conditions for optical microscopy; and the advantages and disadvantages of the most common staining techniques. A few case studies were selected to illustrate the use of autofluorescence (intrinsic fluorescence) and induced fluorescence (using specific staining tests and fluorophore-labeled antibodies) for mapping and identifying organic paint materials in cross sections. New directions of research in cross-section analyses and fluorescence-based techniques for the identification and mapping of artistic materials are presented. The complementary use of different stains on the same cross section, further exploration of intrinsic and induced fluorescence of aged versus fresh materials, and applicability of cross-section observation and staining as complementary methods for assessing the effectiveness of restoration treatments, such as cleaning and consolidation, are discussed in the last section of the article.
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Affiliation(s)
- Irina Crina Anca Sandu
- REQUIMTE, Departamento de Conservação e Restauro, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
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Eyckmans M, Benoot D, Van Raemdonck GA, Zegels G, Van Ostade XW, Witters E, Blust R, De Boeck G. Comparative proteomics of copper exposure and toxicity in rainbow trout, common carp and gibel carp. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:220-32. [DOI: 10.1016/j.cbd.2012.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/09/2012] [Accepted: 03/13/2012] [Indexed: 01/30/2023]
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