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Raza A, Schulz BL, Nouwens A, Naseem MN, Kamran M, Mantilla Valdivieso EF, Kerr ED, Constantinoiu C, Jonsson NN, James P, Tabor AE. Application of quantitative proteomics to discover biomarkers for tick resistance in cattle. Front Immunol 2023; 14:1091066. [PMID: 36793724 PMCID: PMC9924087 DOI: 10.3389/fimmu.2023.1091066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Introduction Breeding for tick resistance is a sustainable alternative to control cattle ticks due to widespread resistance to acaricidal drugs and the lack of a protective vaccine. The most accurate method used to characterise the phenotype for tick resistance in field studies is the standard tick count, but this is labour-intensive and can be hazardous to the operator. Efficient genetic selection requires reliable phenotyping or biomarker(s) for accurately identifying tick-resistant cattle. Although breed-specific genes associated with tick resistance have been identified, the mechanisms behind tick resistance have not yet been fully characterised. Methods This study applied quantitative proteomics to examine the differential abundance of serum and skin proteins using samples from naïve tick-resistant and -susceptible Brangus cattle at two-time points following tick exposure. The proteins were digested into peptides, followed by identification and quantification using sequential window acquisition of all theoretical fragment ion mass spectrometry. Results Resistant naïve cattle had a suite of proteins associated with immune response, blood coagulation and wound healing that were significantly (adjusted P < 10- 5) more abundant compared with susceptible naïve cattle. These proteins included complement factors (C3, C4, C4a), alpha-1-acid glycoprotein (AGP), beta-2-glycoprotein-1, keratins (KRT1 & KRT3) and fibrinogens (alpha & beta). The mass spectrometry findings were validated by identifying differences in the relative abundance of selected serum proteins with ELISA. The proteins showing a significantly different abundance in resistant cattle following early and prolonged tick exposures (compared to resistant naïve) were associated with immune response, blood coagulation, homeostasis, and wound healing. In contrast, susceptible cattle developed some of these responses only after prolonged tick exposure. Discussion Resistant cattle were able to transmigrate immune-response related proteins towards the tick bite sites, which may prevent tick feeding. Significantly differentially abundant proteins identified in this research in resistant naïve cattle may provide a rapid and efficient protective response to tick infestation. Physical barrier (skin integrity and wound healing) mechanisms and systemic immune responses were key contributors to resistance. Immune response-related proteins such as C4, C4a, AGP and CGN1 (naïve samples), CD14, GC and AGP (post-infestation) should be further investigated as potential biomarkers for tick resistance.
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Affiliation(s)
- Ali Raza
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Benjamin L Schulz
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Amanda Nouwens
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Muhammad Noman Naseem
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Muhammad Kamran
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Emily F Mantilla Valdivieso
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Edward D Kerr
- The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
| | - Constantin Constantinoiu
- College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Nicholas N Jonsson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Peter James
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia
| | - Ala E Tabor
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia.,The University of Queensland, School of Chemistry and Molecular Biosciences, St. Lucia, QLD, Australia
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Li J, Zhang J, Bui S, Ahat E, Kolli D, Reid W, Xing L, Wang Y. Common Assays in Mammalian Golgi Studies. Methods Mol Biol 2022; 2557:303-332. [PMID: 36512224 DOI: 10.1007/978-1-0716-2639-9_20] [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] [Indexed: 12/15/2022]
Abstract
The Golgi is a complex structure characterized by stacks of tightly aligned flat cisternae. In mammalian cells, Golgi stacks often concentrate in the perinuclear region and link together to form a ribbon. This structure is dynamic to accommodate continuous cargo flow in and out of the Golgi in both directions and undergoes morphological changes under physiological and pathological conditions. The fine, stacked Golgi structure makes it difficult to study by conventional light or even super-resolution microscopy. Furthermore, efforts to understand how Golgi structural dynamics impact cellular processes have been slow because of the knowledge gap in the protein machinery that maintains the complex and dynamic Golgi structure. In this method article, we list the common assays used in our research to help new and established researchers select the most appropriate method to properly address their questions.
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Affiliation(s)
- Jie Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Bui
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Erpan Ahat
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Divya Kolli
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Whitney Reid
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lijuan Xing
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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van Leeuwen L, Venema LH, Heilig R, Leuvenink HGD, Kessler BM. Doxycycline Alters the Porcine Renal Proteome and Degradome during Hypothermic Machine Perfusion. Curr Issues Mol Biol 2022; 44:559-577. [PMID: 35723325 PMCID: PMC8928973 DOI: 10.3390/cimb44020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Ischemia-reperfusion injury (IRI) is a hallmark for tissue injury in donation after circulatory death (DCD) kidneys. The implementation of hypothermic machine perfusion (HMP) provides a platform for improved preservation of DCD kidneys. Doxycycline administration has shown protective effects during IRI. Therefore, we explored the impact of doxycycline on proteolytic degradation mechanisms and the urinary proteome of perfused kidney grafts. Porcine kidneys underwent 30 min of warm ischemia, 24 h of oxygenated HMP (control/doxycycline) and 240 min of ex vivo reperfusion. A proteomic analysis revealed distinctive clustering profiles between urine samples collected at T15 min and T240 min. High-efficiency undecanal-based N-termini (HUNTER) kidney tissue degradomics revealed significantly more proteolytic activity in the control group at T-10. At T240, significantly more proteolytic activity was observed in the doxycycline group, indicating that doxycycline alters protein degradation during HMP. In conclusion, doxycycline administration during HMP led to significant proteomic and proteolytic differences and protective effects by attenuating urinary NGAL levels. Ultimately, we unraveled metabolic, and complement and coagulation pathways that undergo alterations during machine perfusion and that could be targeted to attenuate IRI induced injury.
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Affiliation(s)
- Leonie van Leeuwen
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
- Correspondence:
| | - Leonie H. Venema
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
| | - Raphael Heilig
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
| | - Henri G. D. Leuvenink
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
| | - Benedikt M. Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK
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Almeida AM, Ali SA, Ceciliani F, Eckersall PD, Hernández-Castellano LE, Han R, Hodnik JJ, Jaswal S, Lippolis JD, McLaughlin M, Miller I, Mohanty AK, Mrljak V, Nally JE, Nanni P, Plowman JE, Poleti MD, Ribeiro DM, Rodrigues P, Roschitzki B, Schlapbach R, Starič J, Yang Y, Zachut M. Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis. J Proteomics 2021; 241:104220. [PMID: 33838350 DOI: 10.1016/j.jprot.2021.104220] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.
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Affiliation(s)
- André M Almeida
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milano, Italy
| | - P David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Lorenzo E Hernández-Castellano
- Department of Animal Science, AU-Foulum, Aarhus University, 8830 Tjele, Denmark; Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Rongwei Han
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Jaka J Hodnik
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Shalini Jaswal
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - John D Lippolis
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Mark McLaughlin
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Ashok Kumar Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Vladimir Mrljak
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Jarlath E Nally
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Paolo Nanni
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | | | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - David M Ribeiro
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Pedro Rodrigues
- CCMAR - Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Jože Starič
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Yongxin Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
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Role of Bioinformatics in Biological Sciences. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Suzuki-Hatano S, Tsai AC, Daugherty A, Pacak CA. TMT Sample Preparation for Proteomics Facility Submission and Subsequent Data Analysis. J Vis Exp 2020. [PMID: 32568242 DOI: 10.3791/60970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Proteomic technologies are powerful methodologies that can aid our understanding of mechanisms of action in biological systems by providing a global view of the impact of a disease, treatment, or other condition on the proteome as a whole. This report provides a detailed protocol for the extraction, quantification, precipitation, digestion, labeling, and subsequent data analysis of protein samples. Our optimized TMT labeling protocol requires a lower tag-label concentration and achieves consistently reliable data. We have used this protocol to evaluate protein expression profiles in a variety of mouse tissues (i.e., heart, skeletal muscle, and brain) as well as cells cultured in vitro. In addition, we demonstrate how to evaluate thousands of proteins from the resulting dataset.
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Two-Dimensional Difference Gel Electrophoresis: A Gel-Based Proteomic Approach for Protein Analysis. Methods Mol Biol 2020; 2102:163-176. [PMID: 31989554 DOI: 10.1007/978-1-0716-0223-2_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two-dimensional difference gel electrophoresis (2D-DIGE) remains to be one of the most popular and versatile methods of protein separation among many proteomics technologies. Similar to traditional two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the proteins are separated based on their charges and molecular weight by 2D-DIGE. Different from 2D-PAGE, proteins are pre-labeled with different fluorescent dyes, and different protein samples are run in one gel by this method. Therefore, 2D-DIGE not only carries the advantages of 2D-PAGE but also eliminates gel-to-gel variation and achieves high resolution, sensitivity, and reproducibility.
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Dauth S, Maoz BM, Sheehy SP, Hemphill MA, Murty T, Macedonia MK, Greer AM, Budnik B, Parker KK. Neurons derived from different brain regions are inherently different in vitro: a novel multiregional brain-on-a-chip. J Neurophysiol 2017; 117:1320-1341. [PMID: 28031399 PMCID: PMC5350271 DOI: 10.1152/jn.00575.2016] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/28/2016] [Accepted: 12/28/2016] [Indexed: 12/30/2022] Open
Abstract
Brain in vitro models are critically important to developing our understanding of basic nervous system cellular physiology, potential neurotoxic effects of chemicals, and specific cellular mechanisms of many disease states. In this study, we sought to address key shortcomings of current brain in vitro models: the scarcity of comparative data for cells originating from distinct brain regions and the lack of multiregional brain in vitro models. We demonstrated that rat neurons from different brain regions exhibit unique profiles regarding their cell composition, protein expression, metabolism, and electrical activity in vitro. In vivo, the brain is unique in its structural and functional organization, and the interactions and communication between different brain areas are essential components of proper brain function. This fact and the observation that neurons from different areas of the brain exhibit unique behaviors in vitro underline the importance of establishing multiregional brain in vitro models. Therefore, we here developed a multiregional brain-on-a-chip and observed a reduction of overall firing activity, as well as altered amounts of astrocytes and specific neuronal cell types compared with separately cultured neurons. Furthermore, this multiregional model was used to study the effects of phencyclidine, a drug known to induce schizophrenia-like symptoms in vivo, on individual brain areas separately while monitoring downstream effects on interconnected regions. Overall, this work provides a comparison of cells from different brain regions in vitro and introduces a multiregional brain-on-a-chip that enables the development of unique disease models incorporating essential in vivo features.NEW & NOTEWORTHY Due to the scarcity of comparative data for cells from different brain regions in vitro, we demonstrated that neurons isolated from distinct brain areas exhibit unique behaviors in vitro. Moreover, in vivo proper brain function is dependent on the connection and communication of several brain regions, underlining the importance of developing multiregional brain in vitro models. We introduced a novel brain-on-a-chip model, implementing essential in vivo features, such as different brain areas and their functional connections.
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Affiliation(s)
- Stephanie Dauth
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Ben M Maoz
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Sean P Sheehy
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Matthew A Hemphill
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Tara Murty
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Mary Kate Macedonia
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Angie M Greer
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts
| | - Kevin Kit Parker
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts; and
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Biron D, Nedelkov D, Missé D, Holzmuller P. Proteomics and Host–Pathogen Interactions. GENETICS AND EVOLUTION OF INFECTIOUS DISEASES 2017. [PMCID: PMC7149668 DOI: 10.1016/b978-0-12-799942-5.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ciaramella MA, Nair MN, Suman SP, Allen PJ, Schilling MW. Differential abundance of muscle proteome in cultured channel catfish (Ictalurus punctatus) subjected to ante-mortem stressors and its impact on fillet quality. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2016; 20:10-18. [PMID: 27484844 DOI: 10.1016/j.cbd.2016.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 11/19/2022]
Abstract
The effects of environmental and handling stress during catfish (Ictalurus punctatus) aquaculture were evaluated to identify the biochemical alterations they induce in the muscle proteome and their impacts on fillet quality. Temperature (25°C and 33°C) and oxygen (~2.5mg/L [L] and >5mg/L [H]) were manipulated followed by sequential socking (S) and transport (T) stress to evaluate changes in quality when fish were subjected to handling (25-H-ST; temperature-oxygen-handling), oxygen stress (25-L-ST), temperature stress (33-H-ST) and severe stress (33-L-ST). Instrumental color and texture of fillets were evaluated, and muscle proteome profile was analyzed. Fillet redness, yellowness and chroma decreased, and hue angle increased in all treatments except temperature stress (33-H-ST). Alterations in texture compared to controls were observed when oxygen levels were held high. In general, changes in the abundance of structural proteins and those involved in protein regulation and energy metabolism were identified. Rearing under hypoxic conditions demonstrated a shift in metabolism to ketogenic pathways and a suppression of the stress-induced changes as the severity of the stress increased. Increased proteolytic activity observed through the down-regulation of various structural proteins could be responsible for the alterations in color and texture.
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Affiliation(s)
- Michael A Ciaramella
- Mississippi State University, Department of Food Science, Nutrition and Health Promotion, Herzer Building, 945 Stone Blvd, Box 9805, Mississippi State, MS 39762, United States; Mississippi State University, Department Wildlife, Fisheries and Aquaculture, Box 9690, Mississippi State, MS 39762, United States.
| | - Mahesh N Nair
- University of Kentucky, Department of Animal and Food Sciences, Lexington, KY 40546, United States
| | - Surendranath P Suman
- University of Kentucky, Department of Animal and Food Sciences, Lexington, KY 40546, United States.
| | - Peter J Allen
- Mississippi State University, Department Wildlife, Fisheries and Aquaculture, Box 9690, Mississippi State, MS 39762, United States.
| | - M Wes Schilling
- Mississippi State University, Department of Food Science, Nutrition and Health Promotion, Herzer Building, 945 Stone Blvd, Box 9805, Mississippi State, MS 39762, United States.
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Pontes AH, de Sousa MV. Mass Spectrometry-Based Approaches to Understand the Molecular Basis of Memory. Front Chem 2016; 4:40. [PMID: 27790611 PMCID: PMC5064248 DOI: 10.3389/fchem.2016.00040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/27/2016] [Indexed: 01/15/2023] Open
Abstract
The central nervous system is responsible for an array of cognitive functions such as memory, learning, language, and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS) have enabled the identification and quantification of thousands of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS)-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.
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Affiliation(s)
- Arthur H Pontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
| | - Marcelo V de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia Brasilia, Brazil
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Zhou A. Proteomics in stroke research: potentials of the nascent proteomics. J Investig Med 2016; 64:1236-1240. [PMID: 27430243 DOI: 10.1136/jim-2016-000186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/22/2023]
Abstract
Among omics, the proteomics assumes a unique role in that it offers the effectors or actuators of a biological condition. This brief review attempts to summarize the development in a relatively new but important subdiscipline of proteomics, the so-called nascent proteomics, and its potential applications in stroke research. First, we will discuss a few examples of proteomics-led discoveries in stroke research, and challenges or unmet demands when using commonly practiced proteomics approaches. Then we will introduce nascent proteomics and its studying tools, followed by discussions on its potentials in stroke research.
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Shibasaki S, Karasaki M, Aburaya S, Morisaka H, Takeda Y, Aoki W, Kitano S, Kitano M, Ueda M, Sano H, Iwasaki T. A comparative proteomics study of a synovial cell line stimulated with TNF-α. FEBS Open Bio 2016; 6:418-24. [PMID: 27419047 PMCID: PMC4856420 DOI: 10.1002/2211-5463.12049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
To elucidate the pathogenesis of rheumatoid arthritis (RA), we used proteomic analysis to determine the protein profile in a synovial cell line, MH7A, established from patients with RA. Proteins were extracted from MH7A cells that were or were not stimulated with tumor necrosis factor‐α (TNF‐α), and then analyzed on a liquid chromatography/mass spectrometry system equipped with a unique long monolithic silica capillary. On the basis of the results of this proteomic analysis, we identified 2650 proteins from untreated MH7A cells and 2688 proteins from MH7A cells stimulated with TNF‐α. Next, we selected 269 differentially produced proteins that were detected only under TNF‐α stimulation, and classified these proteins by performing gene ontology analysis by using DAVID as a functional annotation tool. In TNF‐α‐stimulated MH7A cells, we observed substantial production of plasminogen‐activator inhibitor 2 and apoptosis‐regulating proteins such as BH3‐interacting domain death agonist, autophagy protein 5, apolipoprotein E, and caspase‐3. These results indicate that the upregulation of plasminogen‐activator inhibitor 2 and apoptosis‐regulating proteins in synovial cells in response to TNF‐α stimulation might represent a predominant factor that contributes to the pathogenesis of RA.
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Affiliation(s)
- Seiji Shibasaki
- General Education Center Hyogo University of Health Sciences Kobe Japan
| | - Miki Karasaki
- General Education Center Hyogo University of Health Sciences Kobe Japan
| | - Shunsuke Aburaya
- Division of Applied Life Science Graduate School of Agriculture Kyoto University Japan
| | - Hironobu Morisaka
- Division of Applied Life Science Graduate School of Agriculture Kyoto University Japan
| | - Yumiko Takeda
- Division of Applied Life Science Graduate School of Agriculture Kyoto University Japan
| | - Wataru Aoki
- Division of Applied Life Science Graduate School of Agriculture Kyoto University Japan
| | - Sachie Kitano
- Division of Rheumatology Department of Internal Medicine Hyogo College of Medicine Nishinomiya Japan
| | - Masayasu Kitano
- Division of Rheumatology Department of Internal Medicine Hyogo College of Medicine Nishinomiya Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Science Graduate School of Agriculture Kyoto University Japan
| | - Hajime Sano
- Division of Rheumatology Department of Internal Medicine Hyogo College of Medicine Nishinomiya Japan
| | - Tsuyoshi Iwasaki
- Division of Pharmacotherapy Department of Pharmacy School of Pharmacy Hyogo University of Health Sciences Kobe Japan
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14
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Shamekhi S, Miran Baygi MH, Azarian B, Gooya A. A novel multi-scale Hessian based spot enhancement filter for two dimensional gel electrophoresis images. Comput Biol Med 2015; 66:154-69. [PMID: 26409228 DOI: 10.1016/j.compbiomed.2015.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 11/26/2022]
Abstract
Two dimensional gel electrophoresis (2DGE) is a useful method for studying proteins in a wide variety of applications including identifying post-translation modification (PTM), biomarker discovery, and protein purification. Computerized segmentation and detection of the proteins are the two main processes that are carried out on the scanned image of the gel. Due to the complexities of 2DGE images and the presence of artifacts, the segmentation and detection of protein spots in these images are non-trivial, and involve supervised and time consuming processes. This paper introduces a new spot filter for enhancing, and separating the closely overlapping spots of protein in 2DGE images based on the multi-scale eigenvalue analysis of the image Hessian. Using a Gaussian spot model, we have derived closed form equations to compute the eigen components of the image Hessian of two overlapping spots in a multi-scale fashion. Based on this analysis, we have proposed a novel filter that suppresses the overlapping area and results in a better spot separation. The performance of the proposed filter has been evaluated on the synthetic and real 2DGE images. The comparison with three conventional techniques and a commercial software package reveals the superiority and effectiveness of the proposed filter.
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Affiliation(s)
- Sina Shamekhi
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Bahareh Azarian
- Protein-Chemistry Lab., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Gooya
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, Iran
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15
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Han CM, Park JH, Chang CS, Ryoo MC. A spot-matching method using cumulative frequency matrix in 2D gel images. BIOTECHNOL BIOTEC EQ 2014; 28:S37-S43. [PMID: 26019609 PMCID: PMC4434135 DOI: 10.1080/13102818.2014.949036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/19/2014] [Indexed: 12/02/2022] Open
Abstract
A new method for spot matching in two-dimensional gel electrophoresis images using a cumulative frequency matrix is proposed. The method improves on the weak points of the previous method called ‘spot matching by topological patterns of neighbour spots’. It accumulates the frequencies of neighbour spot pairs produced through the entire matching process and determines spot pairs one by one in order of higher frequency. Spot matching by frequencies of neighbour spot pairs shows a fairly better performance. However, it can give researchers a hint for whether the matching results can be trustworthy or not, which can save researchers a lot of effort for verification of the results.
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Affiliation(s)
- Chan-Myeong Han
- Department of Computer Engineering, Yeungnam University , Gyeongsan , Gyeongbuk , Korea
| | - Joon-Ho Park
- Department of Computer Engineering, Kyungwoon University , Gumi-si , Gyeongbuk , Korea
| | - Chu-Seok Chang
- Department of Computer Engineering, Kyungwoon University , Gumi-si , Gyeongbuk , Korea
| | - Myung-Chun Ryoo
- Department of Computer Engineering, Kyungwoon University , Gumi-si , Gyeongbuk , Korea
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16
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Abstract
A protocol for protein analysis using two-dimensional difference gel electrophoresis (2D-DIGE) is described. 2D-DIGE is one of the most popular and versatile methods of protein separation among rapidly increasing proteomics technologies. Similar to traditional two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the proteins are separated based on their charges and molecular weight by 2D-DIGE. Different from 2D-PAGE, proteins are pre-labeled with different fluorescent and different protein samples are run in one gel by this method. Therefore, 2D-DIGE not only carries the advantages of 2D-PAGE but also eliminates gel-to-gel variation and achieves high resolution, sensitivity, and reproducibility.
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17
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Xu S, Liu P, Lu X, Zhang J, Huang L, Hua W, He D, Ouyang J. A highly sensitive “turn-on” fluorescent sensor for the detection of human serum proteins based on the size exclusion of the polyacrylamide gel. Electrophoresis 2013; 35:546-53. [DOI: 10.1002/elps.201300308] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Shenghao Xu
- Key Laboratory of Theoretical and Computational Photochemistry; College of Chemistry, Beijing Normal University; Ministry of Education; Beijing P. R. China
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute; CNTC; Zhengzhou P. R. China
| | - Xin Lu
- National Institutes for Food and Drug Control; Beijing P. R. China
| | - Jing Zhang
- Key Laboratory of Theoretical and Computational Photochemistry; College of Chemistry, Beijing Normal University; Ministry of Education; Beijing P. R. China
| | - Lingyun Huang
- Key Laboratory for Cell Proliferation and Regulation Biology; Beijing Normal University; Ministry of Education; Beijing P. R. China
| | - Wenhao Hua
- Department of Clinical Laboratory; Beijing Ditan Hospital; Capital Medical University; Beijing P. R. China
| | - Dacheng He
- Key Laboratory for Cell Proliferation and Regulation Biology; Beijing Normal University; Ministry of Education; Beijing P. R. China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry; College of Chemistry, Beijing Normal University; Ministry of Education; Beijing P. R. China
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18
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Song YN, Zhang GB, Zhang YY, Su SB. Clinical Applications of Omics Technologies on ZHENG Differentiation Research in Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2013; 2013:989618. [PMID: 23853666 PMCID: PMC3703351 DOI: 10.1155/2013/989618] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022]
Abstract
Traditional Chinese medicine (TCM) ZHENG is the basic concept of TCM theory. The effectiveness of TCM treatment depends on the accuracy of ZHENG differentiation. ZHENG differentiation, using the "four diagnostic methods," has the drawbacks of subjectivity and variability. Following development of omics technologies, which study the functional activities of human body from a system-wide perspective, it has been more and more applied in study of objectivity differentiating TCM ZHENG and understanding its biological mechanisms. This paper reviewed the literatures of clinical TCM ZHENG differentiation researches, underlying omics technologies, and indicated the increased trends of related articles with four kinds of omics technologies, including genomics, transcriptomics, proteomics and metabolomics, and the correlations between ZHENG differentiation and findings in omics studies. Moreover, the paper summarized the typical omics application in common studied diseases and TCM ZHENGs and discussed the main problems and countermeasure of ZHENG differentiation researches. The work here may provide a reference for further research of TCM ZHENG differentiation using omics technologies.
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Affiliation(s)
- Ya-Nan Song
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai 201203, China
| | - Gui-Biao Zhang
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai 201203, China
| | - Yong-Yu Zhang
- Research Center for Traditional Chinese Medicine and Systems Biology, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai 201203, China
| | - Shi-Bing Su
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong, Shanghai 201203, China
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Biron DG, Loxdale HD. Host–parasite molecular cross-talk during the manipulative process of a host by its parasite. J Exp Biol 2013; 216:148-60. [DOI: 10.1242/jeb.073825] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Summary
Many parasite taxa are able to alter a wide range of phenotypic traits of their hosts in ways that seem to improve the parasite’s chance of completing its life cycle. Host behavioural alterations are classically seen as compelling illustrations of the ‘extended phenotype’ concept, which suggests that parasite genes have phenotype effects on the host. The molecular mechanisms and the host–parasite cross-talk involved during the manipulative process of a host by its parasite are still poorly understood. In this Review, the current knowledge on proximate mechanisms related to the ‘parasite manipulation hypothesis’ is presented. Parasite genome sequences do not themselves provide a full explanation of parasite biology nor of the molecular cross-talk involved in host–parasite associations. Recently, first-generation proteomics tools have been employed to unravel some aspects of the parasite manipulation process (i.e. proximate mechanisms and evolutionary convergence) using certain model arthropod-host–parasite associations. The pioneer proteomics results obtained on the manipulative process are here highlighted, along with the many gaps in our knowledge. Candidate genes and biochemical pathways potentially involved in the parasite manipulation are presented. Finally, taking into account the environmental factors, we suggest new avenues and approaches to further explore and understand the proximate mechanisms used by parasite species to alter phenotypic traits of their hosts.
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Affiliation(s)
- David G. Biron
- Clermont Université, Université Blaise Pascal, Laboratoire ‘Microorganismes: Génome et Environnement’, BP 10448, F-63000 Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, F-63177 Aubiere, France
| | - Hugh D. Loxdale
- Royal Entomological Society, Chiswell Green Lane, St Albans AL2 3NS, UK
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20
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Na N, Liu T, Xu S, Zhang Y, He D, Huang L, Ouyang J. Application of fluorescent carbon nanodots in fluorescence imaging of human serum proteins. J Mater Chem B 2013; 1:787-792. [DOI: 10.1039/c2tb00335j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Nasim FUH, Ejaz S, Ashraf M, Asif AR, Oellerich M, Ahmad G, Malik GA, Attiq-Ur-Rehman. Potential biomarkers in the sera of breast cancer patients from bahawalpur, pakistan. BIOMARKERS IN CANCER 2012; 4:19-34. [PMID: 24179392 PMCID: PMC3791917 DOI: 10.4137/bic.s10502] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the approximately 90,000 cases of Breast Cancer (BC) documented annually in Pakistan are not diagnosed properly because of lack of suitable markers. We performed serum proteome expression profiling of BC and benign breast disease (BBD) patients with the aim to identify biomarkers that can be helpful for diagnosis and prognosis of the disease. Sera of patients were analyzed by one-dimensional SDS polyacrylamide gel electrophoresis (PAGE). Differentially expressed proteins were subjected to identification through LC-MS/MS analysis. In majority of the BC cases some acute phase proteins (APP) and some complement system components (C3 and C8) containing fractions were up-regulated with the exception of transthyretin (TTR) which was predominantly (68.75%) down-regulated (n = 33/48) in the sera of these patients. Varying expression patterns were observed in BBD patients and healthy controls. These differentially expressed proteins have the potential to serve as diagnostic biomarkers for BC as well as benign breast diseases.
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Affiliation(s)
- Faiz-Ul-Hassan Nasim
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, Pakistan. ; Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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22
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Applications of New Technologies and New Methods in ZHENG Differentiation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:298014. [PMID: 22675378 PMCID: PMC3364574 DOI: 10.1155/2012/298014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 03/21/2012] [Indexed: 11/18/2022]
Abstract
With the hope to provide an effective approach for personalized diagnosis and treatment clinically, Traditional Chinese Medicine (TCM) is being paid increasing attention as a complementary and alternative medicine. It performs treatment based on ZHENG (TCM syndrome) differentiation, which could be identified as clinical special phenotypes by symptoms and signs of patients. However, it caused skepticism and criticism because ZHENG classification only depends on observation, knowledge, and clinical experience of TCM practitioners, which is lack of objectivity and repeatability. Scientists have done fruitful researches for its objectivity and standardization. Compared with traditional four diagnostic methods (looking, listening and smelling, asking, and touching), in this paper, the applications of new technologies and new methods on the ZHENG differentiation were systemically reviewed, including acquisition, analysis, and integration of clinical data or information. Furthermore, the characteristics and application range of these technologies and methods were summarized. It will provide reference for further researches.
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23
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Wang JG, Xu WD, Zhai WT, Li Y, Hu JW, Hu B, Li M, Zhang L, Guo W, Zhang JP, Wang LH, Jiao BH. Disorders in angiogenesis and redox pathways are main factors contributing to the progression of rheumatoid arthritis: A comparative proteomics study. ACTA ACUST UNITED AC 2012; 64:993-1004. [DOI: 10.1002/art.33425] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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24
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25
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George J, Shukla Y. Pesticides and cancer: Insights into toxicoproteomic-based findings. J Proteomics 2011; 74:2713-22. [DOI: 10.1016/j.jprot.2011.09.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/21/2011] [Accepted: 09/25/2011] [Indexed: 12/19/2022]
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26
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Egan SA, Kurian D, Ward PN, Hunt L, Leigh JA. Identification of sortase A (SrtA) substrates in Streptococcus uberis: evidence for an additional hexapeptide (LPXXXD) sorting motif. J Proteome Res 2010; 9:1088-95. [PMID: 20038184 DOI: 10.1021/pr901025w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Sortase (a transamidase) has been shown to be responsible for the covalent attachment of proteins to the bacterial cell wall. Anchoring is effected on secreted proteins containing a specific cell wall motif toward their C-terminus; that for sortase A (SrtA) in Gram-positive bacteria often incorporates the sequence LPXTG. Such surface proteins are often characterized as virulence determinants and play important roles during the establishment and persistence of infection. Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis, which impacts on animal health and welfare and the economics of milk production. Comparison of stringently produced cell wall fractions from S. uberis and an isogenic mutant strain lacking SrtA permitted identification of 9 proteins likely to be covalently anchored at the cell surface. Analysis of these sequences implied the presence of two anchoring motifs for S. uberis, the classical LPXTG motif and an additional LPXXXD motif.
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Affiliation(s)
- Sharon A Egan
- The School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
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27
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George J, Singh R, Mahmood Z, Shukla Y. Toxicoproteomics: New paradigms in toxicology research. Toxicol Mech Methods 2010; 20:415-23. [DOI: 10.3109/15376511003667842] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Premsler T, Zahedi RP, Lewandrowski U, Sickmann A. Recent advances in yeast organelle and membrane proteomics. Proteomics 2009; 9:4731-43. [DOI: 10.1002/pmic.200900201] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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López-Pedrera C, Barbarroja N, Villalba JM. Novel biomarkers of atherosclerosis and cardiovascular risk in autoimmune diseases: Genomics and proteomics approaches. Proteomics Clin Appl 2009; 3:213-25. [DOI: 10.1002/prca.200800147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Indexed: 01/15/2023]
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30
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Ozdemir V, Suarez-Kurtz G, Stenne R, Somogyi AA, Someya T, Kayaalp SO, Kolker E. Risk assessment and communication tools for genotype associations with multifactorial phenotypes: the concept of "edge effect" and cultivating an ethical bridge between omics innovations and society. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2009; 13:43-61. [PMID: 19290811 PMCID: PMC2727354 DOI: 10.1089/omi.2009.0011] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Applications of omics technologies in the postgenomics era swiftly expanded from rare monogenic disorders to multifactorial common complex diseases, pharmacogenomics, and personalized medicine. Already, there are signposts indicative of further omics technology investment in nutritional sciences (nutrigenomics), environmental health/ecology (ecogenomics), and agriculture (agrigenomics). Genotype-phenotype association studies are a centerpiece of translational research in omics science. Yet scientific and ethical standards and ways to assess and communicate risk information obtained from association studies have been neglected to date. This is a significant gap because association studies decisively influence which genetic loci become genetic tests in the clinic or products in the genetic test marketplace. A growing challenge concerns the interpretation of large overlap typically observed in distribution of quantitative traits in a genetic association study with a polygenic/multifactorial phenotype. To remedy the shortage of risk assessment and communication tools for association studies, this paper presents the concept of edge effect. That is, the shift in population edges of a multifactorial quantitative phenotype is a more sensitive measure (than population averages) to gauge the population level impact and by extension, policy significance of an omics marker. Empirical application of the edge effect concept is illustrated using an original analysis of warfarin pharmacogenomics and the VKORC1 genetic variation in a Brazilian population sample. These edge effect analyses are examined in relation to regulatory guidance development for association studies. We explain that omics science transcends the conventional laboratory bench space and includes a highly heterogeneous cast of stakeholders in society who have a plurality of interests that are often in conflict. Hence, communication of risk information in diagnostic medicine also demands attention to processes involved in production of knowledge and human values embedded in scientific practice, for example, why, how, by whom, and to what ends association studies are conducted, and standards are developed (or not). To ensure sustainability of omics innovations and forecast their trajectory, we need interventions to bridge the gap between omics laboratory and society. Appreciation of scholarship in history of omics science is one remedy to responsibly learn from the past to ensure a sustainable future in omics fields, both emerging (nutrigenomics, ecogenomics), and those that are more established (pharmacogenomics). Another measure to build public trust and sustainability of omics fields could be legislative initiatives to create a multidisciplinary oversight body, at arm's length from conflict of interests, to carry out independent, impartial, and transparent innovation analyses and prospective technology assessment.
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Affiliation(s)
- Vural Ozdemir
- Department of Social and Preventive Medicine, Bioethics Programs, Faculty of Medicine, University of Montréal, Montréal, Québec, Canada
| | | | - Raphaëlle Stenne
- Department of Biomedical Sciences, University of Montréal, Montréal, Québec, Canada
| | - Andrew A. Somogyi
- Discipline of Pharmacology, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - S. Oğuz Kayaalp
- Turkish Academy of Sciences (TUBA) and Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Eugene Kolker
- Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
- Predictive Analytics, Seattle Children's Hospital
- Biomedical and Health Informatics Division, Medical Education and Biomedical Informatics Department, University of Washington, Seattle, Washington
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31
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Srbek J, Eickhoff J, Effelsberg U, Kraiczek K, van de Goor T, Coufal P. Chip-based nano-LC-MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device. J Sep Sci 2007; 30:2046-52. [PMID: 17654622 DOI: 10.1002/jssc.200700053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Although the proteome of each organism is unambiguously coded in its genome, the proteome shows the real biology in action in each particular organism. New powerful tools are being developed for biochemists and biologists to analyze complex biological samples for studying the complete protein supplement of the genome, i. e., the proteome. There are several methods available for proteome analysis including 2-DE and several forms of MS. In recent years, technologies such as microfluidics and array-based systems have appeared in the field of analysis, identification, and quantification of proteins. These novel approaches might help in solving current technical challenges in proteomics. This paper presents a practical application of the first commercially available microfluidic nano-ESI device coupled with nano-LC (i. e., HPLC-chip) for the analysis of samples of some biological protein mixtures.
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Affiliation(s)
- Jan Srbek
- Faculty of Science, Department of Analytical Chemistry, Charles University in Prague, Prague, Czech Republic
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32
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Zhao Y, Fleet JC, Adamec J, Terry DE, Zhang X, Kemeh S, Davisson VJ, Weaver CM. Effects of hindlimb unloading and bisphosphonates on the serum proteome of rats. Bone 2007; 41:646-58. [PMID: 17627911 DOI: 10.1016/j.bone.2007.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 05/30/2007] [Accepted: 06/01/2007] [Indexed: 11/30/2022]
Abstract
Hindlimb unloading has been used as a model for bone loss associated with extended bed rest or space travel. However, this model also reduces muscle mass and influences other biological systems. To evaluate the impact of hindlimb unloading on bone and overall health, we applied 2-D gel electrophoresis (2-DE)-based proteomics to serum samples collected from 24 5-month-old female rats that were treated for 2 weeks under three conditions: control, hindlimb unloading (HU) and unloading plus bisphosphonate (HUA) (n=8/group). Prior to the intervention, rats were injected with 3H-tetracycline to label bone surfaces. At the end of the experiment bone, urine, and serum samples were collected. As expected, HU reduced femur aBMD and BMC and increased daily urinary 3H-tetracycline (a measure of bone resorption rate) and these effects were reversed by bisphosphonate. In addition, serum osteocalcin and TRAP5b were decreased in the HUA compared to control and HU. Abundant proteins, albumin, IgG and transferrin were removed from serum samples prior to 2-DE analysis (n=5 analytical replicates). Statistical analysis of spot intensities revealed 53 differentially expressed spots among the 3 groups. Cluster analysis shows that 30 spots reflect changes unique to the HU group (i.e. potential bone biomarkers), 6 unique to HUA (i.e. drug related), and 17 common to HU and HUA (e.g. potential mental stress or muscle loss markers). Spots were identified by LC-MS/MS after in-gel trypsin digestion and were found to relate to a variety of physiological functions.
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Affiliation(s)
- Yongdong Zhao
- Department of Foods and Nutrition, Purdue University, 700 W. State St., West Lafayette, IN 47907-2059, USA
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33
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Siest G, Marteau JB, Maumus S, Berrahmoune H, Jeannesson E, Samara A, Batt AM, Visvikis-Siest S. Pharmacogénomique et pharmacoprotéomique. ANNALES PHARMACEUTIQUES FRANÇAISES 2007; 65:203-10. [PMID: 17489077 DOI: 10.1016/s0003-4509(07)90037-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The development of personalized medicine will require improved knowledge of biological variability, particularly concerning the important impact of each individual's genetic makeup. A five-step strategy can be followed when trying to identify genes and gene products involved in differential responses to cardiovascular drugs: 1) Pharmacokinetic-related genes and phenotypes; (2) Pharmacodynamic targets, genes and products; (3) Cardiovascular diseases and risks depending on specific or large metabolic cycles; (4) Physiological variations of previously identified genes and proteins; (5) Environmental influences on them. After summarizing the most well known genes involved in drug metabolism, we used statins as an example. In addition to their economic impact, statins are generally considered to be of significant importance in terms of public health. Individuals respond differently to these drugs depending on multiple polymorphisms. Applying a pharmacoproteomic strategy, it is important to use available information on peptides, proteins and metabolites, generally gene products, in each of the five steps. A profiling approach dealing with genomics as well as proteomics is useful. In conclusion, the ever growing volume of available data will require an organized interpretation of variations in DNA and mRNA as well as proteins, both on the individual and population level.
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Affiliation(s)
- G Siest
- Inserm U525 Equipe 4, Faculté de pharmacie, Université Henri Poincaré Nancy I, 30 rue Lionnois, F 54000 Nancy.
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López-Farré A, Mateos-Cáceres P, Macaya C. Etiopatogenia de la aterosclerosis: de la importancia de la genética a la utilidad de la proteómica. ANGIOLOGIA 2007. [DOI: 10.1016/s0003-3170(07)75033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
The availability of ‘omics’ technologies is transforming scientific approaches to physiological problems from a reductionist viewpoint to that of a holistic viewpoint. This is of profound importance in nutrition, since the integration of multiple systems at the level of gene expression on the synthetic side through to metabolic enzyme activity on the degradative side combine to govern nutrient availability to tissues. Protein activity is central to the process of nutrition from the initial absorption of nutrients via uptake carriers in the gut, through to distribution and transport in the blood, metabolism by degradative enzymes in tissues and excretion through renal tubule exchange proteins. Therefore, the global profiling of the proteome, defined as the entire protein complement of the genome expressed in a particular cell or organ, or in plasma or serum at a particular time, offers the potential for identification of important biomarkers of nutritional state that respond to alterations in diet. The present review considers the published evidence of nutritional modulation of the proteome in vivo which has expanded exponentially over the last 3 years. It highlights some of the challenges faced by researchers using proteomic approaches to understand the interactions of diet with genomic and metabolic–phenotypic variables in normal populations.
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Stühler K, Pfeiffer K, Joppich C, Stephan C, Jung K, Müller M, Schmidt O, van Hall A, Hamacher M, Urfer W, Meyer HE, Marcus K. Pilot study of the Human Proteome Organisation Brain Proteome Project: Applying different 2-DE techniques to monitor proteomic changes during murine brain development. Proteomics 2006; 6:4899-913. [PMID: 16927428 DOI: 10.1002/pmic.200600089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Human Proteome Organisation Brain Proteome Project aims at coordinating neuroproteomic activities with respect to analysis of development, aging, and evolution in human and mice and at analysing normal aging processes as well as neurodegenerative diseases. Our group participated in the mouse pilot study of this project using two different 2-DE systems, to find out the optimal conditions for comprehensive gel-based differential proteome analysis. Besides the assessment of the best methodical conditions the question of "How many biological replicate analyses have to be performed to get reliable statistically validated results?" was addressed. In total 420 differences were detected in all analyses. Both 2-DE methods were found to be suitable for comprehensive differential proteome analysis. Nevertheless, each of the methods showed substantial advantages and disadvantages resulting in the fact that modification of both systems is essential. From our results we can draw the conclusions that for the future optimal quantitative differential gel-based brain proteome analyses the sample preparation has to be slightly changed, the resolution of the first as well as the second dimension has to be advanced, the number of experiments has to be increased and that the 2D-DIGE system should be applied.
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Affiliation(s)
- Kai Stühler
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany.
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Kamoda S, Nakanishi Y, Kinoshita M, Ishikawa R, Kakehi K. Analysis of glycoprotein-derived oligosaccharides in glycoproteins detected on two-dimensional gel by capillary electrophoresis using on-line concentration method. J Chromatogr A 2006; 1106:67-74. [PMID: 16443453 DOI: 10.1016/j.chroma.2005.08.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 08/10/2005] [Accepted: 08/15/2005] [Indexed: 10/25/2022]
Abstract
Capillary electrophoresis (CE) is an effective tool to analyze carbohydrate mixture derived from glycoproteins with high resolution. However, CE has a disadvantage that a few nanoliters of a sample solution are injected to a narrow capillary. Therefore, we have to prepare a sample solution of high concentration for CE analysis. In the present study, we applied head column field-amplified sample stacking method to the analysis of N-linked oligosaccharides derived from glycoprotein separated by two-dimensional gel electrophoresis. Model studies demonstrated that we achieved 60-360 times concentration effect on the analysis of carbohydrate chains labeled with 3-aminobenzoic acid (3-AA). The method was applied to the analysis of N-linked oligosaccharides from glycoproteins separated and detected on PAGE gel. Heterogeneity of alpha1-acid glycoprotein (AGP), i.e. glycoforms, was examined by 2D-PAGE and N-linked oligosaccharides were released by in-gel digestion with PNGase F. The released oligosaccharides were derivatized with 3-AA and analyzed by CE. The results showed that glycoforms having lower pI values contained a larger amount of tetra- and tri-antennary oligosaccharides. In contrast, glycoforms having higher pI values contained bi-antennary oligosaccharides abundantly. The result clearly indicated that the spot of a glycoprotein glycoform detected by Coomassie brilliant blue staining on 2D-PAGE gel is sufficient for quantitative profiling of oligosaccharides.
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Affiliation(s)
- Satoru Kamoda
- Faculty of Pharmaceutical Sciences, Kinki University, Kowakae 3-4-1, Higashi-osaka 577-8502, Japan
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Agrawal GK, Rakwal R. Rice proteomics: a cornerstone for cereal food crop proteomes. MASS SPECTROMETRY REVIEWS 2006; 25:1-53. [PMID: 15957154 DOI: 10.1002/mas.20056] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proteomics-a systematic study of proteins present in a cell, tissue, organ, or organism at a particular moment during the life cycle-that began with classical two-dimensional electrophoresis and its advancement during the 1990s, has been revolutionized by a series of tremendous technological developments in mass spectrometry (MS), a core technology. Proteomics is exerting its influence on biological function of genes and genomes in the era (21st century) of functional genomics, and for this reason yeast, bacterial, and mammalian systems are the best examples. Although plant proteomics is still in its infancy, evolving proteomic technologies and the availability of the genome sequences of Arabidopsis thaliana (L.) Heyhn, and rice (Oryza sativa L.), model dicotyledoneous and monocotyledoneous (monocot) species, respectively, are propelling it towards new heights, as evidenced by the rapid spurt in worldwide plant proteome research. Rice, with an immense socio-economic impact on human civilization, is a representative model of cereal food crops, and we consider it as a cornerstone for functional genomics of cereal plants. In this review, we look at the history and the current state of monocot proteomes, including barley, maize, and wheat, with a central focus on rice, which has the most extensive proteomic coverage to date. On one side, we highlight advances in technologies that have generated enormous amount of interest in plant proteomics, and the other side summarizes the achievements made towards establishing proteomes during plant growth & development and challenge to environmental factors, including disease, and for studying genetic relationships. In light of what we have learned from the proteomic journey in rice and other monocots, we finally reveal and assess their impact in our continuous strive towards completion of their full proteomes.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Agricultural Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.
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D'Auria E, Agostoni C, Giovannini M, Riva E, Zetterström R, Fortin R, Greppi GF, Bonizzi L, Roncada P. Proteomic evaluation of milk from different mammalian species as a substitute for breast milk. Acta Paediatr 2005; 94:1708-13. [PMID: 16421029 DOI: 10.1111/j.1651-2227.2005.tb01842.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
UNLABELLED As milk represents the main source of nutrition for infants, the question of an effective human milk substitute becomes mandatory when a formula-fed baby is allergic to cows' milk proteins. In this case, formulas containing extensively hydrolysed milk proteins should be preferred, but even such a formula may cause allergic reactions in highly sensitive patients. If there is evidence of cows' milk allergy with IgE-associated symptoms, after 6 mo of age, a soy bean formula may be recommended only when tolerance to soy protein has been established by clinical challenge. In infants with allergic reactions to cows' milk proteins, even after extensive hydrolyzation, proteomic techniques coupled to immunological methods may make it possible to select other milk products that do not contain the same allergens as ordinary cow's milk. In this paper, evidence will be presented that proteomic evaluation of proteins from different mammalian species may be a suitable method of testing whether proteins from the milk of different mammalian species may be used as a substitute for untreated bovine milk. CONCLUSION Proteomic evaluation of milk from different mammalian species may not only be of help when recommending suitable feeding in cases of cows' milk allergy but also gives new insight into the background to allergic reactions caused by milk proteins.
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Affiliation(s)
- Enza D'Auria
- Department of Paediatrics, San Paolo Hospital, University of Milan, Milan, Italy
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Siest G, Marteau JB, Maumus S, Berrahmoune H, Jeannesson E, Samara A, Batt AM, Visvikis-Siest S. Pharmacogenomics and cardiovascular drugs: need for integrated biological system with phenotypes and proteomic markers. Eur J Pharmacol 2005; 527:1-22. [PMID: 16316654 DOI: 10.1016/j.ejphar.2005.10.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 09/23/2005] [Accepted: 10/05/2005] [Indexed: 01/22/2023]
Abstract
Personalized medicine is based on a better knowledge of biological variability, considering the important part due to genetics. When trying to identify involved genes and their products in differential cardiovascular drug responses, a five-step strategy is to be followed: 1) Pharmacokinetic-related genes and phenotypes (2) Pharmacodynamic targets, genes and products (3) Cardiovascular diseases and risks depending on specific or large metabolic cycles (4) Physiological variations of previously identified genes and proteins (5) Environment influences on them. After summarizing the most well-known genes involved in drug metabolism, we will take as example of drugs, the statins, considered as very important drugs from a Public-Health standpoint, but also for economical reasons. These drugs respond differently in human depending on multiple polymorphisms. We will give examples with common ApoE polymorphisms influencing the hypolipemic effects of statins. These drugs also have pleiotropic effects and decrease inflammatory markers. This illustrates the need to separate clinical diseases phenotypes in specific metabolic pathways, which could propose other classifications, of diseases and related genes. Hypertension is also a good example of clinical phenotype which should be followed after various therapeutic approaches by genes polymorphisms and proteins markers. Gene products are under clear environmental expression variations such as age, body mass index and obesity, alcohol, tobacco and dietary interventions which are the first therapeutical actions taken in cardiovascular diseases. But at each of the five steps, within a pharmacoproteomic strategy, we also need to use available information from peptides, proteins and metabolites, which usually are the gene products. A profiling approach, i.e., dealing with genomics, but now also with proteomics, is to be used. In conclusion, the profiling, as well as the large amount of data, will more than before render necessary an organized interpretation of DNA, RNA as well as proteins variations, both at individual and population level.
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Affiliation(s)
- Gérard Siest
- Inserm U525 Equipe 4, Université Henri Poincaré Nancy I, 30 rue Lionnois Faculté de Pharmacie, 54000 Nancy, France.
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Conclusions. Proteomics 2005. [DOI: 10.1007/0-306-46895-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Lee HC, Lee SW, Lee KW, Lee SW, Cha KY, Kim KH, Lee S. Identification of new proteins in follicular fluid from mature human follicles by direct sample rehydration method of two-dimensional polyacrylamide gel electrophoresis. J Korean Med Sci 2005; 20:456-60. [PMID: 15953869 PMCID: PMC2782203 DOI: 10.3346/jkms.2005.20.3.456] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Human follicular fluid (HFF) includes various biologically active proteins which can affect follicle growth and oocyte fertilization. Thus far, these proteins from mature follicles in human follicular fluid have been poorly characterized. Here, two-dimensional polyacrylamide gel electrophoresis (2-DE) with matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was used to identify new proteins in HFF. Mature follicular fluids were obtained from five females after oocyte collection during in vitro fertilization (IVF). We directly rehydrated HFF samples, obtained high-resolution 2-DE maps, and processed them for 2-DE and MALDI-MS. One hundred eighty spots were detected and 10 of these spots were identified. By the 2-DE database, six of them had been reported, as proteins already existing in HFF. Hormone sensitive lipase (HSL), Unnamed protein product 1 (UPP1), Unnamed protein product 2 (UPP2), and apolipoprotein A-IV precursor were newly detected. HSL and apolipoprotein A-IV participate in lipid metabolism. UPP1 has a homology with selenocysteine lyase. We found by RT-PCR that these genes are expressed from human primary granulosa cells. The proteins identified here may emerge as potential candidates for specific functions during folliculogenesis, hormone secretion regulation, or oocyte maturation. Further functional analysis of these proteins is necessitated to determine their biological implications.
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Affiliation(s)
- Han-Chul Lee
- Functional Genomics Lab, CHA Research Institute, Bundang Campus, College of Medicine, Pochon CHA University, Sungnam, Korea
| | - Sang-Wha Lee
- Genome Research Center for Reproductive Medicine and Infertility, CHA General Hospital, Seoul, Korea
| | - Kyo Won Lee
- Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sook-Whan Lee
- Genome Research Center for Reproductive Medicine and Infertility, CHA General Hospital, Seoul, Korea
| | - Kwang-Yul Cha
- Genome Research Center for Reproductive Medicine and Infertility, CHA General Hospital, Seoul, Korea
| | - Kye Hyun Kim
- Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Suman Lee
- Functional Genomics Lab, CHA Research Institute, Bundang Campus, College of Medicine, Pochon CHA University, Sungnam, Korea
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Biron DG, Moura H, Marché L, Hughes AL, Thomas F. Towards a new conceptual approach to ‘parasitoproteomics’. Trends Parasitol 2005; 21:162-8. [PMID: 15780837 DOI: 10.1016/j.pt.2005.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many parasitologists are betting heavily on proteomic studies to explain biochemical host-parasite interactions and, thus, to contribute to disease control. However, many "parasitoproteomic" studies are performed with powerful techniques but without a conceptual approach to determine whether the host genomic responses during a parasite infection represent a nonspecific response that might be induced by any parasite or any other stress. In this article, a new conceptual approach, based on evolutionary concepts of immune responses of a host to a parasite, is suggested for parasitologists to study the host proteome reaction after parasite invasion. Also, this new conceptual approach can be used to study other host-parasite interactions such as behavioral manipulation.
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Affiliation(s)
- David G Biron
- GEMI, UMR CNRS, IRD 2724, IRD, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France.
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Belo CAD, Toyama MH, Toyama DDO, Marangoni S, Moreno FB, Cavada BS, Fontana MD, Hyslop S, Carneiro EM, Boschero AC. Determination of the Amino Acid Sequence of a New Phospholipase A2 (MIDCA1) Isolated from Micrurus dumerilii carinicauda Venom. Protein J 2005; 24:147-53. [PMID: 16096720 DOI: 10.1007/s10930-005-7838-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new Phospholipase A(2) (PLA(2)) from Micrurus dumerilii carinicauda venom was isolated and its primary structure determined. This new PLA(2) showed a low enzymatic activity when compared with other PLA(2)s and it is moderately basic with an isoelectric point of 8.0. Its amino acid sequence showed the presence of 120 amino acid residues and its sequence was: NLIQFLNMIQCTTPGREPLVAFANYGCYCGRGGSGTPVDELDRCCQVHDNCYDTAKKVFGCSPYFTMYSYDCSEGKLTCKDNNTKCKAAVCNCDRTAALCFAKAPYNDKNYKIDLTKRCQ. The structural model of MIDCA1, when compared with other strong neurotoxic PLA(2)s, such as Naja naja, showed significant differences in the beta-wing and neurotoxic sites, despite the high level of amino acid sequence similarity. These observations indicate a dissociation between the biological and catalytic activity of this new PLA(2), supporting the view that other regions of the protein are involved in the biological effects.
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Affiliation(s)
- Cháriston A Dal Belo
- Department of Pharmacology, School of Medical Sciences, State University of Campinas, Campinas, SP, Brazil
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45
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Biron DG, Joly C, Galeotti N, Ponton F, Marché L. The proteomics: a new prospect for studying parasitic manipulation. Behav Processes 2005; 68:249-53. [PMID: 15792701 DOI: 10.1016/j.beproc.2004.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2004] [Accepted: 08/26/2004] [Indexed: 11/26/2022]
Affiliation(s)
- David G Biron
- GEMI, UMR CNRS/IRD 2724, IRD, 911 av. Agropolis BP 64501, 34394 Montpellier Cedex 5, France.
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Shishkin SS, Kovalyov LI, Kovalyova MA. Proteomic studies of human and other vertebrate muscle proteins. BIOCHEMISTRY (MOSCOW) 2004; 69:1283-98. [PMID: 15627382 DOI: 10.1007/s10541-005-0074-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review summarizes results of some systemic studies of muscle proteins of humans and some other vertebrates. The studies, started after introduction of two-dimensional gel electrophoresis of O'Farrell, were significantly extended during development of proteomics, a special branch of functional genomics. Special attention is paid to analysis of characteristic features of strategy for practical realization of the systemic approach during three main stages of these studies: pre-genomic, genomic (with organizational registration of proteomics), and post-genomic characterized by active use of structural genomics data. Proteomic technologies play an important role in detection of changes in isoforms of various muscle proteins (myosins, troponins, etc.). These changes possibly reflecting tissue specificity of gene expression may underline functional state of muscle tissues under normal and pathological conditions, and such proteomic analysis is now used in various fields of medicine.
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Affiliation(s)
- S S Shishkin
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia.
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47
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Proteomic studies of human and other vertebrate muscle proteins. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Aldred S, Grant MM, Griffiths HR. The use of proteomics for the assessment of clinical samples in research. Clin Biochem 2004; 37:943-52. [PMID: 15498520 DOI: 10.1016/j.clinbiochem.2004.09.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2004] [Accepted: 09/02/2004] [Indexed: 11/24/2022]
Abstract
Proteomics, the analysis of expressed proteins, has been an important developing area of research for the past two decades [Anderson, NG, Anderson, NL. Twenty years of two-dimensional electrophoresis: past, present and future. Electrophoresis 1996;17:443-453]. Advances in technology have led to a rapid increase in applications to a wide range of samples; from initial experiments using cell lines, more complex tissues and biological fluids are now being assessed to establish changes in protein expression. A primary aim of clinical proteomics is the identification of biomarkers for diagnosis and therapeutic intervention of disease, by comparing the proteomic profiles of control and disease, and differing physiological states. This expansion into clinical samples has not been without difficulties owing to the complexity and dynamic range in plasma and human tissues including tissue biopsies. The most widely used techniques for analysis of clinical samples are surface-enhanced laser desorption/ionisation mass spectrometry (SELDI-MS) and 2-dimensional gel electrophoresis (2-DE) coupled to matrix-assisted laser desorption ionisation [Person, MD, Monks, TJ, Lau, SS. An integrated approach to identifying chemically induced posttranslational modifications using comparative MALDI-MS and targeted HPLC-ESI-MS/MS. Chem. Res. Toxicol. 2003;16:598-608]-mass spectroscopy (MALDI-MS). This review aims to summarise the findings of studies that have used proteomic research methods to analyse samples from clinical studies and to assess the impact that proteomic techniques have had in assessing clinical samples.
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Affiliation(s)
- Sarah Aldred
- School of Sport and Exercise Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Abstract
Since the completion of the human genome, the interest of the scientific community has evolved toward understanding the human proteome. The genomic and proteomic data will facilitate our understanding of the functions of proteins in diseases and the discovery of novel drug target proteins and biomarkers of diseases. Highly sensitive analytic techniques are necessary to study the complexity of biologic samples. The key to any proteomics experiment is to reduce the complexity of the sample before mass spectrometry (MS) analysis. Numerous separation techniques have been used, including one- and two-dimensional gel electrophoresis, chromatography, and affinity techniques. MS has become a powerful method for analyzing biologic samples. This review does not cover all aspects of proteomics, but is intended to give an introductory explanation of the technology using the example of the proteomics of nasal secretions.
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Affiliation(s)
- Begoña Casado
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Georgetown University, Lower Level Gorman Building, Room GL008, 3800 Reservoir Road, NW, Washington, DC 20057, USA.
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Chen FC, Shen LF, Tsai MC, Chak KF. The IspA protease's involvement in the regulation of the sporulation process of Bacillus thuringiensis is revealed by proteomic analysis. Biochem Biophys Res Commun 2004; 312:708-15. [PMID: 14680823 DOI: 10.1016/j.bbrc.2003.10.155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Indexed: 11/20/2022]
Abstract
We have observed that the process of sporulation of the ispA-deficient mutant was delayed under phase-contrast microscopy. The protein profiles of the ispA-deficient mutant have been analyzed using two-dimensional gel electrophoresis. The results of a proteomic analysis using MALDI-TOF MS indicated that a sporulation-associated protein, pro- [Formula: see text], was upregulated, while two other sporulation-associated proteins, SpoVD and SpoVR, were downregulated in the ispA-deficient mutant. It has been known that pro- [Formula: see text] is a precursor of [Formula: see text] and is required for gene expression related to the late stage of sporulation. Moreover, SpoVD and SpoVR are known to be involved in the formation of the spore cortex. Based on these observations, we propose that the delay in the sporulation process observed in the ispA-deficient mutant may be due to a failure of [Formula: see text] to signal sporulation. This phenomenon may be further enhanced by insufficient amount of SpoVD and SpoVR for cortex formation. In this study, we have revealed for the first time a possible pathway for the regulation of sporulation-associated proteins via IspA.
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Affiliation(s)
- Fu-Chu Chen
- Institute of Biochemistry, National Yang Ming University, Shih-Pai, Taipei 11221, Taiwan, R.O.C
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