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Wadood AA, Xiquan Z. Unraveling the mysteries of chicken proteomics: Insights into follicle development and reproduction. J Proteomics 2024; 308:105281. [PMID: 39154802 DOI: 10.1016/j.jprot.2024.105281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Chicken proteomics is a valuable method for comprehending the many mechanisms involved in follicle growth and reproduction in birds. This study offers a thorough summary of the latest progress in chicken proteomics research, specifically highlighting the knowledge obtained regarding follicle development and reproductive physiology. Proteomic studies have revealed essential proteins and pathways that play a role in follicle development, including those that control oocyte size, maturation, and ovulation. Proteomic investigations have provided insight into the molecular pathways that govern reproductive processes. By utilizing advanced proteomic technologies, including mass spectrometry and protein microarray analysis, we have been able to identify and measure many proteins in chicken follicles at their different developmental stages. The utilization of proteomic methods has enabled the identification of previously unknown biomarkers for reproductive efficiency that expedited the creation of innovative diagnostic instruments for monitoring reproductive health in chicken. Chicken proteomics not only offers insights into follicle growth and reproduction but also uncovers the effects of environmental influences on reproductive function. This provides new opportunities for exploring the molecular pathways that cause these effects. The integration of current data with upcoming proteomic technologies offers the potential for innovative strategies to enhance chicken reproduction.
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Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Zhang Xiquan
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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2
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Kamble P, Nagar PR, Bhakhar KA, Garg P, Sobhia ME, Naidu S, Bharatam PV. Cancer pharmacoinformatics: Databases and analytical tools. Funct Integr Genomics 2024; 24:166. [PMID: 39294509 DOI: 10.1007/s10142-024-01445-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
Cancer is a subject of extensive investigation, and the utilization of omics technology has resulted in the generation of substantial volumes of big data in cancer research. Numerous databases are being developed to manage and organize this data effectively. These databases encompass various domains such as genomics, transcriptomics, proteomics, metabolomics, immunology, and drug discovery. The application of computational tools into various core components of pharmaceutical sciences constitutes "Pharmacoinformatics", an emerging paradigm in rational drug discovery. The three major features of pharmacoinformatics include (i) Structure modelling of putative drugs and targets, (ii) Compilation of databases and analysis using statistical approaches, and (iii) Employing artificial intelligence/machine learning algorithms for the discovery of novel therapeutic molecules. The development, updating, and analysis of databases using statistical approaches play a pivotal role in pharmacoinformatics. Multiple software tools are associated with oncoinformatics research. This review catalogs the databases and computational tools related to cancer drug discovery and highlights their potential implications in the pharmacoinformatics of cancer.
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Affiliation(s)
- Pradnya Kamble
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prinsa R Nagar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Kaushikkumar A Bhakhar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Srivatsava Naidu
- Center of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Prasad V Bharatam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
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Badhe MR, Das P, Sahoo S, Paul A, Sahoo PK, Reddy RRK, Suryawanshi AR, Nandanpawar PC, Das Mahapatra K, Nagpure NS, Goswami M, Mohanty J. Physiological Responses to Acute Heat Stress in Rohu, Labeo rohita: Insights from Liver Proteomics. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10360-6. [PMID: 39207653 DOI: 10.1007/s10126-024-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Heat stress is a major problem in aquaculture species, causing changes in physiology such as decreased feed intake, growth rate, reproduction, and internal cellular damage, thereby affecting fish's health. The effects of an acute heat stress simulating a daily rise and fall in temperature on summer days were evaluated in the liver proteome of rohu (Labeo rohita) fingerlings in the present study. The fish maintained at 30 °C were gradually exposed to a higher temperature of 36 °C at an increment rate of 1 °C per 1.5 h, and after 3 h at that temperature, it was gradually reduced to 30 °C. The liver tissue samples were collected at 5 am, 5 pm, and 5 am the next day from the exposed and control fish. Protein samples were prepared from the liver tissues, and the extracted proteins were compared using 2-dimensional (2D) gel electrophoresis (2DGE) and mass spectrometry (MS) using a MALDI-TOF/TOF mass spectrometer. A total of 44 differentially expressed protein spots were visualized in 2D gel analysis from heat stress exposed fish at three time points, out of which 21 proteins including one hypothetical protein could be identified by MS. The abundance of five selected differentially expressed proteins (DEPs) was validated using qPCR. The majority of DEPs were found to be involved primarily in lipid, protein and energy metabolism, immune system regulation, cytoskeletal stability, and ROS management. The findings of this study would help in the development of strategies to mitigate heat stress in L. rohita.
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Affiliation(s)
- Mohan R Badhe
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Priyanka Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Sonalina Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Anirban Paul
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Pramoda Kumar Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | | | | | | | - Kanta Das Mahapatra
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Naresh S Nagpure
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Jyotirmaya Mohanty
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India.
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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Xia D, Xu GP, Zhang YT, Yan WW, Pan XR, Tong JH. Targeting inhibition of TCTP could inhibit proliferation and induce apoptosis in AML cells. Cell Signal 2024; 117:111074. [PMID: 38309549 DOI: 10.1016/j.cellsig.2024.111074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
Translationally controlled tumor protein (TCTP) is a highly conserved multifunctional protein, which participates in many important physiological processes. Recently, the roles of TCTP in cell proliferation and apoptosis, especially its close relationship with various tumors, have attracted widespread attention. In this study, we found that the protein level of TCTP was significantly reduced in acute promyelocytic leukemia cell line NB4 transfected with retinoic acid-induced gene G (RIG-G). The RIG-G was found in our previous work as a key mediator of anti-proliferative activity in retinoid/interferon-related pathways. Here, we tried to further explore the function of TCTP in the development of acute myeloid leukemia (AML) from different levels. Our results showed that inhibiting TCTP expression could attenuate AML cells proliferation and induce apoptosis both in AML cell lines and in xenograft of NOD-SCID mice. In addition, either compared with patients in complete remission or non-leukemia patients, we detected that the expression of TCTP was generally high in the fresh bone marrow of AML patients, suggesting that there was a certain correlation between TCTP and AML disease progression. Taken together, our study revealed the role of TCTP in AML development, and provided a potential target for AML treatment.
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Affiliation(s)
- Di Xia
- Central Laboratory, Rui-jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-jin Er Road, Shanghai 200025, China
| | - Gui-Ping Xu
- Transfusion Department, The Second Affiliated Hospital of Chongqing Medical University, No.74 Linjiang Road, Yuzhong District, Chongqing 400010, China
| | - Ying-Ting Zhang
- Central Laboratory, Rui-jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-jin Er Road, Shanghai 200025, China
| | - Wei-Wei Yan
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Xiao-Rong Pan
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-jin Er Road, Shanghai 200025, China.
| | - Jian-Hua Tong
- Central Laboratory, Rui-jin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Rui-jin Er Road, Shanghai 200025, China.
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Spermatozoa and seminal plasma proteomics: too many molecules, too few markers. The case of bovine and porcine semen. Anim Reprod Sci 2022; 247:107075. [DOI: 10.1016/j.anireprosci.2022.107075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/06/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022]
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Hirano H, Shirakawa J. Recent developments in Phos-tag electrophoresis for the analysis of phosphoproteins in proteomics. Expert Rev Proteomics 2022; 19:103-114. [PMID: 35285370 DOI: 10.1080/14789450.2022.2052850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Phosphate-binding tag (Phos-tag) sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is an important development capable of analyzing the phosphorylation state of proteins. Conventionally, proteins were separated via SDS-PAGE and Phos-tag SDS-PAGE that use different gels to identify phosphorylated proteins. However, it was often difficult to compare the electrophoretic mobility of the proteins in the different gels used. The recently developed Phos-tag diagonal electrophoresis has been able to solve this problem. It can indicate the SDS-PAGE and Phos-tag SDS-PAGE patterns on a single gel; therefore, phosphorylated proteins can be distinguished easily from non-phosphorylated proteins. AREAS COVERED This review assesses the importance of Phos-tag electrophoresis, which enables the analysis of protein phosphorylation states, in the field of proteomics. Additionally, this review describes the significance and actual experimental technique of Phos-tag diagonal electrophoresis, which was recently developed to overcome the drawbacks of Phos-tag SDS-PAGE. EXPERT OPINION Although shotgun analysis of proteins allows detecting many phosphorylation sites, it is challenging to clarify the differences in the phosphorylation states of protein molecules using this technique. Therefore, Phos-tag SDS-PAGE is frequently used to determine the phosphorylation state of proteins. This technique has become more powerful with the recent development of Phos-tag diagonal electrophoresis.
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Affiliation(s)
- Hisashi Hirano
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Jun Shirakawa
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
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Proteomic analysis of Caenorhabditis elegans against Salmonella Typhi toxic proteins. Genes Immun 2021; 22:75-92. [PMID: 33986511 DOI: 10.1038/s41435-021-00132-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 02/03/2023]
Abstract
Bacterial effector molecules are crucial infectious agents that can cause pathogenesis. In the present study, the pathogenesis of toxic Salmonella enterica serovar Typhi (S. Typhi) proteins on the model host Caenorhabditis elegans was investigated by exploring the host's regulatory proteins during infection through the quantitative proteomics approach. Extracted host proteins were analyzed using two-dimensional gel electrophoresis (2D-GE) and differentially regulated proteins were identified using MALDI TOF/TOF/MS analysis. Of the 150 regulated proteins identified, 95 were downregulated while 55 were upregulated. The interaction network of regulated proteins was predicted using the STRING tool. Most downregulated proteins were involved in muscle contraction, locomotion, energy hydrolysis, lipid synthesis, serine/threonine kinase activity, oxidoreductase activity, and protein unfolding. Upregulated proteins were involved in oxidative stress pathways. Hence, cellular stress generated by S. Typhi proteins in the model host was determined using lipid peroxidation as well as oxidant and antioxidant assays. In addition, candidate proteins identified via extract analysis were validated by western blotting, and the roles of several crucial molecules were analyzed in vivo using transgenic strains (myo-2 and col-19) and mutant (ogt-1) of C. elegans. To the best of our knowledge, this is the first study to report protein regulation in host C. elegans exposed to toxic S. Typhi proteins. It highlights the significance of p38 MAPK and JNK immune pathways.
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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Differential Expression of Multiple Disease-Related Protein Groups Induced by Valproic Acid in Human SH-SY5Y Neuroblastoma Cells. Brain Sci 2020; 10:brainsci10080545. [PMID: 32806546 PMCID: PMC7465595 DOI: 10.3390/brainsci10080545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022] Open
Abstract
Valproic acid (VPA) is a multifunctional medication used for the treatment of epilepsy, mania associated with bipolar disorder, and migraine. The pharmacological effects of VPA involve a variety of neurotransmitter and cell signaling systems, but the molecular mechanisms underlying its clinical efficacy is to date largely unknown. In this study, we used the isobaric tags for relative and absolute quantitation shotgun proteomic analysis to screen differentially expressed proteins in VPA-treated SH-SY5Y cells. We identified changes in the expression levels of multiple proteins involved in Alzheimer’s disease, Parkinson’s disease, chromatin remodeling, controlling gene expression via the vitamin D receptor, ribosome biogenesis, ubiquitin-mediated proteolysis, and the mitochondrial oxidative phosphorylation and electron transport chain. Our data indicate that VPA may modulate the differential expression of proteins involved in mitochondrial function and vitamin D receptor-mediated chromatin transcriptional regulation and proteins implicated in the pathogenesis of neurodegenerative diseases.
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An Evidence-Based Update on the Molecular Mechanisms Underlying Periodontal Diseases. Int J Mol Sci 2020; 21:ijms21113829. [PMID: 32481582 PMCID: PMC7312805 DOI: 10.3390/ijms21113829] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/15/2022] Open
Abstract
Several investigators have reported about the intricate molecular mechanism underlying periodontal diseases (PD). Nevertheless, the role of specific genes, cells, or cellular mechanisms involved in the pathogenesis of periodontitis are still unclear. Although periodontitis is one of the most prevalent oral diseases globally, there are no pre-diagnostic markers or therapeutic targets available for such inflammatory lesions. A pivotal role is played by pro- and anti-inflammatory markers in modulating pathophysiological and physiological processes in repairing damaged tissues. In addition, effects on osteoimmunology is ever evolving due to the ongoing research in understanding the molecular mechanism lying beneath periodontal diseases. The aim of the current review is to deliver an evidence-based update on the molecular mechanism of periodontitis with a particular focus on recent developments. Reports regarding the molecular mechanism of these diseases have revealed unforeseen results indicative of the fact that significant advances have been made to the periodontal medicine over the past decade. There is integrated hypothesis-driven research going on. Although a wide picture of association of periodontal diseases with immune response has been further clarified with present ongoing research, small parts of the puzzle remain a mystery and require further investigations.
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Chen Q, Huang R, Xu Z, Zhang Y, Li L, Fu J, Wang G, Wang J, Du X, Gu R. Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels. Int J Mol Sci 2020; 21:ijms21041369. [PMID: 32085613 PMCID: PMC7072901 DOI: 10.3390/ijms21041369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/20/2022] Open
Abstract
The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.
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Affiliation(s)
- Quanquan Chen
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Ran Huang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Zhenxiang Xu
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Yaxin Zhang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Li Li
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Jianhua Wang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Xuemei Du
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
- Correspondence: (X.D.); (R.G.)
| | - Riliang Gu
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
- Correspondence: (X.D.); (R.G.)
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D'Antona L, Dattilo V, Catalogna G, Scumaci D, Fiumara CV, Musumeci F, Perrotti G, Schenone S, Tallerico R, Spoleti CB, Costa N, Iuliano R, Cuda G, Amato R, Perrotti N. In Preclinical Model of Ovarian Cancer, the SGK1 Inhibitor SI113 Counteracts the Development of Paclitaxel Resistance and Restores Drug Sensitivity. Transl Oncol 2019; 12:1045-1055. [PMID: 31163384 PMCID: PMC6545392 DOI: 10.1016/j.tranon.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/19/2022] Open
Abstract
Ovarian cancer is the second most common gynecological malignancy worldwide. Paclitaxel is particularly important in the therapy of ovarian carcinomas, but the treatment efficacy is counteracted by the development of resistance to chemotherapy. The identification of target molecules that can prevent or control the development of chemoresistance might provide important tools for the management of patients affected by ovarian cancer. Serum- and glucocorticoid-regulated kinase 1 (SGK1) appears to be a key determinant of resistance to chemo- and radiotherapy. Specifically, SGK1 affects paclitaxel sensitivity in RKO colon carcinoma cells by modulating the specificity protein 1 (SP1)–dependent expression of Ran-specific GTPase-activating protein (RANBP1), a member of the GTP-binding nuclear protein Ran (RAN) network that is required for the organization and function of the mitotic spindle. SGK1 inhibition might thus be useful for counteracting the development of paclitaxel resistance. Here, we present in vitro data obtained using ovarian carcinoma cell lines that indicate that the SGK1 inhibitor SI113 inhibits cancer cell proliferation, potentiates the effects of paclitaxel-based chemotherapy, counteracts the development of paclitaxel resistance, and restores paclitaxel sensitivity in paclitaxel-resistant A2780 ovarian cancer cells. The results were corroborated by preclinical studies of xenografts generated in nude mice through the implantation of paclitaxel-resistant human ovarian cancer cells. The SGK1 inhibitor SI113 synergizes with paclitaxel in the treatment of xenografted ovarian cancer cells. Taken together, these data suggest that SGK1 inhibition should be investigated in clinical trials for the treatment of paclitaxel-resistant ovarian cancer.
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Affiliation(s)
- Lucia D'Antona
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Vincenzo Dattilo
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Giada Catalogna
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Domenica Scumaci
- Department of "Medicina Sperimentale e Clinica", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Claudia Vincenza Fiumara
- Department of "Medicina Sperimentale e Clinica", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | | | - Giuseppe Perrotti
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | | | - Rossana Tallerico
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Cristina B Spoleti
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Nicola Costa
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Rodolfo Iuliano
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Giovanni Cuda
- Department of "Medicina Sperimentale e Clinica", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro
| | - Rosario Amato
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro.
| | - Nicola Perrotti
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Viale Europa, Catanzaro.
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14
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Keppanan R, Krutmuang P, Sivaperumal S, Hussain M, Bamisile BS, Aguila LCR, Dash CK, Wang L. Synthesis of mycotoxin protein IF8 by the entomopathogenic fungus Isaria fumosorosea and its toxic effect against adult Diaphorina citri. Int J Biol Macromol 2018; 125:1203-1211. [PMID: 30227211 DOI: 10.1016/j.ijbiomac.2018.09.093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/05/2023]
Abstract
Entomopathogenic fungi based microbial insecticides are considered as safe alternatives to chemical pesticides, which secretes several bioactive compounds to kill the host insects. In this study, we report a new approach for the synthesis and characterization of insecticide toxic protein IF8 produced by the Isaria fumosorosea 08, and to evaluate the mycotoxin level against the vector of Huanglongbing (HLB) or citrus greening disease, the Asian citrus psyllid, Diaphorina citri. Soluble toxic metabolites extracted from I. fumosorosea 08 through submerged liquid state culture had a molecular weight of 43 kDa when subjected by to sodium dodecyl sulfate-poly-acrylamide (SDS-PAGE) gel electrophoresis. The most abundant of toxic protein IF8 was determined by High-performance liquid chromatography (HPLC) and liquid chromatography electrospray ionization-mass spectroscopy (LC-ESI-MS) for the analysis of its molecular mass weight and purity. Further Matrix-assisted laser desorption ionization-time of flight (MALDI-TOFF) analysis confirmed the presence of toxic metabolites in liquid culture. Subsequently, mycotoxic effect of toxic protein IF8 was tested against D. citri at three different concentrations (1%, 2%, and 3%). The results showed the insecticidal activity of >80% when administered at three different concentrations at 48-120 hour post-application. Additionally, we also investigated the physicochemical properties and stability of IF8 by using computational biological tools. This is the first study to report the characterization of fungal mediated synthesis of the protein IF8 toxic to the insect D. citri. These results suggest the mycotoxin control of D. citri and prevention of HLB transmission by using a natural toxic compound which is eco-friendly and can be potentially used for the integrated management of D. citri.
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Affiliation(s)
- Ravindran Keppanan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Sivaramakrishnan Sivaperumal
- Department of Biotechnology and Genetic Engineering, School of Life Sciences, Bharathidasan University, Tamil Nadu, India
| | - Mubasher Hussain
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bamisope Steve Bamisile
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Luis Carlos Ramos Aguila
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chandra Kanta Dash
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liande Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China; College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
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15
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Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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16
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Noaman N, Abbineni PS, Withers M, Coorssen JR. Coomassie staining provides routine (sub)femtomole in-gel detection of intact proteoforms: Expanding opportunities for genuine Top-down Proteomics. Electrophoresis 2017; 38:3086-3099. [PMID: 28872692 DOI: 10.1002/elps.201700190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/11/2017] [Accepted: 08/25/2017] [Indexed: 01/22/2023]
Abstract
Modified colloidal Coomassie Brilliant Blue (cCBB) staining utilising a novel destain protocol and near-infrared fluorescence detection (nIRFD) rivals the in-gel protein detection sensitivity (DS) of SYPRO Ruby. However, established DS estimates are likely inaccurate in terms of 2DE-resolved proteoform 'spots' since DS is routinely measured from comparatively diffuse protein 'bands' following wide-well 1DE. Here, cCBB DS for 2DE-based proteomics was more accurately determined using narrow-well 1DE. As precise estimates of protein standard monomer concentrations are essential for accurate quantitation, coupling UV absorbance with gel-based purity assessments is described. Further, as cCBB is compatible with both nIRFD and densitometry, the impacts of imaging method (and image resolution) on DS were assessed. Narrow-well 1DE enabled more accurate quantitation of cCBB DS for 2DE, achieving (sub)femtomole DS with either nIRFD or densitometry. While densitometry offers comparative simplicity and affordability, nIRFD has the unique potential for enhanced DS with Deep Imaging. Higher-resolution nIRFD also improved analysis of a 2DE-resolved proteome, surpassing the DS of standard nIRFD and densitometry, with nIRFD Deep Imaging further maximising proteome coverage. cCBB DS for intact proteins rivals that of mass spectrometry (MS) for peptides in complex mixtures, reaffirming that 2DE-MS currently provides the most routine, broadly applicable, robust, and information-rich Top-down approach to Discovery Proteomics.
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Affiliation(s)
- Nour Noaman
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Prabhodh S Abbineni
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Withers
- Department of Molecular Physiology, and the WSU Molecular Medicine Research Group, School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Jens R Coorssen
- Departments of Health Sciences and Biological Sciences, Brock University, St Catharines, Ontario, Canada
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17
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Cao Z, Mou R, Cao Z, Lin X, Ma Y, Zhu Z, Chen M. Quantitation of glutathione S-transferases in rice ( Oryza sativa L.) roots exposed to cadmium by liquid chromatography-tandem mass spectrometry using isotope-labeled wing peptides as an internal standard. PLANT METHODS 2017; 13:64. [PMID: 28785299 PMCID: PMC5543549 DOI: 10.1186/s13007-017-0214-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/27/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plant glutathione S-transferases (GSTs, EC 2.5.1.18) are multifunctional enzymes involved in heavy metal cellular detoxification by conjugating the tripeptide (g-Glu-Cys-Gly) glutathione to heavy metals. Previous studies demonstrated that individual rice GSTs were differentially induced by heavy metal exposure at the mRNA transcript level. However, little information is available concerning changes in protein concentration of rice GSTs under heavy metal stress. Because the correlation between changes in protein concentration and gene expression under abiotic stress is poor, direct determination of rice GSTs protein concentrations during cadmium (Cd) exposure is a more effective and reliable approach to explore possible mechanisms of rice Cd translocation and accumulation. RESULTS This study established an optimized and advanced liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics assay for quantification of OsGSTF14 and OsGSTU6 proteins in Cd-stressed rice roots. The tryptic signature peptides were chosen as surrogate analytes and winged peptides containing the isotope-labeled signature peptides were used as the internal standards. The signature peptides exhibited good linearity in the range of 0.6-60 and 0.3-30 nM, respectively. The limit of detection and limit of quantification were 4.5 and 14.5 µg/g for OsGSTF14, respectively, and 2.1 and 7.0 µg/g for OsGSTU6. The spiking recoveries rates at low, medium and high levels were in the range of 72.5-93.4%, with intra- and inter-day precisions of 5.5-9.1 and 4.2-10.2%, respectively. CONCLUSIONS The assay successfully quantified the temporal and dose responses of OsGSTF14 and OsGSTU6 proteins in Cd-stressed rice roots, with good accuracy, precision and high-throughput. This assay will have significant application in developing quantification methods of other proteins in Cd-stressed rice, which may provide more insight into the mechanisms of Cd translocation and accumulation in rice.
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Affiliation(s)
- Zhenzhen Cao
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Renxiang Mou
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhaoyun Cao
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Xiaoyan Lin
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Youning Ma
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhiwei Zhu
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
| | - Mingxue Chen
- Rice Product Quality Supervision and Inspection Center, China National Rice Research Institute, Hangzhou, 310006 China
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18
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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19
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Coleman O, Henry M, McVey G, Clynes M, Moriarty M, Meleady P. Proteomic strategies in the search for novel pancreatic cancer biomarkers and drug targets: recent advances and clinical impact. Expert Rev Proteomics 2016; 13:383-94. [PMID: 26985644 DOI: 10.1586/14789450.2016.1167601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers; despite a low incidence rate it is the fourth leading cause of cancer-related death in the world. Improvement of the diagnosis, prognosis and treatment remains the main focus of pancreatic cancer research. Rapid developments in proteomic technologies has improved our understanding of the pancreatic cancer proteome. Here, the authors summarise the recent proteomic strategies undertaken in the search for: novel biomarkers for early diagnosis, pancreatic cancer-specific proteins which may be used for novel targeted therapies and proteins which may be useful for monitoring disease progression post-therapy. Recent advances and findings discussed here provide great promise of having a significant clinical impact and improving the outcome of patients with this malignancy.
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Affiliation(s)
- Orla Coleman
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Michael Henry
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Gerard McVey
- b St. Lukes Hospital , Rathgar , Dublin 6 , Ireland
| | - Martin Clynes
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Michael Moriarty
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland.,b St. Lukes Hospital , Rathgar , Dublin 6 , Ireland
| | - Paula Meleady
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
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20
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Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L. Int J Mol Sci 2016; 17:ijms17111794. [PMID: 27801782 PMCID: PMC5133795 DOI: 10.3390/ijms17111794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.
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21
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Ma C, Cao J, Li J, Zhou B, Tang J, Miao A. Phenotypic, histological and proteomic analyses reveal multiple differences associated with chloroplast development in yellow and variegated variants from Camellia sinensis. Sci Rep 2016; 6:33369. [PMID: 27633059 PMCID: PMC5025893 DOI: 10.1038/srep33369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/26/2016] [Indexed: 11/20/2022] Open
Abstract
Leaf colour variation is observed in several plants. We obtained two types of branches with yellow and variegated leaves from Camellia sinensis. To reveal the mechanisms that underlie the leaf colour variations, combined morphological, histological, ionomic and proteomic analyses were performed using leaves from abnormal branches (variants) and normal branches (CKs). The measurement of the CIE-Lab coordinates showed that the brightness and yellowness of the variants were more intense than the CKs. When chloroplast profiles were analysed, HY1 (branch with yellow leaves) and HY2 (branch with variegated leaves) displayed abnormal chloroplast structures and a reduced number and size compared with the CKs, indicating that the abnormal chloroplast development might be tightly linked to the leaf colour variations. Moreover, the concentration of elemental minerals was different between the variants and the CKs. Furthermore, DEPs (differentially expressed proteins) were identified in the variants and the CKs by a quantitative proteomics analysis using the label-free approach. The DEPs were significantly involved in photosynthesis and included PSI, PSII, cytochrome b6/f complex, photosynthetic electron transport, LHC and F-type ATPase. Our results suggested that a decrease in the abundance of photosynthetic proteins might be associated with the changes of leaf colours in tea plants.
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Affiliation(s)
- Chengying Ma
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Junxi Cao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Bo Zhou
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Jinchi Tang
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
| | - Aiqing Miao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation &Utilization, Guangzhou 510640, China
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22
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Zhang X, Li Y, Chen Z, Liu Z, Ren Q, Yang J, Zhu X, Guan G, Liu A, Luo J, Yin H. Comparative proteomic and bioinformatic analysis of Theileria luwenshuni and Theileria uilenbergi. Exp Parasitol 2016; 166:51-9. [DOI: 10.1016/j.exppara.2016.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 12/07/2015] [Accepted: 03/15/2016] [Indexed: 01/12/2023]
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23
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Khurshid Z, Najeeb S, Mali M, Moin SF, Raza SQ, Zohaib S, Sefat F, Zafar MS. Histatin peptides: Pharmacological functions and their applications in dentistry. Saudi Pharm J 2016; 25:25-31. [PMID: 28223859 PMCID: PMC5310145 DOI: 10.1016/j.jsps.2016.04.027] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/26/2016] [Indexed: 01/10/2023] Open
Abstract
There are many human oral antimicrobial peptides responsible for playing important roles including maintenance, repairing of oral tissues (hard or soft) and defense against oral microbes. In this review we have highlighted the biochemistry, physiology and proteomics of human oral histatin peptides, secreted from parotid and submandibular salivary glands in human. The significance of these peptides includes capability for ionic binding that can kill fungal Candida albicans. They have histidine rich amino acid sequences (7-12 family members; corresponding to residues 12-24, 13-24, 12-25, 13-25, 5-11, and 5-12, respectively) for Histatin-3. However, Histatin-3 can be synthesized proteolytically from histatin 5 or 6. Due to their fungicidal response and high biocompatibility (little or no toxicity), these peptides can be considered as therapeutic agents with most probable applications for example, artificial saliva for denture wearers and salivary gland dysfunction conditions. The objectives of current article are to explore the human histatin peptides for its types, chemical and biological aspects. In addition, the potential for therapeutic bio-dental applications has been elaborated.
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Affiliation(s)
- Zohaib Khurshid
- Department of Dental Biomaterials, College of Dentistry, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Shariq Najeeb
- School of Dentistry, University of Sheffield, Sheffield, UK
| | - Maria Mali
- Department of Endodontics, Fatima Jinnah Dental College, Karachi, Pakistan
| | - Syed Faraz Moin
- National Centre for Proteomics, Karachi University, Pakistan
| | - Syed Qasim Raza
- Institute of Research and Consulting, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Sana Zohaib
- Department of Biomedical Engineering, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Farshid Sefat
- Department of Biomedical Engineering, King Faisal University, Al-Hofuf, Saudi Arabia; Department of Medical Engineering, University of Bradford, Bradford, UK
| | - Muhammad Sohail Zafar
- Department of Restorative Dentistry, College of Dentistry, Taibah University, Al Madinah Al Munawwarah, Saudi Arabia
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24
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Dick LW, Mehl JT, Loughney JW, Mach A, Rustandi RR, Ha S, Zhang L, Przysiecki CT, Dieter L, Hoang VM. Label-free quantitative mass spectrometry for analysis of protein antigens in a meningococcal group B outer membrane vesicle vaccine. Hum Vaccin Immunother 2016; 11:1518-25. [PMID: 25997113 DOI: 10.1080/21645515.2015.1016678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The development of a multivalent outer membrane vesicle (OMV) vaccine where each strain contributes multiple key protein antigens presents numerous analytical challenges. One major difficulty is the ability to accurately and specifically quantitate each antigen, especially during early development and process optimization when immunoreagents are limited or unavailable. To overcome this problem, quantitative mass spectrometry methods can be used. In place of traditional mass assays such as enzyme-linked immunosorbent assays (ELISAs), quantitative LC-MS/MS using multiple reaction monitoring (MRM) can be used during early-phase process development to measure key protein components in complex vaccines in the absence of specific immunoreagents. Multiplexed, label-free quantitative mass spectrometry methods using protein extraction by either detergent or 2-phase solvent were developed to quantitate levels of several meningococcal serogroup B protein antigens in an OMV vaccine candidate. Precision was demonstrated to be less than 15% RSD for the 2-phase extraction and less than 10% RSD for the detergent extraction method. Accuracy was 70 to 130% for the method using a 2-phase extraction and 90-110% for detergent extraction. The viability of MS-based protein quantification as a vaccine characterization method was demonstrated and advantages over traditional quantitative methods were evaluated. Implementation of these MS-based quantification methods can help to decrease the development time for complex vaccines and can provide orthogonal confirmation of results from existing antigen quantification techniques.
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Key Words
- BCA, bicinchoninic acid
- ELISA, enzyme-linked immunosorbent assay
- HPLC –high performance liquid chromatography
- LC-MS/MS, liquid chromatography, tandem mass spectrometry
- MRM, multiple reaction monitoring
- MS, mass spectrometry
- MenB, Meningococcal serogroup B
- NadA, Neisseria adhesin A
- OMPC, outer membrane protein complex
- OMV, outer membrane vesicle
- PorA, major outer membrane protein (class I outer membrane protein)
- QC, quality control
- RSD, relative standard deviation
- SDS-PAGE, sodium dodecyl sulfate, polyacrylamide gel electrophoresis
- WRAIR, Walter Reed Army Institute of Research
- fHbp, factor H binding protein
- mass spectrometry
- membrane proteins
- meningococcal group B
- multiple reaction monitoring
- outer membrane vesicle
- protein quantification
- vaccine
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Affiliation(s)
- Lawrence W Dick
- a Vaccine Bioprocess Research and Development; Merck Research Labs; Merck & Co., Inc. ; Whitehouse Station , NJ , USA
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Bal G, Futschik ME, Hartl D, Ringel F, Kamhieh-Milz J, Sterzer V, Hoheisel JD, Alhamdani MSS, Salama A. Identification of novel biomarkers in chronic immune thrombocytopenia (ITP) by microarray-based serum protein profiling. Br J Haematol 2015; 172:602-15. [PMID: 26628061 DOI: 10.1111/bjh.13861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/06/2015] [Indexed: 01/15/2023]
Abstract
The pathological mechanisms underlying the development of immune thrombocytopenia (ITP) are unclear and its diagnosis remains a process of exclusion. Currently, there are no known specific biomarkers for ITP to support differential diagnosis and treatment decisions. Profiling of serum proteins may be valuable for identifying such biomarkers. Sera from 46 patients with primary chronic ITP and 34 healthy blood donors were analysed using a microarray of 755 antibodies. We identified 161 differentially expressed proteins. In addition to oncoproteins and tumour-suppressor proteins, including apoptosis regulator BCL2, breast cancer type 1 susceptibility protein (BRCA1), Fanconi anaemia complementation group C (FANCC) and vascular endothelial growth factor A (VEGFA), we detected six anti-nuclear autoantibodies in a subset of ITP patients: anti-PCNA, anti-SmD, anti-Ro/SSA60, anti-Ro/SSA52, anti-La/SSB and anti-RNPC antibodies. This finding may provide a rational explanation for the association of ITP with malignancies and other autoimmune diseases. While RUNX1mRNA expression in the peripheral blood mononuclear cells (PBMC) of patients was significantly downregulated, an accumulation of RUNX1 protein was observed in the platelets of ITP patients. This may indicate dysregulation of RUNX1 expression in PBMC and megakaryocytes and may lead to an imbalanced immune response and impaired thrombopoiesis. In conclusion, we provide novel insights into the pathogenic mechanisms of ITP that warrant further exploration.
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Affiliation(s)
- Gürkan Bal
- Institute for Transfusion Medicine, Charité Universitätsmedizin, Berlin, Germany
| | | | - Daniela Hartl
- Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Berlin, Germany
| | - Frauke Ringel
- Institute for Transfusion Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Julian Kamhieh-Milz
- Institute for Transfusion Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Viktor Sterzer
- Institute for Transfusion Medicine, Charité Universitätsmedizin, Berlin, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Abdulgabar Salama
- Institute for Transfusion Medicine, Charité Universitätsmedizin, Berlin, Germany
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Dattilo S, Mancuso C, Koverech G, Di Mauro P, Ontario ML, Petralia CC, Petralia A, Maiolino L, Serra A, Calabrese EJ, Calabrese V. Heat shock proteins and hormesis in the diagnosis and treatment of neurodegenerative diseases. Immun Ageing 2015; 12:20. [PMID: 26543490 PMCID: PMC4634585 DOI: 10.1186/s12979-015-0046-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022]
Abstract
Modulation of endogenous cellular defense mechanisms via the vitagene system represents an innovative approach to therapeutic intervention in diseases causing chronic tissue damage, such as in neurodegeneration. The possibility of high-throughoutput screening using proteomic techniques, particularly redox proteomics, provide more comprehensive overview of the interaction of proteins, as well as the interplay among processes involved in neuroprotection. Here by introducing the hormetic dose response concept, the mechanistic foundations and applications to the field of neuroprotection, we discuss the emerging role of heat shock protein as prominent member of vitagene network in neuroprotection and redox proteomics as a tool for investigating redox modulation of stress responsive vitagenes. Hormetic mechanisms are reviewed as possibility of targeted therapeutic manipulation in a cell-, tissue- and/or pathway-specific manner at appropriate points in the neurodegenerative disease process.
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Affiliation(s)
- Sandro Dattilo
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Cesare Mancuso
- />Institute of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - Guido Koverech
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Paola Di Mauro
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Maria Laura Ontario
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | | | - Antonino Petralia
- />Department of Clinical and Experimental Medicine, School of Medicine, University of Catania, Catania, Italy
| | - Luigi Maiolino
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Agostino Serra
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Edward J. Calabrese
- />Environmental Health Sciences Division, School of Public Health, University of Massachusetts, Amherst, MA USA
| | - Vittorio Calabrese
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
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Wang L, Cao H, Chen C, Yue C, Hao X, Yang Y, Wang X. Complementary transcriptomic and proteomic analyses of a chlorophyll-deficient tea plant cultivar reveal multiple metabolic pathway changes. J Proteomics 2015; 130:160-9. [PMID: 26344129 DOI: 10.1016/j.jprot.2015.08.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/04/2015] [Accepted: 08/27/2015] [Indexed: 02/03/2023]
Abstract
To uncover the mechanisms that underlie the chlorina phenotype of the tea plant, this study employs morphological, biochemical, transcriptomic, and iTRAQ-based proteomic analyses to compare the green tea cultivar LJ43 and the yellow-leaf tea cultivar ZH1. ZH1 exhibited the chlorina phenotype, with significantly decreased chlorophyll content and abnormal chloroplast development compared with LJ43. ZH1 also displayed higher theanine and free amino acid content and lower carotenoid and catechin content. Microarray and iTRAQ analyses indicated that the differentially expressed genes and proteins could be mapped to the following pathways: 'phenylpropanoid biosynthesis,' 'glutathione metabolism,' 'phenylalanine metabolism,' 'photosynthesis,' and 'flavonoid biosynthesis.' Altered gene and protein levels in these pathways may account for the increased amino acid content and reduced chlorophyll and flavonoid content of ZH1. Altogether, this study combines transcriptomic and proteomic approaches to better understand the mechanisms responsible for the chlorina phenotype.
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Affiliation(s)
- Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Hongli Cao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu'an 355000, China.
| | - Chuan Yue
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China.
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Baraúna RA, Santos AV, Graças DA, Santos DM, Ghilardi R, Pimenta AMC, Carepo MSP, Schneider MPC, Silva A. Exposure to an extremely low-frequency electromagnetic field only slightly modifies the proteome of Chromobacterium violaceumATCC 12472. Genet Mol Biol 2015; 38:227-30. [PMID: 26273227 PMCID: PMC4530650 DOI: 10.1590/s1415-4757382220140240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/30/2014] [Indexed: 11/21/2022] Open
Abstract
Several studies of the physiological responses of different organisms exposed to extremely low-frequency electromagnetic fields (ELF-EMF) have been described. In this work, we report the minimal effects of in situ exposure to ELF-EMF on the global protein expression of Chromobacterium violaceum using a gel-based proteomic approach. The protein expression profile was only slightly altered, with five differentially expressed proteins detected in the exposed cultures; two of these proteins (DNA-binding stress protein, Dps, and alcohol dehydrogenase) were identified by MS/MS. The enhanced expression of Dps possibly helped to prevent physical damage to DNA. Although small, the changes in protein expression observed here were probably beneficial in helping the bacteria to adapt to the stress generated by the electromagnetic field.
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Affiliation(s)
- Rafael A Baraúna
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Agenor V Santos
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Diego A Graças
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Daniel M Santos
- Laboratório de Venenos e Toxinas, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rubens Ghilardi
- Superintendência do Meio Ambiente, Centrais Elétricas do Norte do Brasil S/A, Brasília, DF, Brazil
| | - Adriano M C Pimenta
- Laboratório de Venenos e Toxinas, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marta S P Carepo
- Rede de Química e Tecnologia, Centro de Química Fina e Biotecnologia, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Maria P C Schneider
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Artur Silva
- Laboratório de Polimorfismo de DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
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Labella C, Kanawati B, Vogel H, Schmitt-Kopplin P, Laurino S, Bianco G, Falabella P. Identification of two arginine kinase forms of endoparasitoid Leptomastix dactylopii venom by bottom up-sequence tag approach. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:756-765. [PMID: 26259659 DOI: 10.1002/jms.3585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Abstract
Leptomastix dactylopii (Howard) is an endoparasitoid wasp, natural enemy of mealybug Planococcus citri (Risso). Despite the acquired knowledge regarding this host-parasitoid interaction, only little information is available on the factors of parasitoid origin able to modulate the mealybug physiology. The major alteration observed in P. citri is a strong reduction in fecundity, which is evident soon after parasitization by L. dactylopii or venom injection in unparasitized hosts indicating that this proteinaceus secretion injected at the oviposition plays a key-role in host regulation. Protein identification of L. dactilopii venom has been limited by the lack of literature sources and public protein databases. Here, we identified two venom proteins by an integrated trascriptomic and proteomic approach. A custom-made transcriptomic database from the L. dactylopii venom glands was created by applying the high-throughput RNA sequencing approach. Two-dimensional gel electrophoresis (2DE) trypsinized protein spots were analyzed by high-resolution mass spectrometry (FTICRMS-12 T). The most abundant peptide ions were fragmented by collision induced dissociation and the obtained sequence tags were subjected to custom-made protein database searching. Two putative arginine kinases (full-length and truncated form) were identified. This is the first case in which both, truncated and full length arginine kinases, are identified in an endoparasitoid non-paralyzing venom.
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Affiliation(s)
- Cristiana Labella
- Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Basem Kanawati
- Department of Environmental Sciences, Research Unit Analytical BioGeoChemistry (BGC), Ingolstaedter Landstrasse, 85764, Neuherberg, Germany
| | - Heiko Vogel
- Department of Entomology, Host Plant Adaptation, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Philippe Schmitt-Kopplin
- Department of Environmental Sciences, Research Unit Analytical BioGeoChemistry (BGC), Ingolstaedter Landstrasse, 85764, Neuherberg, Germany
- Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, D-85354, Freising-Weihenstephan, Germany
| | - Simona Laurino
- Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Giuliana Bianco
- Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
| | - Patrizia Falabella
- Dipartimento di Scienze, Università degli Studi della Basilicata, Via dell'Ateneo Lucano 10, 85100, Potenza, Italy
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Calabrese V, Dattilo S, Petralia A, Parenti R, Pennisi M, Koverech G, Calabrese V, Graziano A, Monte I, Maiolino L, Ferreri T, Calabrese EJ. Analytical approaches to the diagnosis and treatment of aging and aging-related disease: redox status and proteomics. Free Radic Res 2015; 49:511-24. [PMID: 25824967 DOI: 10.3109/10715762.2015.1020799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Basal levels of oxidants are indispensible for redox signaling to produce adaptive cellular responses such as vitagenes linked to cell survival; however, at higher levels, they are detrimental to cells, contributing to aging and to the pathogenesis of numerous age-related diseases. Aging is a complex systemic process and the major gap in aging research reminds the insufficient knowledge about pathways shifting from normal "healthy" aging to disease-associated pathological aging. The major complication of normal "healthy" aging is in fact the increasing risk of age-related diseases such as cardiovascular diseases, diabetes mellitus, and neurodegenerative pathologies that can adversely affect the quality of life in general, with enhanced incidences of comorbidities and mortality. In this context, global "omics" approaches may help to dissect and fully study the cellular and molecular mechanisms of aging and age-associated processes. The proteome, being more close to the phenotype than the transcriptome and more stable than the metabolome, represents the most promising "omics" field in aging research. In the present study, we exploit recent advances in the redox biology of aging and discuss the potential of proteomics approaches as innovative tools for monitoring at the proteome level the extent of protein oxidative insult and related modifications with the identification of targeted proteins.
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Affiliation(s)
- V Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania , Catania , Italy
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31
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Sheng L, Zhu G, Tong Q. Comparative proteomic analysis of Aureobasidium pullulans in the presence of high and low levels of nitrogen source. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10529-10534. [PMID: 25290967 DOI: 10.1021/jf503390f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Pullulan, produced by Aureobasidium pullulans strain, has been broadly used in the food and medical industries. However, relatively little is known concerning the molecular basis of pullulan biosynthesis of this strain. In this paper, the effect of different concentrations of (NH4)2SO4 on pullulan fermentation was studied. Proteomics containing two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) were used to analyze the protein with different expressions of A. pullulans cells between the nitrogen limitation and nitrogen repletion. Maximum pullulan production reached 37.72 g/L when 0.6 g/L of initial (NH4)2SO4 was added. Excess nitrogen source would impel carbon flux flow toward biomass production, but decreased the pullulan production. Nitrogen limitation in A. pullulans seemed to influence the flux change of carbon flux flow toward exopolysaccharide accumulation. The findings indicated that 12 identified protein spots were involved in energy-generating enzymes, antioxidant-related enzymes, amino acid biosynthesis, glycogen biosynthesis, glycolysis, protein transport, and transcriptional regulation. These results presented more evidence of pullulan biosynthesis under nitrogen-limited environment, which would provide a molecular understanding of the physiological response of A. pullulans for optimizing the performance of industrial pullulan fermentation.
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Affiliation(s)
- Long Sheng
- The State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University , Wuxi 214122, China
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32
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Butterfield DA, Gu L, Di Domenico F, Robinson RAS. Mass spectrometry and redox proteomics: applications in disease. MASS SPECTROMETRY REVIEWS 2014; 33:277-301. [PMID: 24930952 DOI: 10.1002/mas.21374] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 06/03/2023]
Abstract
Proteomics techniques are continuously being developed to further understanding of biology and disease. Many of the pathways that are relevant to disease mechanisms rely on the identification of post-translational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation. Much attention has also been focused on oxidative PTMs which include protein carbonyls, protein nitration, and the incorporation of fatty acids and advanced glycation products to amino acid side chains, amongst others. The introduction of these PTMs in the cell can occur due to the attack of reactive oxygen and nitrogen species (ROS and RNS, respectively) on proteins. ROS and RNS can be present as a result of normal metabolic processes as well as external factors such as UV radiation, disease, and environmental toxins. The imbalance of ROS and RNS with antioxidant cellular defenses leads to a state of oxidative stress, which has been implicated in many diseases. Redox proteomics techniques have been used to characterize oxidative PTMs that result as a part of normal cell signaling processes as well as oxidative stress conditions. This review highlights many of the redox proteomics techniques which are currently available for several oxidative PTMs and brings to the reader's attention the application of redox proteomics for understanding disease pathogenesis in neurodegenerative disorders and others such as cancer, kidney, and heart diseases.
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Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40506
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33
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Xuan C, Gao G, Yang Q, Wang XL, Liu ZG, Liu XC, He GW. Proteomic Study Reveals Plasma Protein Changes in Congenital Heart Diseases. Ann Thorac Surg 2014; 97:1414-9. [DOI: 10.1016/j.athoracsur.2013.11.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/18/2013] [Accepted: 11/25/2013] [Indexed: 12/11/2022]
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Efecto del alprostadil en los cultivos de músculo esquelético isquémico. Estudio proteómico comparativo frente a músculo sano. ANGIOLOGIA 2014. [DOI: 10.1016/j.angio.2013.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Ghosh D, Xu J. Abiotic stress responses in plant roots: a proteomics perspective. FRONTIERS IN PLANT SCIENCE 2014; 5:6. [PMID: 24478786 PMCID: PMC3900766 DOI: 10.3389/fpls.2014.00006] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/06/2014] [Indexed: 05/18/2023]
Abstract
Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.
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Affiliation(s)
- Dipanjana Ghosh
- Department of Biological Sciences, NUS Centre for BioImaging Sciences, National University of SingaporeSingapore
| | - Jian Xu
- Department of Biological Sciences, NUS Centre for BioImaging Sciences, National University of SingaporeSingapore
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36
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Petriz BA, Franco OL. Application of Cutting-Edge Proteomics Technologies for Elucidating Host–Bacteria Interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:1-24. [DOI: 10.1016/b978-0-12-800453-1.00001-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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37
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Zi J, Zhang J, Wang Q, Zhou B, Zhong J, Zhang C, Qiu X, Wen B, Zhang S, Fu X, Lin L, Liu S. Stress responsive proteins are actively regulated during rice (Oryza sativa) embryogenesis as indicated by quantitative proteomics analysis. PLoS One 2013; 8:e74229. [PMID: 24058531 PMCID: PMC3776822 DOI: 10.1371/journal.pone.0074229] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
Embryogenesis is the initial step in a plant’s life, and the molecular changes that occur during embryonic development are largely unknown. To explore the relevant molecular events, we used the isobaric tags for relative and absolute quantification (iTRAQ) coupled with the shotgun proteomics technique (iTRAQ/Shotgun) to study the proteomic changes of rice embryos during embryogenesis. For the first time, a total of 2 165 unique proteins were identified in rice embryos, and the abundances of 867 proteins were actively changed based on the statistical evaluation of the quantitative MS/MS signals. The quantitative data were then confirmed using multiple reactions monitoring (MRM) and were also supported by our previous study based on two-dimensional gel electrophoresis (2 DE). Using the proteome at 6 days after pollination (DAP) as a reference, cluster analysis of these differential proteins throughout rice embryogenesis revealed that 25% were up-regulated and 75% were down-regulated. Gene Ontology (GO) analysis implicated that most of the up-regulated proteins were functionally categorized as stress responsive, mainly including heat shock-, lipid transfer-, and reactive oxygen species-related proteins. The stress-responsive proteins were thus postulated to play an important role during seed maturation.
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Affiliation(s)
- Jin Zi
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiyuan Zhang
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Quanhui Wang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Baojin Zhou
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Junyan Zhong
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | | | - Xuemei Qiu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Bo Wen
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
| | - Shenyan Zhang
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiqin Fu
- Hunan Hybrid Rice Research Center, Changsha, China
| | - Liang Lin
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- * E-mail: (LL); (SL)
| | - Siqi Liu
- Proteomics Division, BGI-Shenzhen, Shenzhen, China
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (LL); (SL)
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Shi Y, Deng X, Zhan Q, Shen B, Jin X, Zhu Z, Chen H, Li H, Peng C. A prospective proteomic-based study for identifying potential biomarkers for the diagnosis of cholangiocarcinoma. J Gastrointest Surg 2013; 17:1584-91. [PMID: 23868055 PMCID: PMC3753471 DOI: 10.1007/s11605-013-2182-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/05/2013] [Indexed: 01/31/2023]
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is becoming a common fatal hepatic tumor. Early detection of CCA is hampered by the absence of a sufficiently accurate and noninvasive diagnostic test. Proteomic analysis would be a powerful tool to identify potential biomarkers of this cancer. AIMS This study aims to identify new protein markers that are specific for CCA using proteomic approaches and to evaluate the performance of S100 calcium-binding protein A9 (S100A9) and chaperonin-containing TCR1, subunit 3 (CCTγ) as diagnostic markers for screening test of CCA. METHODS Two-dimensional differential gel electrophoresis (2-D DIGE) coupled with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were used to analyze and screen biomarker candidates in the proteomes of five human CCA samples and five healthy control samples. Subsequently, two potential biomarkers, S100A9 and CCTγ, were chosen for validation and analysis by immunohistochemical methods using CCA tissue microarrays. RESULTS Twenty protein spots were significantly elevated and five protein spots were downregulated in all patients (p < 0.05). The positive rate was significantly higher in patients with CCA (48 ± 35%) compared with the normal liver control group (5 ± 10%, p < 0.001), the hepatocellular carcinoma group (15 ± 20%, p < 0.001), and the cirrhosis group (12 ± 16%, p < 0.001). A greater proportion of patients with CCA were positive for CCTγ (72 ± 18%) compared with the normal liver control group (43 ± 22%, p < 0.001), the hepatocellular carcinoma group (45 ± 20%, p < 0.001), and the cirrhosis group (39 ± 25%, p < 0.001). CONCLUSIONS Combined comparative proteomic analysis using 2-D DIGE and MALDI-TOF is an effective method for identifying differentially expressed proteins in CCA tissues. The expression of S100A9 and CCTγ showed promise as novel diagnostic markers for CCA.
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Affiliation(s)
- Yuan Shi
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Xiaxing Deng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Qian Zhan
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Baiyong Shen
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Xiaolong Jin
- Department of Pathology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025 China
| | - Zhecheng Zhu
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Hao Chen
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Hongwei Li
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
| | - Chenghong Peng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er RD, Shanghai, 200025 People’s Republic of China
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Gao G, Xuan C, Yang Q, Liu XC, Liu ZG, He GW. Identification of altered plasma proteins by proteomic study in valvular heart diseases and the potential clinical significance. PLoS One 2013; 8:e72111. [PMID: 24015209 PMCID: PMC3754973 DOI: 10.1371/journal.pone.0072111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/06/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Little is known about genetic basis and proteomics in valvular heart disease (VHD) including rheumatic (RVD) and degenerative (DVD) valvular disease. The present proteomic study examined the hypothesis that certain proteins may be associated with the pathological changes in the plasma of VHD patients. METHODS AND RESULTS Differential protein analysis in the plasma identified 18 differentially expressed protein spots and 14 corresponding proteins or polypeptides by two-dimensional electrophoresis and mass spectrometry in 120 subjects. Two up-regulated (complement C4A and carbonic anhydrase 1) and three down-regulated proteins (serotransferrin, alpha-1-antichymotrypsin, and vitronectin) were validated by ELISA in enlarging samples. The plasma levels (n = 40 for each) of complement C4A in RVD (715.8±35.6 vs. 594.7±28.2 ng/ml, P = 0.009) and carbonic anhydrase 1 (237.70±15.7 vs. 184.7±10.8 U/L, P = 0.007) in DVD patients were significantly higher and that of serotransferrin (2.36±0.20 vs. 2.93±0.16 mg/ml, P = 0.025) and alpha-1-antichymotrypsin (370.0±13.7 vs. 413.0±11.6 µg/ml, P = 0.019) in RVD patients were significantly lower than those in controls. The plasma vitronectin level in both RVD (281.3±11.0 vs. 323.2±10.0 µg/ml, P = 0.006) and DVD (283.6±11.4 vs. 323.2±10.0 µg/ml, P = 0.011) was significantly lower than those in normal controls. CONCLUSIONS We have for the first time identified alterations of 14 differential proteins or polypeptides in the plasma of patients with various VHD. The elevation of plasma complement C4A in RVD and carbonic anhydrase 1 in DVD and the decrease of serotransferrin and alpha-1-antichymotrypsin in RVD patients may be useful biomarkers for these valvular diseases. The decreased plasma level of vitronectin - a protein related to the formation of valvular structure - in both RVD and DVD patients might indicate the possible genetic deficiency in these patients.
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Affiliation(s)
- Ge Gao
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
| | - Chao Xuan
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Qin Yang
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao-Cheng Liu
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Zhi-Gang Liu
- TEDA International Cardiovascular Hospital, Tianjin, China
| | - Guo-Wei He
- TEDA International Cardiovascular Hospital and The Affiliated Hospital, Hangzhou Normal University, Tianjin and Hangzhou, China
- Department of Surgery, Oregon Health and Science University, Portland, Oregon, United States of America
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Slibinskas R, Ražanskas R, Zinkevičiūtė R, Čiplys E. Comparison of first dimension IPG and NEPHGE techniques in two-dimensional gel electrophoresis experiment with cytosolic unfolded protein response in Saccharomyces cerevisiae. Proteome Sci 2013; 11:36. [PMID: 23889826 PMCID: PMC3729415 DOI: 10.1186/1477-5956-11-36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 07/23/2013] [Indexed: 12/13/2022] Open
Abstract
Background Two-dimensional gel electrophoresis (2DE) is one of the most popular methods in proteomics. Currently, most 2DE experiments are performed using immobilized pH gradient (IPG) in the first dimension; however, some laboratories still use carrier ampholytes-based isoelectric focusing technique. The aim of this study was to directly compare IPG-based and non-equilibrium pH gradient electrophoresis (NEPHGE)-based 2DE techniques by using the same samples and identical second dimension procedures. We have used commercially available Invitrogen ZOOM IPGRunner and WITAvision systems for IPG and NEPHGE, respectively. The effectiveness of IPG-based and NEPHGE-based 2DE methods was compared by analysing differential protein expression during cytosolic unfolded protein response (UPR-Cyto) in Saccharomyces cerevisiae. Results Protein loss during 2DE procedure was higher in IPG-based method, especially for basic (pI > 7) proteins. Overall reproducibility of spots was slightly better in NEPHGE-based method; however, there was a marked difference when evaluating basic and acidic protein spots. Using Coomassie staining, about half of detected basic protein spots were not reproducible by IPG-based 2DE, whereas NEPHGE-based method showed excellent reproducibility in the basic gel zone. The reproducibility of acidic proteins was similar in both methods. Absolute and relative volume variability of separate protein spots was comparable in both 2DE techniques. Regarding proteomic analysis of UPR-Cyto, the results exemplified parameters of general comparison of the methods. New highly basic protein Sis1p, overexpressed during UPR-Cyto stress, was identified by NEPHGE-based 2DE method, whereas IPG-based method showed unreliable results in the basic pI range and did not provide any new information on basic UPR-Cyto proteins. In the acidic range, the main UPR-Cyto proteins were detected and quantified by both methods. The drawback of NEPHGE-based 2DE method is its failure to detect some highly acidic proteins. The advantage of NEPHGE is higher protein capacity with good reproducibility and quality of spots at high protein load. Conclusions Comparison of broad range (pH 3–10) gradient-based 2DE methods suggests that NEPHGE-based method is preferable over IPG (Invitrogen) 2DE method for the analysis of basic proteins. Nevertheless, the narrow range (pH 4–7) IPG technique is a method of choice for the analysis of acidic proteins.
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Affiliation(s)
- Rimantas Slibinskas
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Vilnius University, V, Graiciuno 8, Vilnius LT-02241, Lithuania.
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Maslinic acid, a triterpenic anti-tumoural agent, interferes with cytoskeleton protein expression in HT29 human colon-cancer cells. J Proteomics 2013; 83:15-25. [PMID: 23499989 DOI: 10.1016/j.jprot.2013.02.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/31/2013] [Accepted: 02/25/2013] [Indexed: 12/14/2022]
Abstract
UNLABELLED Maslinic acid (MA) is an anti-tumoural agent which shows potent anti-proliferative properties against the HT29 colon-cancer cells. To shed light upon the active mechanism of MA we have investigated its effects upon the cytoskeleton. We used a proteomics procedure based on two-dimensional gel electrophoresis, mass analysis and peptide mass fingerprinting. The incubation of HT29 cells with MA led to G1 cell-cycle arrest. After 24hours' exposure to 3.7μM (IC50/8) and 30μM (IC50) MA fourteen differentially expressed cytoskeletal proteins could be discerned. One group of these proteins, made up of keratin 2, keratin 8, keratin type II cytoskeletal 8, keratin type I cytoskeletal 9, keratin type I cytoskeletal 18, cytokeratins 18 and 19, and β-actin, exert a structural function, whilst another group, made up of lamin B1, gelsolin 1, septin 2, villin 1, actin-related protein 2 and moesin, is related to the nucleation of actin and cytoskeleton formation. Changes in the expression of moesin, villin 1 and β-actin identified by the proteomics techniques were corroborated by Western blotting. This is the first evidence obtained of the regulatory effects of MA on the cytoskeleton, which may prove to be one of the bases of its anti-proliferative effect against colon-cancer cells. BIOLOGICAL SIGNIFICANCE In this paper we describe the changes in the expression of different cytoskeleton proteins identified by the proteomics techniques and corroborated by Western blotting. This is the first evidence obtained of the regulatory effects of MA on the cytoskeleton, which may prove to be one of the bases of its anti-proliferative effect against colon-cancer cells.
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Zheng Q, Song J, Campbell-Palmer L, Thompson K, Li L, Walker B, Cui Y, Li X. A proteomic investigation of apple fruit during ripening and in response to ethylene treatment. J Proteomics 2013; 93:276-94. [PMID: 23435059 DOI: 10.1016/j.jprot.2013.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 01/23/2023]
Abstract
UNLABELLED A proteomic approach employing a two dimensional electrophoresis (2-DE) technique with SYPRO Ruby, a fluorescent stain with improved sensitivity and quantitative accuracy, was performed to separate the total proteins from apple fruit at different stages of ripening and senescence. After imaging and statistical analyses were performed on 2340 spots, a total of 316 spots, or approximately 13.5% of the total protein population, was found to be significantly changed in this study. Of the 316 proteins, 219 spots were only present at a specific ripening stage, while 97 spots were significantly different (p<0.05) throughout fruit ripening and in response to ethylene treatment. From 316 candidate spots, 221 proteins were further identified by liquid chromatography and mass spectrometry analysis with protein sequence and express sequence tag (EST) data searching. Analysis and identification of proteins revealed that apple fruit ripening is associated with increase of abundance of many proteins with functions such as ethylene production, antioxidation and redox, carbohydrate metabolism, oxidative stress, energy, and defense response. Ethylene treatment increased a group of unique proteins that were not present during normal fruit ripening and have not been previously reported. It also reduced some proteins involved in primary metabolism, including those of the last few steps of the glycolytic pathway. This study demonstrated the complexity and dynamic changes of protein profiles of apple fruit during ripening and in response to exogenous ethylene treatment. Identifying and tracking protein changes may allow us to better understand the mechanism of ripening in climacteric fruit. BIOLOGICAL SIGNIFICANCE Postharvest physiology and biochemistry has been conducted on apple fruit for many years. Ethylene plays an important role in ripening and senescence in many climacteric fruit. However, little information is available at the proteome level to investigate fruit ripening and effect of ethylene treatment. The significance of this paper is that it is the first study employing 2-DE and fluorescent dye in the investigation of the apple fruit ripening and influence of ethylene treatment. It reveals some significant biological changes in association with these events and demonstrates significant changed proteins under these conditions. Therefore, our study links the biological events with proteomic information and provides detailed peptide information on all identified proteins. Through the function analysis, those significantly changed proteins are also analyzed. These findings from this paper provide not only proteome information on fruit ripening, but also pave the ground for further quantitative studies using SMR to investigate certain proteins and pathways under the hypothesis involved in fruit ripening. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Qifa Zheng
- Agriculture and Agri-Food Canada, Atlantic Food and Horticulture Research Centre, 32 Main St., Kentville, NS., Canada B4N 1J5
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George J, Shukla Y. Early changes in proteome levels upon acute deltamethrin exposure in mammalian skin system associated with its neoplastic transformation potential. J Toxicol Sci 2013; 38:629-42. [DOI: 10.2131/jts.38.629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jasmine George
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), India
| | - Yogeshwer Shukla
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), India
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Lodha TD, Hembram P, Basak NTJ. Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.46149] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Qiu J, Su Y, Gelbǐc I, Qiu Y, Xie X, Guan X. Proteomic analysis of proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Aschersonia placenta. Can J Microbiol 2012; 58:1327-34. [DOI: 10.1139/w2012-111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The infection of insects by the entomopathogenic fungus Aschersonia placenta depends on conidia. To identify proteins differentially expressed in A. placenta conidia vs mycelia, we performed a comparative proteomic analysis of A. placenta using 2-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS). We detected 1022 2-DE protein spots in conidia and 1049 in mycelia and analyzed 48 (13 from conidia and 35 from mycelia) using MALDI-TOF-MS. Finally, we identified 28 proteins (7 from conidia and 21 from mycelia). The identified proteins exclusive to conidia included major proteins participating in oxidation–reduction processes and vegetative insecticidal protein 1 (Vip1), a protein that is likely involved in pathogenicity. The identified proteins exclusive to mycelia were those involved in biosynthesis and metabolism, including uridine diphosphate galactopyranose mutase, which might play key roles in hyphal morphogenesis. This report provides the first proteomic analysis of different developmental stages of an Aschersonia species. Although only a small number of proteins were identified, the data represent a useful foundation for future studies concerning the molecular basis of entomopathogenicity in the species A. placenta and in the genus Aschersonia.
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Affiliation(s)
- Junzhi Qiu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Yubin Su
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Ivan Gelbǐc
- Biological Centre of the Academy of Sciences of the Czech Republic, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Yunfeng Qiu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Xiaocong Xie
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People’s Republic of China
| | - Xiong Guan
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People’s Republic of China
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Kaltwaßer B, Schulenborg T, Beck F, Klotz M, Schäfer KH, Schmitt M, Sickmann A, Friauf E. Developmental changes of the protein repertoire in the rat auditory brainstem: a comparative proteomics approach in the superior olivary complex and the inferior colliculus with DIGE and iTRAQ. J Proteomics 2012. [PMID: 23201114 DOI: 10.1016/j.jprot.2012.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Protein profiles of developing neural circuits undergo manifold changes. The aim of this proteomic analysis was to quantify postnatal changes in two auditory brainstem areas in a comparative approach. Protein samples from the inferior colliculus (IC) and the superior olivary complex (SOC) were obtained from neonatal (P4) and young adult (P60) rats. The cytosolic fractions of both areas were examined by 2-D DIGE, and the plasma membrane-enriched fraction of the IC was analyzed via iTRAQ. iTRAQ showed a regulation in 34% of the quantified proteins. DIGE revealed 12% regulated spots in both the SOC and IC and, thus, numeric congruency. Although regulation in KEGG pathways displayed a similar pattern in both areas, only 13 of 71 regulated DIGE proteins were regulated in common, implying major area-specific differences. 89% of regulated glycolysis/gluconeogenesis and citrate cycle proteins were up-regulated in the SOC or IC, suggesting a higher energy demand in adulthood. Seventeen cytoskeleton proteins were regulated, consistent with complex morphological reorganization between P4 and P60. Fourteen were uniquely regulated in the SOC, providing further evidence for area-specific differences. Altogether, we provide the first elaborate catalog of proteins involved in auditory brainstem development, several of them possibly of particular developmental relevance.
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Affiliation(s)
- Bernd Kaltwaßer
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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Maurer MH. Genomic and proteomic advances in autism research. Electrophoresis 2012; 33:3653-8. [PMID: 23160986 DOI: 10.1002/elps.201200382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/10/2023]
Abstract
Recent studies suggest that adult neural stem cells (NSCs) may play a role in the pathogenesis of a number of the developmental disorders subsumed under the term autism spectrum disorders (ASD) that have in common impaired social interaction, communication deficits, and stereotypical behavior or interests. Since there is no "unifying hypothesis" about the etiology and pathogenesis of ASD, several factors have been associated with ASD, including genetic factors, physical co-morbidity, disturbances of brain structure and function, biochemical anomalies, cognitive impairment, and disorders of speech and emotional development, mostly the lack of empathy. Most of disturbances of brain interconnectivity are regarded as main problem in autism. Since NSCs have a distinct life cycle in the mammalian brain consisting of proliferation, migration, arborization, integration into existing neuronal circuits, and myelinization, disturbances in NSCs differentiation is thought to be deleterious. In the current review, I will summarize the results of genomic and proteomic studies finding susceptibility genes and proteins for autism with regard to NSCs differentiation and maturation.
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Affiliation(s)
- Martin H Maurer
- Department of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.
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Kapoor I, Pal P, Lochab S, Kanaujiya JK, Trivedi AK. Proteomics approaches for myeloid leukemia drug discovery. Expert Opin Drug Discov 2012; 7:1165-75. [DOI: 10.1517/17460441.2012.724055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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HE PENGCHENG, LIU YANFENG, ZHANG MEI, WANG XIAONING, WANG HUAIYU, XI JIEYING, WEI KAIHUA, WANG HONGLI, ZHAO JING. Establishment of two-dimensional gel electrophoresis profiles of the human acute promyelocytic leukemia cell line NB4. Mol Med Rep 2012; 6:570-4. [DOI: 10.3892/mmr.2012.963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/11/2012] [Indexed: 11/06/2022] Open
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Volk S, Schreiber TD, Eisen D, Wiese C, Planatscher H, Pynn CJ, Stoll D, Templin MF, Joos TO, Pötz O. Combining ultracentrifugation and peptide termini group-specific immunoprecipitation for multiplex plasma protein analysis. Mol Cell Proteomics 2012; 11:O111.015438. [PMID: 22527512 DOI: 10.1074/mcp.o111.015438] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Blood plasma is a valuable source of potential biomarkers. However, its complexity and the huge dynamic concentration range of its constituents complicate its analysis. To tackle this problem, an immunoprecipitation strategy was employed using antibodies directed against short terminal epitope tags (triple X proteomics antibodies), which allow the enrichment of groups of signature peptides derived from trypsin-digested plasma. Isolated signature peptides are subsequently detected using MALDI-TOF/TOF mass spectrometry. Sensitivity of the immunoaffinity approach was, however, compromised by the presence of contaminant peaks derived from the peptides of nontargeted high abundant proteins. A closer analysis of the enrichment strategy revealed nonspecific peptide binding to the solid phase affinity matrix as the major source of the contaminating peptides. We therefore implemented a sucrose density gradient ultracentrifugation separation step into the procedure. This yielded a 99% depletion of contaminating peptides from a sucrose fraction containing 70% of the peptide-antibody complexes and enabled the detection of the previously undetected low abundance protein filamin-A. Assessment of this novel approach using 15 different triple X proteomics antibodies demonstrated a more consistent detection of a greater number of targeted peptides and a significant reduction in the intensity of nonspecific peptides. Ultracentrifugation coupled with immunoaffinity MS approaches presents a powerful tool for multiplexed plasma protein analysis without the requirement for demanding liquid chromatography separation techniques.
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Affiliation(s)
- Sonja Volk
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany
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