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Srivastava S, Jayaswal N, Kumar S, Sharma PK, Behl T, Khalid A, Mohan S, Najmi A, Zoghebi K, Alhazmi HA. Unveiling the potential of proteomic and genetic signatures for precision therapeutics in lung cancer management. Cell Signal 2024; 113:110932. [PMID: 37866667 DOI: 10.1016/j.cellsig.2023.110932] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Lung cancer's enduring global significance necessitates ongoing advancements in diagnostics and therapeutics. Recent spotlight on proteomic and genetic biomarker research offers a promising avenue for understanding lung cancer biology and guiding treatments. This review elucidates genetic and proteomic lung cancer biomarker progress and their treatment implications. Technological strides in mass spectrometry-based proteomics and next-generation sequencing enable pinpointing of genetic abnormalities and abnormal protein expressions, furnishing vital data for precise diagnosis, patient classification, and customized treatments. Biomarker-driven personalized medicine yields substantial treatment improvements, elevating survival rates and minimizing adverse effects. Integrating omics data (genomics, proteomics, etc.) enhances understanding of lung cancer's intricate biological milieu, identifying novel treatment targets and biomarkers, fostering precision medicine. Liquid biopsies, non-invasive tools for real-time treatment monitoring and early resistance detection, gain popularity, promising enhanced management and personalized therapy. Despite advancements, biomarker repeatability and validation challenges persist, necessitating interdisciplinary efforts and large-scale clinical trials. Integrating artificial intelligence and machine learning aids analyzing vast omics datasets and predicting treatment responses. Single-cell omics reveal cellular connections and intratumoral heterogeneity, valuable for combination treatments. Biomarkers enable accurate diagnosis, tailored medicines, and treatment response tracking, significantly impacting personalized lung cancer care. This approach spurs patient-centered trials, empowering active patient engagement. Lung cancer proteomic and genetic biomarkers illuminate disease biology and treatment prospects. Progressing towards individualized efficient therapies is imminent, alleviating lung cancer's burden through ongoing research, omics integration, and technological strides.
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Affiliation(s)
- Shriyansh Srivastava
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), Sector 3 Pushp Vihar, New Delhi 110017, India; Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Nandani Jayaswal
- Accurate College of Pharmacy, 49, Knowledge Park-III, Greater Noida, UP, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), Sector 3 Pushp Vihar, New Delhi 110017, India
| | - Pramod Kumar Sharma
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Sahibzada Ajit Singh Nagar, Punjab, India.
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box: 2424, Khartoum 11111, Sudan
| | - Syam Mohan
- Substance Abuse and Toxicology Research Centre, Jazan University, Jazan 45142, Saudi Arabia; Center for Global Health Research, Saveetha Medical College, and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; School of Health Sciences, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India.
| | - Asim Najmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| | - Khalid Zoghebi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
| | - Hassan A Alhazmi
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, P.O. Box 114, Jazan, Saudi Arabia
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Brajkovic S, Rugen N, Agius C, Berner N, Eckert S, Sakhteman A, Schwechheimer C, Kuster B. Getting Ready for Large-Scale Proteomics in Crop Plants. Nutrients 2023; 15:nu15030783. [PMID: 36771489 PMCID: PMC9921824 DOI: 10.3390/nu15030783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.
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Affiliation(s)
- Sarah Brajkovic
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nils Rugen
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Institute of Plant Genetics, Leibniz University Hannover, 30167 Hannover, Germany
| | - Carlos Agius
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Nicola Berner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Claus Schwechheimer
- Chair of Plant Systems Biology, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354 Freising, Germany
- Correspondence:
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Du M, Hou Z, Liu L, Xuan Y, Chen X, Fan L, Li Z, Xu B. 1Progress, applications, challenges and prospects of protein purification technology. Front Bioeng Biotechnol 2022; 10:1028691. [PMID: 36561042 PMCID: PMC9763899 DOI: 10.3389/fbioe.2022.1028691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Protein is one of the most important biological macromolecules in life, which plays a vital role in cell growth, development, movement, heredity, reproduction and other life activities. High quality isolation and purification is an essential step in the study of the structure and function of target proteins. Therefore, the development of protein purification technologies has great theoretical and practical significance in exploring the laws of life activities and guiding production practice. Up to now, there is no forthcoming method to extract any proteins from a complex system, and the field of protein purification still faces significant opportunities and challenges. Conventional protein purification generally includes three steps: pretreatment, rough fractionation, and fine fractionation. Each of the steps will significantly affect the purity, yield and the activity of target proteins. The present review focuses on the principle and process of protein purification, recent advances, and the applications of these technologies in the life and health industry as well as their far-reaching impact, so as to promote the research of protein structure and function, drug development and precision medicine, and bring new insights to researchers in related fields.
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Affiliation(s)
- Miao Du
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Zhuru Hou
- Science and Technology Centre, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
| | - Yan Xuan
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Xiaocong Chen
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Lei Fan
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Zhuoxi Li
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, China
| | - Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China,Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, China,*Correspondence: Ling Liu, ; Benjin Xu,
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Brevé TG, Filius M, Weerdenburg S, van der Griend SJ, Groeneveld TP, Denkova AG, Eelkema R. Light sensitive phenacyl crosslinked dextran hydrogels for controlled delivery. Chemistry 2021; 28:e202103523. [PMID: 34939694 PMCID: PMC9306828 DOI: 10.1002/chem.202103523] [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: 09/28/2021] [Indexed: 11/16/2022]
Abstract
Stimuli‐responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agents is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered by using Cerenkov luminescence, we have developed polymer hydrogels that can release bovine serum albumin and immunoglobulin G by using light (254 nm–375 nm) as a trigger. We describe the synthesis and photochemical characterization of two light sensitive phenacyl bis‐azide crosslinkers that are used to prepare transparent self‐supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an π‐extended phenacyl core, resulting in a high quantum yield (14 %) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein‐loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Cerenkov‐triggered release is as yet inconclusive due to unexpected side‐reactivity. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release.
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Affiliation(s)
- Tobias G Brevé
- Delft University of Technology: Technische Universiteit Delft, Department of Chemical Engineering, NETHERLANDS
| | - Mike Filius
- Delft University of Technology: Technische Universiteit Delft, Department of Bionanoscience, NETHERLANDS
| | - Sven Weerdenburg
- Delft University of Technology: Technische Universiteit Delft, Department of Chemical engineering, NETHERLANDS
| | - Stefan J van der Griend
- Delft University of Technology: Technische Universiteit Delft, Department of Chemical Engineering, NETHERLANDS
| | - Tim P Groeneveld
- Delft University of Technology: Technische Universiteit Delft, Department of Chemical Engineering, NETHERLANDS
| | - Antonia G Denkova
- Delft University of Technology: Technische Universiteit Delft, Department of Radiation Science and Technology, NETHERLANDS
| | - Rienk Eelkema
- Delft University of Technology: Technische Universiteit Delft, Department of Chemical Engineering, van der Maasweg 9, 2629HZ, Delft, NETHERLANDS
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Fei J, Wang YS, Cheng H, Su YB. An efficient protein extraction method applied to mangrove plant Kandelia obovata leaves for proteomic analysis. PLANT METHODS 2021; 17:100. [PMID: 34587982 PMCID: PMC8482605 DOI: 10.1186/s13007-021-00800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Mangroves plants, an important wetland system in the intertidal shores, play a vital role in estuarine ecosystems. However, there is a lack of a very effective method for extracting protein from mangrove plants for proteomic analysis. Here, we evaluated the efficiency of three different protein extraction methods for proteomic analysis of total proteins obtained from mangrove plant Kandelia obovata leaves. RESULTS The protein yield of the phenol-based (Phe-B) method (4.47 mg/g) was significantly higher than the yields of the traditional phenol (Phe) method (2.38 mg/g) and trichloroacetic acid-acetone (TCA-A) method (1.15 mg/g). The Phe-B method produced better two-dimensional electrophoresis (2-DE) protein patterns with high reproducibility regarding the number, abundance and coverage of protein spots. The 2-DE gels showed that 847, 650 and 213 unique protein spots were separated from the total K. obovata leaf proteins extracted by the Phe-B, Phe and TCA-A methods, respectively. Fourteen pairs of protein spots were randomly selected from 2-DE gels of Phe- and Phe-B- extracted proteins for identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) technique, and the results of three pairs were consistent. Further, oxygen evolving enhancer protein and elongation factor Tu could be observed in the 2-DE gels of Phe and Phe-B methods, but could only be detected in the results of the Phe-B methods, showing that Phe-B method might be the optimized choice for proteomic analysis. CONCLUSION Our data provides an improved Phe-B method for protein extraction of K. obovata and other mangrove plant tissues which is rich in polysaccharides and polyphenols. This study might be expected to be used for proteomic analysis in other recalcitrant plants.
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Affiliation(s)
- Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Yu-Bin Su
- College of Life Science and Technology, Jinan University, Guangzhou, 510632 China
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Abstract
The use of antibodies in the treatment of lung diseases is of increasing interest especially as the search for COVID-19 therapies has unfolded. Historically, the use of antibody therapy was based on multiple targets including receptors involved in local hyper-reactivity in asthma, viruses and micro-organisms involved in a variety of pulmonary infectious disease. Generally, protein therapeutics pose challenges with respect to formulation and delivery to retain activity and assure therapy. The specificity of antibodies amplifies the need for attention to molecular integrity not only in formulation but also during aerosol delivery for pulmonary administration. Drug product development can be viewed from considerations of route of administration, dosage form, quality, and performance measures. Nebulizers and dry powder inhalers have been used to deliver protein therapeutics and each has its advantages that should be matched to the needs of the drug and the disease. This review offers insight into quality and performance barriers and the opportunities that arise from meeting them effectively.
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Impact of Extraction Method on the Detection of Quality Biomarkers in Normal vs. DFD Meat. Foods 2021; 10:foods10051097. [PMID: 34063396 PMCID: PMC8156798 DOI: 10.3390/foods10051097] [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: 04/06/2021] [Revised: 04/20/2021] [Accepted: 05/13/2021] [Indexed: 11/17/2022] Open
Abstract
The objective of this work was to demonstrate how the extraction method affects the reliability of biomarker detection and how this detection depends on the biomarker location within the cell compartment. Different extraction methods were used to study the sarcoplasmic and myofibrillar fractions of the Longissimus thoracis et lumborum muscle of young bulls of the Asturiana de los Valles breed in two quality grades, standard (Control) or dark, firm, and dry (DFD) meat. Protein extractability and the expression of some of the main meat quality biomarkers—oxidative status (lipoperoxidation (LPO) and catalase activity (CAT)), proteome (SDS-PAGE electrophoretic pattern), and cell stress protein (Hsp70)—were analyzed. In the sarcoplasmic fraction, buffers containing Triton X-100 showed significantly higher protein extractability, LPO, and higher intensity of high-molecular-weight protein bands, whereas the TES buffer was more sensitive to distinguishing differences in the protein pattern between the Control and DFD meat. In the myofibrillar fraction, samples extracted with the lysis buffer showed significantly higher protein extractability, whereas samples extracted with the non-denaturing buffer showed higher results for LPO, CAT, and Hsp70, and higher-intensity bands in the electrophoretic pattern. These findings highlight the need for the careful selection of the extraction method used to analyze the different biomarkers considering their cellular location to adapt the extractive process.
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Sedaghat B, Hajjaran H, Sadjjadi FS, Heidari S, Sadjjadi SM. Proteomic characterization of hydatid cyst fluid: two-dimensional electrophoresis (2-DE) setup through optimizing protein extraction. BMC Res Notes 2021; 14:22. [PMID: 33430965 PMCID: PMC7802163 DOI: 10.1186/s13104-020-05433-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/24/2020] [Indexed: 12/04/2022] Open
Abstract
Objective Proper characterization of hydatid cyst fluid (HCF) is useful for diagnostic and follow up purposes of cystic echinococcosis/hydatidosis, which is an important zoonotic disease. In this regard, proteomics methods are very helpful. The present study was conducted to compare three protein extraction methods for HCF collected from sheep liver hydatid cysts including, trichloracetic acid (TCA)/Acetone precipitation, TCA/Acetone along with dialysis, and combination of 2-D Clean-up Kit and dialysis followed by two-dimensional electrophoresis (2-DE), to achieve better resolution in the proteomic characterization of HCF proteins. Results The 2-DE of TCA/Acetone products showed a lot of smears in the background of gels; TCA/Acetone with dialysis showed greatly reduced smears while the 2-D Clean-up Kit together with dialysis showed sharp spots and least smears. Three-dimensional images of separated spots created by Progenesis SameSpots software showed the best result was achieved by 2-D Clean-up Kit and dialysis.
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Affiliation(s)
- Bahareh Sedaghat
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Homa Hajjaran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Fatemeh Sadat Sadjjadi
- Faculty of Paramedical Sciences, Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudabeh Heidari
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mahmoud Sadjjadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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Pérez-Rodriguez S, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis of Chinese hamster ovary cell homogenates. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Cunha EN, de Souza MFB, Lanza DCF, Lima JPMS. A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum. PLoS One 2020; 15:e0240536. [PMID: 33057447 PMCID: PMC7561130 DOI: 10.1371/journal.pone.0240536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.
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Affiliation(s)
- Eduardo Nogueira Cunha
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
| | - Maria Fernanda Bezerra de Souza
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - Daniel Carlos Ferreira Lanza
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - João Paulo Matos Santos Lima
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Natal, Brazil
- * E-mail:
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Blundon M, Ganesan V, Redler B, Van PT, Minden JS. Two-Dimensional Difference Gel Electrophoresis. Methods Mol Biol 2019; 1855:229-247. [PMID: 30426421 DOI: 10.1007/978-1-4939-8793-1_20] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Two-dimensional difference gel electrophoresis (2D DIGE) is a modified form of 2D electrophoresis (2D E) that allows one to compare two or three protein samples simultaneously on the same gel. The proteins in each sample are covalently tagged with different color fluorescent dyes that are designed to have no effect on the relative migration of proteins during electrophoresis. Proteins that are common to the samples appear as "spots" with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. With conventional imaging systems, DIGE is capable of reliably detecting as little as 0.2 fmol of protein, and protein differences down to ± 15%, over a ~10,000-fold protein concentration range. DIGE combined with digital image analysis therefore greatly improves the statistical assessment of proteome variation. Here we describe a protocol for conducting DIGE experiments, which takes 2-3 days to complete. We have further improved upon 2D DIGE by introducing in-gel equilibration to improve protein retention during transfer between the first and second dimensions of electrophoresis and by developing a fluorescent gel imaging system with a millionfold dynamic range.
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Affiliation(s)
- Malachi Blundon
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Vinitha Ganesan
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Brendan Redler
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Phu T Van
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan S Minden
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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Gel electrophoresis-based plant proteomics: Past, present, and future. Happy 10th anniversary Journal of Proteomics! J Proteomics 2019; 198:1-10. [DOI: 10.1016/j.jprot.2018.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/21/2018] [Accepted: 08/26/2018] [Indexed: 02/03/2023]
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13
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Niu L, Zhang H, Wu Z, Wang Y, Liu H, Wu X, Wang W. Modified TCA/acetone precipitation of plant proteins for proteomic analysis. PLoS One 2018; 13:e0202238. [PMID: 30557402 PMCID: PMC6296544 DOI: 10.1371/journal.pone.0202238] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Protein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hang Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhaokun Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yibo Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Liu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- * E-mail: (WW); (HL)
| | - Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- * E-mail: (WW); (HL)
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Methods for Extraction of Muscle Proteins from Meat and Fish Using Denaturing and Nondenaturing Solutions. J FOOD QUALITY 2018. [DOI: 10.1155/2018/8478471] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The objective of the present study was to test two extraction methods including solutions with different ionic strengths on the extraction and separation of the myofibrillar proteins from meat and fish muscles of different species. Meat samples from longissimus thoracis muscle of beef and lamb, pectoralis major muscle of chicken, and dorsal white muscle of fish from sole (Solea solea), European hake (Merluccius merluccius), and sea bass (Dicentrarchus labrax) were analyzed. The extraction method using nondenaturing solution led to a major extraction of high molecular-weight proteins as myosin heavy chain, α-actinin, and desmin; on the contrary, the denaturing method provided a good protein extractability of proteins and fragments with low molecular-weight as actin, troponin-T, tropomyosin, and myosin light chain 1 and 2 proteins for the most meat and fish samples. The nondenaturing extraction method showed several advantages resulting in time and labour saving and in minimizing the use of toxic and polluting agents.
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15
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Li Z, Luo R, Zhang Y, Yan X, Pang Q. Effective protein extraction from mycelium and fruiting body of Auricularia auricula for proteomics studies. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2018. [DOI: 10.1080/10942912.2018.1499111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ziwei Li
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Rui Luo
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Yuexin Zhang
- Heilongjiang Forest By-product and Speciality Institute, Mudanjiang, Heilongjiang, China
| | - Xiufeng Yan
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Harbin, Heilongjiang, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, Heilongjiang, China
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16
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Proteomic features of delayed ocular symptoms caused by exposure to sulfur mustard: As studied by protein profiling of corneal epithelium. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1445-1454. [DOI: 10.1016/j.bbapap.2017.08.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 08/11/2017] [Accepted: 08/31/2017] [Indexed: 12/21/2022]
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17
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Schulte F, Hardt M, Niehaus K. A robust protocol for the isolation of cellular proteins from Xanthomonas campestris to analyze the methionine effect in 2D-gel experiments. Electrophoresis 2017; 38:2603-2609. [PMID: 28605028 DOI: 10.1002/elps.201700064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 11/06/2022]
Abstract
Two-dimensional PAGE (2D-PAGE) is a key technique for the separation of complex protein samples to survey the protein inventory of prokaryotic microorganisms. Although the preparation of proteins is a critical step in 2D gel experiments, its effect on the outcome of proteome data is often underestimated. In this work, we show that the choice of protein isolation method can have a profound impact on the quality of 2D gels of protein extracts from prokaryotes. Based on Xanthomonas campestris, a commercially relevant producer of the thickening agent xanthan, we validated a phenol extraction protocol for the purification of bacterial proteins that provides excellent 2D gel separation. As a proof of concept, this method was used to study the effect of methionine-a medium compound that reduces the xanthan output of industrial fermentations-on the cellular proteome of Xanthomonas. The detection of nine regulated proteins associated with sulfur metabolism (Cgl, CysI, CysJ, CysK, MetH1, MetY) and sugar nucleotide biosynthesis (Pgi, Ugd, XanA) proved the efficiency of phenol extraction for the screening of statistically significant abundance changes in 2D gel spots and MALDI-TOF-MS based identification in bacteria. Since this method is very robust, it may be useful for the study of other prokaryotes that are relevant in industrial biotechnology.
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Affiliation(s)
- Fabian Schulte
- Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA
| | - Markus Hardt
- Department of Applied Oral Sciences, The Forsyth Institute, Cambridge, MA, USA.,Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA.,Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, NY, USA
| | - Karsten Niehaus
- Fakultät für Biologie, Proteom- und Metabolomforschung, Universität Bielefeld, Bielefeld, Germany
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Duran-Ortiz S, Brittain AL, Kopchick JJ. The impact of growth hormone on proteomic profiles: a review of mouse and adult human studies. Clin Proteomics 2017; 14:24. [PMID: 28670222 PMCID: PMC5492507 DOI: 10.1186/s12014-017-9160-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
Growth hormone (GH) is a protein that is known to stimulate postnatal growth, counter regulate insulin's action and induce expression of insulin-like growth factor-1. GH exerts anabolic or catabolic effects depending upon on the targeted tissue. For instance, GH increases skeletal muscle and decreases adipose tissue mass. Our laboratory has spent the past two decades studying these effects, including the effects of GH excess and depletion, on the proteome of several mouse and human tissues. This review first discusses proteomic techniques that are commonly used for these types of studies. We then examine the proteomic differences found in mice with excess circulating GH (bGH mice) or mice with disruption of the GH receptor gene (GHR-/-). We also describe the effects of increased and decreased GH action on the proteome of adult patients with either acromegaly, GH deficiency or patients after short-term GH treatment. Finally, we explain how these proteomic studies resulted in the discovery of potential biomarkers for GH action, particularly those related with the effects of GH on aging, glucose metabolism and body composition.
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Affiliation(s)
- Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA
| | - Alison L Brittain
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Department of Biological Sciences, College of Arts and Sciences, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
| | - John J Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH USA.,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701 USA
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A Routine 'Top-Down' Approach to Analysis of the Human Serum Proteome. Proteomes 2017; 5:proteomes5020013. [PMID: 28587287 PMCID: PMC5489773 DOI: 10.3390/proteomes5020013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 12/21/2022] Open
Abstract
Serum provides a rich source of potential biomarker proteoforms. One of the major obstacles in analysing serum proteomes is detecting lower abundance proteins owing to the presence of hyper-abundant species (e.g., serum albumin and immunoglobulins). Although depletion methods have been used to address this, these can lead to the concomitant removal of non-targeted protein species, and thus raise issues of specificity, reproducibility, and the capacity for meaningful quantitative analyses. Altering the native stoichiometry of the proteome components may thus yield a more complex series of issues than dealing directly with the inherent complexity of the sample. Hence, here we targeted method refinements so as to ensure optimum resolution of serum proteomes via a top down two-dimensional gel electrophoresis (2DE) approach that enables the routine assessment of proteoforms and is fully compatible with subsequent mass spectrometric analyses. Testing included various fractionation and non-fractionation approaches. The data show that resolving 500 µg protein on 17 cm 3–10 non-linear immobilised pH gradient strips in the first dimension followed by second dimension resolution on 7–20% gradient gels with a combination of lithium dodecyl sulfate (LDS) and sodium dodecyl sulfate (SDS) detergents markedly improves the resolution and detection of proteoforms in serum. In addition, well established third dimension electrophoretic separations in combination with deep imaging further contributed to the best available resolution, detection, and thus quantitative top-down analysis of serum proteomes.
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20
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Papala A, Sylvester M, Dyballa-Rukes N, Metzger S, D'Haese J. Isolation and characterization of human CapG expressed and post-translationally modified in Pichia pastoris. Protein Expr Purif 2017; 134:25-37. [DOI: 10.1016/j.pep.2017.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/08/2017] [Accepted: 03/18/2017] [Indexed: 12/13/2022]
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21
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Kwak JH, Kim HK, Kim K, Noh BR, Cheon HI, Yeo M, Shakya R, Shrestha SA, Kim D, Choe S, Pyo JS. Proteomic Evaluation of Biomarkers to Determine the Postmortem Interval. ANAL LETT 2016. [DOI: 10.1080/00032719.2016.1172080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Rodríguez RA, Urrego WA, Sanabria MC, Sánchez Gómez M, Umaña Perez A. IMPLEMENTACIÓN DE UNA METODOLOGÍA PARA LA SEPARACIÓN DE PROTEOMAS DE PLASMA HUMANO MEDIANTE ELECTROFORESIS BIDIMENSIONAL. REVISTA COLOMBIANA DE QUÍMICA 2016. [DOI: 10.15446/rev.colomb.quim.v44n3.55810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>El análisis proteómico en derivados sanguíneos es una importante herramienta en el descubrimiento de biomarcadores para el diagnóstico de enfermedades, aunque su caracterización exhibe desafíos relacionados con el amplio rango dinámico de las proteínas.<strong> </strong>En este trabajo se implementaron las condiciones para la separación de proteomas de plasma sanguíneo por electroforesis bidimensional. En muestras de plasma de infante y adulto se evaluaron dos sistemas de pretratamiento de la muestra para reducir el rango dinámico de las proteínas: inmunodepleción de proteínas abundantes y enriquecimiento de proteínas de baja abundancia. Los proteomas se separaron por electroforesis bidimensional y las imágenes se analizaron con el programa Melanie 7.0.<strong> </strong>Se encontró que ambos métodos de pretratamiento fueron reproducibles y permitieron ver las diferencias en los proteomas de infante y adulto, como muestran los análisis de componentes principales y de clasificación jerárquica tipo heatmap. El porcentaje de recuperación de proteínas fue mayor con la inmunodepleción en comparación con el enriquecimiento proteico.<strong> </strong>Estos resultados permitieron concluir que con la inmunodepleción, se tiene mayor control de las proteínas eliminadas y por tanto menor pérdida de información, lo que permite su aplicación en estudios exploratorios para la identificación de potenciales biomarcadores de enfermedad.</p>
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Pan K, Zhong Q. Organic Nanoparticles in Foods: Fabrication, Characterization, and Utilization. Annu Rev Food Sci Technol 2016; 7:245-66. [PMID: 26735797 DOI: 10.1146/annurev-food-041715-033215] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the context of food systems, organic nanoparticles (ONPs) are fabricated from proteins, carbohydrates, lipids, and other organic compounds to a characteristic dimension, such as a radius smaller than 100 nm. ONPs can be fabricated with bottom-up and top-down approaches, or a combination of both, on the basis of the physicochemical properties of the source materials and the fundamental principles of physical chemistry, colloidal and polymer sciences, and materials science and engineering. ONPs are characterized for dimension, morphology, surface properties, internal structures, and biological properties to understand structure-function correlations and to explore their applications. These potential applications include modifying physical properties, improving sensory attributes and food quality, protecting labile compounds, and delivering encapsulated bioactive compounds for improved bioactivity and bioavailability. Because ONPs can have digestion and absorption properties different from conventional materials, the eventual applications of ONPs require in vitro and in vivo studies to guide the development of safe food products that utilize the unique functionalities of ONPs.
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Affiliation(s)
- Kang Pan
- Department of Food Science and Technology, University of Tennessee, Knoxville, Tennessee 37996;
| | - Qixin Zhong
- Department of Food Science and Technology, University of Tennessee, Knoxville, Tennessee 37996;
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24
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Papalamprou A, Griffiths LG. Cardiac Extracellular Matrix Scaffold Generated Using Sarcomeric Disassembly and Antigen Removal. Ann Biomed Eng 2015. [DOI: 10.1007/s10439-015-1404-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Abstract
Current proteomic technologies can effectively be used to study the proteins of the vitreous body and retina in health and disease. The use of appropriate samples, analytical platform and bioinformatic method are essential factors to consider when undertaking such studies. Certain proteins may hinder the detection and evaluation of more relevant proteins associated with pathological processes if not carefully considered, particularly in the sample preparation and data analysis stages. The utilization of more than one quantification technique and database search program to expand the level of proteome coverage and analysis will help to generate more robust and worthwhile results. This review discusses important aspects of sample processing and the use of label and label-free quantitative proteomics strategies applied to the vitreous and retina.
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Malafaia CB, Guerra ML, Silva TD, Paiva PM, Souza EB, Correia MT, Silva MV. Selection of a protein solubilization method suitable for phytopathogenic bacteria: a proteomics approach. Proteome Sci 2015; 13:5. [PMID: 25670925 PMCID: PMC4322814 DOI: 10.1186/s12953-015-0062-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/12/2015] [Indexed: 12/12/2022] Open
Abstract
Background Finding the best extraction method of proteins from lysed cells is the key step for detection and identification in all proteomics applications. These are important to complement the knowledge about the mechanisms of interaction between plants and phytopathogens causing major economic losses. To develop an optimized extraction protocol, strains of Acidovorax citrulli, Pectobacterium carotovorum subsp. carotovorum and Ralstonia solanacearum were used as representative cells in the study of phytopathogenic bacteria. This study aims to compare four different protein extraction methods, including: Trizol, Phenol, Centrifugation and Lysis in order to determine which are more suitable for proteomic studies using as parameters the quantity and quality of extracted proteins observed in two-dimensional gels. Results The bacteria studied showed different results among the tested methods. The Lysis method was more efficient for P. carotovorum subsp. carotovorum and R. solanacearum phytobacteria, as well as simple and fast, while for A. citrulli, the Centrifugation method was the best. This evaluation is based on results obtained in polyacrylamide gels that presented a greater abundance of spots and clearer and more consistent strips as detected by two-dimensional gels. Conclusions These results attest to the adequacy of these proteins extraction methods for proteomic studies.
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Affiliation(s)
- Carolina B Malafaia
- Programa de Pós-Graduação em Ciências Biológicas - Centro de Ciências Biológicas - Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, Cidade Universitária, CEP 50670-901 Recife, PE Brasil
| | - Myrzânia L Guerra
- Programa de Pós-Graduação em Fitopatologia - Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n - Dois Irmãos, CEP: 52171-900 Recife, PE Brasil
| | - Túlio D Silva
- Programa de Pós-Graduação em Ciências Biológicas - Centro de Ciências Biológicas - Universidade Federal de Pernambuco, Rua Prof. Nelson Chaves s/n, Cidade Universitária, CEP 50670-901 Recife, PE Brasil
| | - Patrícia Mg Paiva
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
| | - Elineide B Souza
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n - Dois Irmãos, CEP: 52171-900 Recife, PE Brasil
| | - Maria Ts Correia
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
| | - Márcia V Silva
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Rua Prof. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE Brasil
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27
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A new enabling proteomics methodology to investigate membrane associated proteins from parasitic nematodes: case study using ivermectin resistant and ivermectin susceptible isolates of Caenorhabditis elegans and Haemonchus contortus. Vet Parasitol 2014; 207:266-75. [PMID: 25537855 DOI: 10.1016/j.vetpar.2014.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 11/23/2014] [Accepted: 12/06/2014] [Indexed: 01/06/2023]
Abstract
The mechanisms involved in anthelmintic resistance (AR) are complex but a greater understanding of AR management is essential for effective and sustainable control of parasitic helminth worms in livestock. Current tests to measure AR are time consuming and can be technically problematic, gold standard diagnostics are therefore urgently required to assist in combatting the threat from drug resistant parasites. For anthelmintics such as ivermectin (IVM), target proteins may be present in the cellular membrane. As proteins usually act in complexes and not in isolation, AR may develop and be measurable in the target associated proteins present in the parasite membrane. The model nematode Caenorhabditis elegans was used to develop a sub-proteomic assay to measure protein expression differences, between IVM resistant and IVM susceptible isolates in the presence and absence of drug challenge. Evaluation of detergents including CHAPS, ASB-14, C7BzO, Triton ×100 and TBP (tributyl phosphine) determined optimal conditions for the resolution of membrane proteins in Two Dimensional Gel Electrophoresis (2DE). These sub-proteomic methodologies were then translated and evaluated using IVM-susceptible and IVM-resistant Haemonchus contortus; a pathogenic blood feeding parasitic nematode which is of global importance in livestock health, welfare and productivity. We have demonstrated the successful resolution of membrane associated proteins from both C. elegans and H. contortus isolates, using a combination of CHAPS and the zwitterionic amphiphilic surfactant ASB-14 to further support the detection of markers for AR.
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Franconi F, Rosano G, Campesi I. Need for gender-specific pre-analytical testing: the dark side of the moon in laboratory testing. Int J Cardiol 2014; 179:514-35. [PMID: 25465806 DOI: 10.1016/j.ijcard.2014.11.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/27/2014] [Accepted: 11/03/2014] [Indexed: 01/16/2023]
Abstract
Many international organisations encourage studies in a sex-gender perspective. However, research with a gender perspective presents a high degree of complexity, and the inclusion of sex-gender variable in experiments presents many methodological questions, the majority of which are still neglected. Overcoming these issues is fundamental to avoid erroneous results. Here, pre-analytical aspects of the research, such as study design, choice of utilised specimens, sample collection and processing, animal models of diseases, and the observer's role, are discussed. Artefacts in this stage of research could affect the predictive value of all analyses. Furthermore, the standardisation of research subjects according to their lifestyles and, if female, to their life phase and menses or oestrous cycle, is urgent to harmonise research worldwide. A sex-gender-specific attention to pre-analytical aspects could produce a decrease in the time for translation from the bench to bedside. Furthermore, sex-gender-specific pre-clinical pharmacological testing will enable adequate assessment of pharmacokinetic and pharmacodynamic actions of drugs and will enable, where appropriate, an adequate gender-specific clinical development plan. Therefore, sex-gender-specific pre-clinical research will increase the gender equity of care and will produce more evidence-based medicine.
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Affiliation(s)
- Flavia Franconi
- Department of Biomedical Sciences, University of Sassari, National Laboratory of Gender Medicine of the National Institute of Biostructures and Biosystems, Osilo, Sassari, Italy; Vicepresident of Basilicata Region.
| | - Giuseppe Rosano
- Cardiovascular and Cell Sciences Research Institute, St George's University of London, United Kingdom
| | - Ilaria Campesi
- Department of Biomedical Sciences, University of Sassari, National Laboratory of Gender Medicine of the National Institute of Biostructures and Biosystems, Osilo, Sassari, Italy
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Carvalhais V, França A, Pier GB, Vilanova M, Cerca N, Vitorino R. Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium. Talanta 2014; 132:705-12. [PMID: 25476368 DOI: 10.1016/j.talanta.2014.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/01/2014] [Accepted: 10/08/2014] [Indexed: 01/07/2023]
Abstract
Staphylococcus epidermidis is an important nosocomial agent among carriers of indwelling medical devices, due to its strong ability to form biofilms on inert surfaces. Contrary to some advances made in the transcriptomic field, proteome characterization of S. epidermidis biofilms is less developed. To highlight the relation between transcripts and proteins of S. epidermidis biofilms, we analyzed the proteomic profile obtained by two mechanical lysis methods (sonication and bead beating), associated with two distinct detergent extraction buffers, namely SDS and CHAPS. Based on gel electrophoresis-LC-MS/MS, we identified a total of 453 proteins. While lysis with glass beads provided greater amounts of protein, CHAPS extraction buffer allowed identification of a higher number of proteins compared to SDS. Our data shows the impact of different protein isolation methods in the characterization of the S. epidermidis biofilm proteome. Furthermore, the correlation between proteomic and transcriptomic profiles was evaluated. The results confirmed that proteomic and transcriptomic data should be analyzed simultaneously in order to have a comprehensive understanding of a specific microbiological condition.
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Affiliation(s)
- Virginia Carvalhais
- CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela França
- CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gerald B Pier
- Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Manuel Vilanova
- ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal
| | - Nuno Cerca
- CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rui Vitorino
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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Doubly Phosphorylated Peptide Vaccines to Protect Transgenic P301S Mice against Alzheimer's Disease Like Tau Aggregation. Vaccines (Basel) 2014; 2:601-23. [PMID: 26344748 PMCID: PMC4494214 DOI: 10.3390/vaccines2030601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 12/13/2022] Open
Abstract
Intracellular neurofibrillary tangles and extracellular senile plaques are potential targets for active and passive immunotherapies. In this study we used the transgenic mouse model P301S for active immunizations with peptide vaccines composed of a double phosphorylated tau neoepitope (pSer202/pThr205, pThr212/pSer214, pThr231/pSer235) and an immunomodulatory T cell epitope from the tetanus toxin or tuberculosis antigen Ag85B. Importantly, the designed vaccine combining Alzheimer’s disease (AD) specific B cell epitopes with foreign (bacterial) T cell epitopes induced fast immune responses with high IgG1 titers after prophylactic immunization that subsequently decreased over the observation period. The effectiveness of the immunization was surveyed by evaluating the animal behavior, as well as the pathology in the brain by biochemical and histochemical techniques. Immunized mice clearly lived longer with reduced paralysis than placebo-treated mice. Additionally, they performed significantly better in rotarod and beam walk tests at the age of 20 weeks, indicating that the disease development was slowed down. Forty-eight weeks old vaccinated mice passed the beam walk test significantly better than control animals, which together with the increased survival rates undoubtedly prove the treatment effect. In conclusion, the data provide strong evidence that active immune therapies can reduce toxic effects of deposits formed in AD.
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Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts. J Biosci 2014; 39:631-42. [DOI: 10.1007/s12038-014-9453-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Lee JJ, Simborio HL, Reyes AWB, Kim DG, Hop HT, Min W, Her M, Jung SC, Yoo HS, Kim S. Proteomic analyses of the time course responses of mice infected with Brucella abortus 544 reveal immunogenic antigens. FEMS Microbiol Lett 2014; 357:164-74. [PMID: 24975114 DOI: 10.1111/1574-6968.12522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/02/2014] [Accepted: 06/18/2014] [Indexed: 11/28/2022] Open
Abstract
Brucellosis is a major zoonotic disease caused by pathogens of the genus Brucella. The eradication of brucellosis in domestic animals, associated with the prevention of human infection, can be attained through accurate diagnosis. However, the conventional serological diagnosis of brucellosis has limitations, particularly in detecting the infection period. Accordingly, the aim of this study was to determine reliable immunogenic proteins to detect Brucella abortus infection according to time course responses to aid in the appropriate management of this disease. Proteomic identification through two-dimensional electrophoresis (2DE), followed by immunoblotting, revealed 13, 24, and 55 immunodominant B. abortus 544 proteins that were reactive to sera from experimentally infected mice at early (10 days), middle (30 days), and late (60 days) infection periods, respectively. After excluding several spots reactive to sera from Yersinia enterocolitica O:9-infected and noninfected mice, 17 of the 67 immunodominant proteins were identified through MALDI-TOF MS. Consequently, the identified proteins showed time course-dependent immunogenicity against Brucella infection. Thus, the results of this study suggest that the production of immunogenic proteins during infection periods improves the diagnosis and discovery of vaccine candidates.
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Affiliation(s)
- Jin Ju Lee
- Animal and Plant Quarantine Agency, Anyang, Gyeonggi-do, Korea
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Wong ML, Griffiths LG. Immunogenicity in xenogeneic scaffold generation: antigen removal vs. decellularization. Acta Biomater 2014; 10:1806-16. [PMID: 24486910 DOI: 10.1016/j.actbio.2014.01.028] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 12/15/2013] [Accepted: 01/23/2014] [Indexed: 12/11/2022]
Abstract
Decades of research have been undertaken towards the goal of tissue engineering using xenogeneic scaffolds. The primary advantages associated with use of xenogeneic tissue-derived scaffolds for in vitro development of replacement tissues and organs stem from the inherent extracellular matrix (ECM) composition and architecture. Native ECM possesses appropriate mechanical properties for physiological function of the biomaterial and signals for cell binding, growth and differentiation. Additionally, xenogeneic tissue is readily available. However, translation of xenogeneic scaffold-derived engineered tissues or organs into clinical therapies requires xenoantigenicity of the material to be adequately addressed prior to implantation. Failure to achieve this goal will result in a graft-specific host immune rejection response, jeopardizing in vivo survival of the resultant scaffold, tissue or organ. This review explores (i) the appropriateness of scaffold acellularity as an outcome measure for assessing reduction of the immunological barriers to the use of xenogeneic scaffolds for tissue engineering applications and (ii) the need for tissue engineers to strive for antigen removal during xenogeneic scaffold generation.
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Affiliation(s)
- Maelene L Wong
- Department of Veterinary Medicine: Medicine and Epidemiology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA; Department of Biomedical Engineering, University of California, Davis, One Shields Ave., Davis, CA 95616, USA
| | - Leigh G Griffiths
- Department of Veterinary Medicine: Medicine and Epidemiology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA.
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Fernandez-Gomez FJ, Jumeau F, Derisbourg M, Burnouf S, Tran H, Eddarkaoui S, Obriot H, Dutoit-Lefevre V, Deramecourt V, Mitchell V, Lefranc D, Hamdane M, Blum D, Buée L, Buée-Scherrer V, Sergeant N. Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting. J Vis Exp 2014. [PMID: 24747743 DOI: 10.3791/51339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets.
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Affiliation(s)
| | - Fanny Jumeau
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837; EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille
| | - Maxime Derisbourg
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Sylvie Burnouf
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Hélène Tran
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Sabiha Eddarkaoui
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Hélène Obriot
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | | | | | - Valérie Mitchell
- EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille
| | - Didier Lefranc
- EA2686-Laboratorie d'Immunologie, Faculté de Médecine - Pôle Recherche
| | - Malika Hamdane
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - David Blum
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | - Luc Buée
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837
| | | | - Nicolas Sergeant
- Team Alzheimer & Tauopathies, Jean-Pierre Aubert Research Centre, Inserm UMR 837;
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Amoako-Andoh FO, Daniëls B, Keulemans W, Davey MW. A systematic evaluation of protocols for a proteomics analysis of (lyophilized) fruit tissues. Electrophoresis 2014; 35:1395-1405. [DOI: 10.1002/elps.201300443] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Francis O. Amoako-Andoh
- Laboratory of Fruit Breeding and Biotechnology; Department of Biosystems; Katholieke Universiteit Leuven; Belgium
| | - Bruno Daniëls
- Laboratory of Fruit Breeding and Biotechnology; Department of Biosystems; Katholieke Universiteit Leuven; Belgium
| | - Wannes Keulemans
- Laboratory of Fruit Breeding and Biotechnology; Department of Biosystems; Katholieke Universiteit Leuven; Belgium
| | - Mark W. Davey
- Laboratory of Fruit Breeding and Biotechnology; Department of Biosystems; Katholieke Universiteit Leuven; Belgium
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36
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Wu X, Gong F, Wang W. Protein extraction from plant tissues for 2DE and its application in proteomic analysis. Proteomics 2014; 14:645-58. [PMID: 24395710 DOI: 10.1002/pmic.201300239] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/03/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
Abstract
Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).
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Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Wheat & Maize Crop Science in Henan Province, Synergetic Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, Zhengzhou, China
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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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Paoletti AC, Zybailov B, Washburn MP. Principles and applications of Multidimensional Protein Identification Technology. Expert Rev Proteomics 2014; 1:275-82. [PMID: 15966824 DOI: 10.1586/14789450.1.3.275] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Multidimensional chromatography coupled to tandem mass spectrometry is an emerging technique for the analysis of proteomes and is rapidly being implemented by many researchers for proteomic analysis. In this technology profile, a particular proteomic approach known as multidimensional protein identification technology (MudPIT) is discussed. In MudPIT, a biphasic microcapillary column is packed with high-performance liquid chromatography grade reversed phase and strong cation exchange packing materials, loaded with a complex peptide mixture and placed in line with quaternary high-performance liquid chromatography and a tandem mass spectrometer. MudPIT has the capability to analyze highly complex proteomic mixtures such as whole proteomes, organelles and protein complexes.
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Affiliation(s)
- Andrew C Paoletti
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA.
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39
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Amado F, Lobo MJC, Domingues P, Duarte JA, Vitorino R. Salivary peptidomics. Expert Rev Proteomics 2014; 7:709-21. [DOI: 10.1586/epr.10.48] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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40
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Shi J, Feng H, Lee J, Ning Chen W. Comparative proteomics profile of lipid-cumulating oleaginous yeast: an iTRAQ-coupled 2-D LC-MS/MS analysis. PLoS One 2013; 8:e85532. [PMID: 24386479 PMCID: PMC3873444 DOI: 10.1371/journal.pone.0085532] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/28/2013] [Indexed: 12/03/2022] Open
Abstract
Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts.
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Affiliation(s)
- Jiahua Shi
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore
| | - Huixing Feng
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore
| | - Jaslyn Lee
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore
| | - Wei Ning Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore
- * E-mail:
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Abstract
Most biophysical experiments require protein samples of high quality and accurately determined concentration. This chapter attempts to compile basic information on the most common methods to assess the purity, dispersity, and stability of protein samples. It also reminds of methods to measure protein concentration and of their limits. The idea is to make aware and remind of the range of methods available and of commonly overlooked pitfalls. The aim is to enable experimenters to fully characterize their preparations of soluble or membrane proteins and gain reliable and reproducible results from their experimental work.
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Affiliation(s)
- Tina Daviter
- ISMB Biophysics Centre, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
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42
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Natarajan S, Luthria D, Bae H, Lakshman D, Mitra A. Transgenic soybeans and soybean protein analysis: an overview. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:11736-43. [PMID: 24099420 DOI: 10.1021/jf402148e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To meet the increasing global demand for soybeans for food and feed consumption, new high-yield varieties with improved quality traits are needed. To ensure the safety of the crop, it is important to determine the variation in seed proteins along with unintended changes that may occur in the crop as a result various stress stimuli, breeding, and genetic modification. Understanding the variation of seed proteins in the wild and cultivated soybean cultivars is useful for determining unintended protein expression in new varieties of soybeans. Proteomic technology is useful to analyze protein variation due to various stimuli. This short review discusses transgenic soybeans, different soybean proteins, and the approaches used for protein analysis. The characterization of soybean protein will be useful for researchers, nutrition professionals, and regulatory agencies dealing with soy-derived food products.
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Affiliation(s)
- Savithiry Natarajan
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
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43
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Szuba A, Wojakowska A, Lorenc-Plucińska G. An optimized method to extract poplar leaf proteins for two-dimensional gel electrophoresis guided by analysis of polysaccharides and phenolic compounds. Electrophoresis 2013; 34:3234-43. [DOI: 10.1002/elps.201300223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Agnieszka Szuba
- Laboratory of Proteomics; Institute of Dendrology; Polish Academy of Sciences; Kórnik Poland
| | - Anna Wojakowska
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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44
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Pigosso LL, Parente AFA, Coelho ASG, Silva LP, Borges CL, Bailão AM, Soares CMDA. Comparative proteomics in the genus Paracoccidioides. Fungal Genet Biol 2013; 60:87-100. [PMID: 23911955 DOI: 10.1016/j.fgb.2013.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The genus Paracoccidioides comprises a complex of phylogenetic species of dimorphic pathogenic fungi, the etiologic agents of paracoccidioidomycosis (PCM), a disease confined to Latin America and of marked relevance in its endemic areas due to its high frequency and severity. The members of the Paracoccidioides genus are distributed in distinct phylogenetic species (S1, PS2, PS3 and 01-like) that potentially differ in their biochemical and molecular characteristics. In this work, we performed the proteomic characterization of different members of the genus Paracoccidioides. We compared the proteomic profiles of Pb01 (01-like), Pb2 (PS2), Pb339 (S1) and PbEPM83 (PS3) using 2D electrophoresis and mass spectrometry. The proteins/isoforms were selected based on the staining intensity of the spots as determined by image analysis. The proteins/isoforms were in-gel digested and identified by peptide mass fingerprinting and ion fragmentation. A total of 714 spots were detected, of which 343 were analyzed. From these spots, 301 represented differentially expressed proteins/isoforms among the four analyzed isolates, as determined by ANOVA. After applying the FDR correction, a total of 267 spots were determined to be differentially expressed. From the total, 193 proteins/isoforms were identified by PMF and confirmed by ion fragmentation. Comparing the expression profiles of the isolates, the proteins/isoforms that were related to glycolysis/gluconeogenesis and to alcohol fermentation were more abundant in Pb01 than in other representatives of the genus Paracoccidioides, indicating ahigher use of anaerobic pathways for energy production. Those enzymes related to the oxidative stress response were more abundant in Pb01, Pb2 and Pb339, indicating a better response to ROS in these members of the Paracoccidioides complex. The enzymes of the pentose phosphate pathway were abundant in Pb2. Antigenic proteins, such as GP43 and a 27-kDa antigenic protein, were less abundant in Pb01 and Pb2. The proteomic profile indicates metabolic differences among the analyzed members of the Paracoccidioides genus.
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Affiliation(s)
- Laurine Lacerda Pigosso
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
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45
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Rapa RA, Shimmon R, Djordjevic SP, Stokes HW, Labbate M. Deletion of integron-associated gene cassettes impact on the surface properties of Vibrio rotiferianus DAT722. PLoS One 2013; 8:e58430. [PMID: 23484028 PMCID: PMC3590141 DOI: 10.1371/journal.pone.0058430] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 02/06/2013] [Indexed: 01/21/2023] Open
Abstract
Background The integron is a genetic recombination system that catalyses the acquisition of genes on mobilisable elements called gene cassettes. In Vibrio species, multiple acquired gene cassettes form a cassette array that can comprise 1–3% of the bacterial genome. Since 75% of these gene cassettes contain genes encoding proteins of uncharacterised function, how the integron has driven adaptation and evolution in Vibrio species remains largely unknown. A feature of cassette arrays is the presence of large indels. Using Vibrio rotiferianus DAT722 as a model organism, the aim of this study was to determine how large cassette deletions affect vibrio physiology with a view to improving understanding into how cassette arrays influence bacterial host adaptation and evolution. Methodology/Principal Findings Biological assays and proteomic techniques were utilised to determine how artificially engineered deletions in the cassette array of V. rotiferianus DAT722 affected cell physiology. Multiple phenotypes were identified including changes to growth and expression of outer membrane porins/proteins and metabolic proteins. Furthermore, the deletions altered cell surface polysaccharide with Proton Nuclear Magnetic Resonance on whole cell polysaccharide identifying changes in the carbohydrate ring proton region indicating that gene cassette products may decorate host cell polysaccharide via the addition or removal of functional groups. Conclusions/Significance From this study, it was concluded that deletion of gene cassettes had a subtle effect on bacterial metabolism but altered host surface polysaccharide. Deletion (and most likely rearrangement and acquisition) of gene cassettes may provide the bacterium with a mechanism to alter its surface properties, thus impacting on phenotypes such as biofilm formation. Biofilm formation was shown to be altered in one of the deletion mutants used in this study. Reworking surface properties may provide an advantage to the bacterium’s interactions with organisms such as bacteriophage, protozoan grazers or crustaceans.
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Affiliation(s)
- Rita A. Rapa
- The ithree Institute, University of Technology, Sydney, Australia
| | - Ronald Shimmon
- Chemical Technology and Forensic Science, University of Technology, Sydney, Australia
| | | | - H. W. Stokes
- The ithree Institute, University of Technology, Sydney, Australia
| | - Maurizio Labbate
- The ithree Institute, University of Technology, Sydney, Australia
- * E-mail:
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46
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Effective Solubilization Procedure for Analysis of Silkworm Hemolymph Proteins by Two-Dimensional Gel Electrophoresis. Appl Biochem Biotechnol 2013; 169:1459-66. [DOI: 10.1007/s12010-012-0067-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022]
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Weber SS, Parente AFA, Borges CL, Parente JA, Bailão AM, de Almeida Soares CM. Analysis of the secretomes of Paracoccidioides mycelia and yeast cells. PLoS One 2012; 7:e52470. [PMID: 23272246 PMCID: PMC3525554 DOI: 10.1371/journal.pone.0052470] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/13/2012] [Indexed: 11/19/2022] Open
Abstract
Paracoccidioides, a complex of several phylogenetic species, is the causative agent of paracoccidioidomycosis. The ability of pathogenic fungi to develop a multifaceted response to the wide variety of stressors found in the host environment is important for virulence and pathogenesis. Extracellular proteins represent key mediators of the host-parasite interaction. To analyze the expression profile of the proteins secreted by Paracoccidioides, Pb01 mycelia and yeast cells, we used a proteomics approach combining two-dimensional electrophoresis with matrix-assisted laser desorption ionization quadrupole time-of-flight mass spectrometry (MALDI-Q-TOF MS/MS). From three biological replicates, 356 and 388 spots were detected, in mycelium and yeast cell secretomes, respectively. In this study, 160 non-redundant proteins/isoforms were indentified, including 30 and 24 proteins preferentially secreted in mycelia and yeast cells, respectively. In silico analyses revealed that 65% of the identified proteins/isoforms were secreted primarily via non-conventional pathways. We also investigated the influence of protein export inhibition in the phagocytosis of Paracoccidioides by macrophages. The addition of Brefeldin A to the culture medium significantly decreased the production of secreted proteins by both Paracoccidioides and internalized yeast cells by macrophages. In contrast, the addition of concentrated culture supernatant to the co-cultivation significantly increased the number of internalized yeast cells by macrophages. Importantly, the proteins detected in the fungal secretome were also identified within macrophages. These results indicate that Paracoccidioides extracellular proteins are important for the fungal interaction with the host.
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Affiliation(s)
- Simone Schneider Weber
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Ana Flávia Alves Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Juliana Alves Parente
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Alexandre Melo Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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48
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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49
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Alam I, Sharmin SA, Kim KH, Kim YG, Lee JJ, Lee BH. An improved plant leaf protein extraction method for high resolution two-dimensional polyacrylamide gel electrophoresis and comparative proteomics. Biotech Histochem 2012; 88:61-75. [DOI: 10.3109/10520295.2012.729863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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50
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Mesquita RO, de Almeida Soares E, de Barros EG, Loureiro ME. Method optimization for proteomic analysis of soybean leaf: Improvements in identification of new and low-abundance proteins. Genet Mol Biol 2012; 35:353-61. [PMID: 22802721 PMCID: PMC3392888 DOI: 10.1590/s1415-47572012000200017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes of TCA precipitated protein with acetone, using a final wash with 80% ethanol and using sonication to ressuspend the pellet increased the number of detected proteins as well the resolution of the 2-DE gels. Using this approach we have constructed a soybean protein map. The major group of identified proteins corresponded to genes of unknown function. The second and third most abundant groups of proteins were composed of photosynthesis and metabolism related genes. The resulting protocol improved protein solubility and gel resolution allowing the identification of 122 soybean leaf proteins, 72 of which were not detected in other published soybean leaf 2-DE gel datasets, including a transcription factor and several signaling proteins.
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