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Prims S, Van Ginneken C, Van Ostade X, Casteleyn C. Welfare Assessment in Pigs Using the Salivary Proteome. Animals (Basel) 2024; 14:1703. [PMID: 38891749 PMCID: PMC11171187 DOI: 10.3390/ani14111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Identifying the potential presence of stress at the pig farm is fundamental since it affects pig welfare. As a result, a reliable and straightforward tool to monitor stress could record the welfare status of the animals. Although numerous methods to assess the welfare of pigs have been developed in the past, no gold standard has been established yet. Recently, the value of saliva as a tool to identify chronic stress in piglets was explored, as it can be collected fast and non-invasively. Since the protein composition, i.e., the proteome of porcine saliva, responds to stress, the affected proteins could be used as salivary stress biomarkers. The present review first defines stress and its relationship with welfare. Next, the porcine gland-specific salivary proteome is characterized. Finally, six potential salivary biomarkers for stress are proposed, i.e., odorant-binding protein, vomeromodulin-like protein, chitinase, lipocalin-1, long palate lung and nasal epithelium protein, and alpha-2-HS-glycoprotein.
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Affiliation(s)
- Sara Prims
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Xaveer Van Ostade
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
| | - Christophe Casteleyn
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
- Department of Morphology, Medical Imaging, Orthopedics, Physiotherapy and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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2
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Rezaeerod K, Heinzmann H, Torrence AV, Patel J, Forsythe JG. Qualitative Monitoring of Proto-Peptide Condensation by Differential FTIR Spectroscopy. ACS EARTH & SPACE CHEMISTRY 2024; 8:937-944. [PMID: 38774359 PMCID: PMC11103710 DOI: 10.1021/acsearthspacechem.3c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024]
Abstract
Condensation processes such as wet-dry cycling are thought to have played significant roles in the emergence of proto-peptides. Here, we describe a simple and low-cost method, differential Fourier transform infrared (FTIR) spectroscopy, for qualitative analysis of peptide condensation products in model primordial reactions. We optimize differential FTIR for depsipeptides and apply this method to investigate their polymerization in the presence of extraterrestrial dust simulants.
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Affiliation(s)
- Keon Rezaeerod
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Hanna Heinzmann
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
- Analytical
and Bioanalytical Chemistry, Aalen University, 73430 Aalen, Germany
| | - Alexis V. Torrence
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jui Patel
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jay G. Forsythe
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
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3
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Wang S, Teng H, Wang L, Li P, Yuan X, Sang X, Wu J, Yang L, Xu G. A Simple Screening and Optimization Bioprocess for Long-Chain Peptide Catalysts Applied to Asymmetric Aldol Reaction. Molecules 2023; 28:6985. [PMID: 37836827 PMCID: PMC10574572 DOI: 10.3390/molecules28196985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Peptides have demonstrated their efficacy as catalysts in asymmetric aldol reactions. But the constraints inherent in chemical synthesis have imposed limitations on the viability of long-chain peptide catalysts. A noticeable dearth of tools has impeded the swift and effective screening of peptide catalysts using biological methods. To address this, we introduce a straightforward bioprocess for the screening of peptide catalysts for asymmetric aldol reactions. We synthesized several peptides through this method and obtained a 15-amino acid peptide. This peptide exhibited asymmetric aldol catalytic activity, achieving 77% ee in DMSO solvent and 63% ee with over an 80.8% yield in DMSO mixed with a pH 9.0 buffer solution. The successful application of our innovative approach not only represents an advancement but also paves the way for currently unexplored research avenues.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gang Xu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
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4
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Tubatsi G, Kebaabetswe LP, Musee N. Proteomic evaluation of nanotoxicity in aquatic organisms: A review. Proteomics 2022; 22:e2200008. [PMID: 36107811 DOI: 10.1002/pmic.202200008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 12/29/2022]
Abstract
The alteration of organisms protein functions by engineered nanoparticles (ENPs) is dependent on the complex interplay between their inherent physicochemical properties (e.g., size, surface coating, shape) and environmental conditions (e.g., pH, organic matter). To date, there is increasing interest on the use of 'omics' approaches, such as proteomics, genomics, and others, to study ENPs-biomolecules interactions in aquatic organisms. However, although proteomics has recently been applied to investigate effects of ENPs and associated mechanisms in aquatic organisms, its use remain limited. Herein, proteomics techniques widely applied to investigate ENPs-protein interactions in aquatic organisms are reviewed. Data demonstrates that 2DE and mass spectrometry and/or their combination, thereof, are the most suitable techniques to elucidate ENPs-protein interactions. Furthermore, current status on ENPs and protein interactions, and possible mechanisms of nanotoxicity with emphasis on those that exert influence at protein expression levels, and key influencing factors on ENPs-proteins interactions are outlined. Most reported studies were done using synthetic media and essay protocols and had wide variability (not standardized); this may consequently limit data application in actual environmental systems. Therefore, there is a need for studies using realistic environmental concentrations of ENPs, and actual environmental matrixes (e.g., surface water) to aid better model development of ENPs-proteins interactions in aquatic systems.
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Affiliation(s)
- Gosaitse Tubatsi
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology (BIUST), Palapye, Botswana
| | - Lemme Prica Kebaabetswe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology (BIUST), Palapye, Botswana
| | - Ndeke Musee
- Emerging Contaminants Ecological and Risk Assessment (ECERA) Research Group, Department of Chemical Engineering, University of Pretoria, Pretoria, South Africa
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5
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Jeckel AM, Beran F, Züst T, Younkin G, Petschenka G, Pokharel P, Dreisbach D, Ganal-Vonarburg SC, Robert CAM. Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches. Front Physiol 2022; 13:1001032. [PMID: 36237530 PMCID: PMC9552321 DOI: 10.3389/fphys.2022.1001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Herbivorous insects encounter diverse plant specialized metabolites (PSMs) in their diet, that have deterrent, anti-nutritional, or toxic properties. Understanding how they cope with PSMs is crucial to understand their biology, population dynamics, and evolution. This review summarizes current and emerging cutting-edge methods that can be used to characterize the metabolic fate of PSMs, from ingestion to excretion or sequestration. It further emphasizes a workflow that enables not only to study PSM metabolism at different scales, but also to tackle and validate the genetic and biochemical mechanisms involved in PSM resistance by herbivores. This review thus aims at facilitating research on PSM-mediated plant-herbivore interactions.
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Affiliation(s)
- Adriana Moriguchi Jeckel
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Franziska Beran
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tobias Züst
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Gordon Younkin
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Georg Petschenka
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Prayan Pokharel
- Department of Applied Entomology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Domenic Dreisbach
- Institute for Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Stephanie Christine Ganal-Vonarburg
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Christelle Aurélie Maud Robert
- Laboratory of Chemical Ecology, Institute of Plant Sciences, University of Bern, Bern, Switzerland
- *Correspondence: Christelle Aurélie Maud Robert,
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6
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Autoreactive antibodies control blood glucose by regulating insulin homeostasis. Proc Natl Acad Sci U S A 2022; 119:2115695119. [PMID: 35131852 PMCID: PMC8833180 DOI: 10.1073/pnas.2115695119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 12/31/2022] Open
Abstract
The random nature of antibody repertoire generation includes the potential of producing autoantibodies recognizing self-structures. It is believed that establishing immunological tolerance and prevention of autoimmune diseases require the removal of antibody specificities recognizing self. Using insulin as a common and physiologically important autoantigen, we show that anti-insulin antibodies associated with autoimmune diabetes can readily be detected in mice and humans and are involved in the physiological regulation of blood glucose levels. Importantly, human high-affinity, anti-insulin IgM antibodies protect insulin from autoimmune degradation by anti-insulin IgG antibodies. Thus, in contrast to the proposed negative selection, self-recognition and the production of highly autoreactive IgM antibodies are important for tolerance induction. Homeostasis of metabolism by hormone production is crucial for maintaining physiological integrity, as disbalance can cause severe metabolic disorders such as diabetes mellitus. Here, we show that antibody-deficient mice and immunodeficiency patients have subphysiological blood glucose concentrations. Restoring blood glucose physiology required total IgG injections and insulin-specific IgG antibodies detected in total IgG preparations and in the serum of healthy individuals. In addition to the insulin-neutralizing anti-insulin IgG, we identified two fractions of anti-insulin IgM in the serum of healthy individuals. These autoreactive IgM fractions differ in their affinity to insulin. Interestingly, the low-affinity IgM fraction (anti-insulin IgMlow) neutralizes insulin and leads to increased blood glucose, whereas the high-affinity IgM fraction (anti-insulin IgMhigh) protects insulin from neutralization by anti-insulin IgG, thereby preventing blood glucose dysregulation. To demonstrate that anti-insulin IgMhigh acts as a protector of insulin and counteracts insulin neutralization by anti-insulin IgG, we expressed the variable regions of a high-affinity anti-insulin antibody as IgG and IgM. Remarkably, the recombinant anti-insulin IgMhigh normalized insulin function and prevented IgG-mediated insulin neutralization. These results suggest that autoreactive antibodies recognizing insulin are key regulators of blood glucose and metabolism, as they control the concentration of insulin in the blood. Moreover, our data suggest that preventing autoimmune damage and maintaining physiological homeostasis requires adaptive tolerance mechanisms generating high-affinity autoreactive IgM antibodies during memory responses.
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7
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Cruz-Casas DE, Aguilar CN, Ascacio-Valdés JA, Rodríguez-Herrera R, Chávez-González ML, Flores-Gallegos AC. Enzymatic hydrolysis and microbial fermentation: The most favorable biotechnological methods for the release of bioactive peptides. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 3:100047. [PMID: 35415659 PMCID: PMC8991988 DOI: 10.1016/j.fochms.2021.100047] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022]
Abstract
Peptide release methods influence its bioactivity by generating different sequences. The absorption, toxicity and taste of peptides is influenced by the production method. The most used methods are enzymatic hydrolysis and microbial fermentation. The most used methods are biotechnological and differ in their process.
Bioactive peptides are biomolecules derived from proteins. They contain anywhere from 2 to 20 amino acids and have different bioactivities. For example, they have antihypertensive activity, antioxidant activity, antimicrobial activity, etc. However, bioactive peptides are encrypted and inactive in the parental protein, so it is necessary to release them to show their bioactivity. For this, there are different methods, where biotechnological methods are highly favorable, highlighting enzymatic hydrolysis and microbial fermentation. The choice of the method to be used depends on different factors, which is why it is essential to know about the process, its principle, and its advantages and disadvantages. The process of peptide release is critical to generate various peptide sequences, which will produce different biological effects in the hydrolysate. This review focuses on providing extensive information on the enzymatic method and microbial fermentation to facilitate selecting the method that provides the most benefits.
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Affiliation(s)
- Dora Elisa Cruz-Casas
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
| | - Cristóbal N Aguilar
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
| | - Juan A Ascacio-Valdés
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
| | - Raúl Rodríguez-Herrera
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
| | - Mónica L Chávez-González
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
| | - Adriana C Flores-Gallegos
- Bioprocesses and Bioproducts Research Group, Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Boulevard Venustiano Carranza e Ing, José Cárdenas Valdés s/n Col, República, 25280 Saltillo, Coahuila, Mexico
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8
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Borberg E, Pashko S, Koren V, Burstein L, Patolsky F. Depletion of Highly Abundant Protein Species from Biosamples by the Use of a Branched Silicon Nanopillar On-Chip Platform. Anal Chem 2021; 93:14527-14536. [PMID: 34668374 PMCID: PMC8592501 DOI: 10.1021/acs.analchem.1c03506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/10/2021] [Indexed: 11/29/2022]
Abstract
Highly abundant serum proteins tend to mask the low- and ultralow-abundance proteins, making low-abundance species detection extremely challenging. While traditional highly abundant protein depletion techniques are effective, they suffer from nonspecific binding problems and laborious sample manipulation procedures, and the kinetics of release of current separation systems is inadequately long, causing dilution of the eluted low-abundance protein samples. Here, we introduce an on-chip light-controlled reusable platform for the direct and fast depletion of highly abundant proteins from serum biosamples. Our nanoarrays display fast and highly selective depletion capabilities, up to 99% depletion of highly abundant protein species, with no undesired depletion effects on the concentration of low-abundance protein biomarkers. Displaying an ultrahigh surface area, ∼3400 m2 g-1, alongside a light-triggerable ultrafast release, this platform allows for a high depletion performance, together with high-yield reusability capabilities. Furthermore, this nanostructured light-controlled separation device could easily be integrated with downstream analytical technologies in a single lab-on-a-chip platform.
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Affiliation(s)
- Ella Borberg
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sofiya Pashko
- George
S. Wise Faculty of Life Sciences, Tel Aviv
University, Tel Aviv 69978, Israel
| | - Vlad Koren
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Larisa Burstein
- The
Wolfson Applied Materials Research Centre, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fernando Patolsky
- School
of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department
of Materials Science and Engineering, the Iby and Aladar Fleischman
Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
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9
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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10
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Agregán R, Echegaray N, López-Pedrouso M, Kharabsheh R, Franco D, Lorenzo JM. Proteomic Advances in Milk and Dairy Products. Molecules 2021; 26:3832. [PMID: 34201770 PMCID: PMC8270265 DOI: 10.3390/molecules26133832] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 02/04/2023] Open
Abstract
Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.
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Affiliation(s)
- Rubén Agregán
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - Noemí Echegaray
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain;
| | - Radwan Kharabsheh
- Business Administration, Faculty of Economics and Administrative Sciences, Applied Science University—Bahrain, Al Hidd 5055, Bahrain;
| | - Daniel Franco
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
| | - José M. Lorenzo
- Centro Tecnológico de la Carne de Galicia, Adva. Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, 32900 Ourense, Spain; (R.A.); (N.E.); (D.F.)
- Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, 32004 Ourense, Spain
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11
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Ulug SK, Jahandideh F, Wu J. Novel technologies for the production of bioactive peptides. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.12.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Towards translation of surface-enhanced Raman spectroscopy (SERS) to clinical practice: Progress and trends. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116122] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits. Methods 2020; 186:42-51. [PMID: 32758682 DOI: 10.1016/j.ymeth.2020.07.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/12/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022] Open
Abstract
The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi. Collectively, rumen microbial populations interact closely in order to degrade and ferment complex plant material into nutrients for host metabolism, a process which also produces other by-products, such as methane gas. Our understanding of the rumen microbiome and its functions are of both scientific and industrial interest, as the metabolic functions are connected to animal health and nutrition, but at the same time contribute significantly to global greenhouse gas emissions. While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active microbial populations involved in essential rumen metabolic functions. Meaningful and accurate metaproteomic analyses are highly dependent on representative samples, precise protein extraction and fractionation, as well as a comprehensive and high-quality protein sequence database that enables precise protein identification and quantification. This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions. We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for accurate reconstruction of active microbial populations in the rumen.
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14
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Fractionation of Protein Hydrolysates of Fish Waste Using Membrane Ultrafiltration: Investigation of Antibacterial and Antioxidant Activities. Probiotics Antimicrob Proteins 2020; 11:1015-1022. [PMID: 30415461 DOI: 10.1007/s12602-018-9483-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this study, yellowfin tuna (Thunnus albacores) viscera were hydrolyzed with protamex to obtain hydrolysate that is separated by a membrane ultrafiltration into four molecular size fractions (< 3, 3-10, 10-30, and 30 kDa <). Antibacterial and antioxidant properties of the resulting hydrolysates and membrane fractions were characterized, and results showed that the lowermost molecular weight fraction (< 3 kDa) had significantly the highest (P < 0.05) percentage of bacteria inhibition against Gram-positive (Listeria and Staphylococcus) and Gram-negative (E. coli and Pseudomonas) pathogenic and fish spoilage-associated microorganisms and scavenging activity against DPPH and ABTS radical and ferric reducing antioxidant power among the fractionated enzymatic hydrolysates. These results suggest that the protein hydrolysate derived from yellowfin tuna by-products and its peptide fractions could be used as an antimicrobial and antioxidant ingredient in both nutraceutical applications and functional food.
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15
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Borberg E, Zverzhinetsky M, Krivitsky A, Kosloff A, Heifler O, Degabli G, Soroka HP, Fainaro RS, Burstein L, Reuveni S, Diamant H, Krivitsky V, Patolsky F. Light-Controlled Selective Collection-and-Release of Biomolecules by an On-Chip Nanostructured Device. NANO LETTERS 2019; 19:5868-5878. [PMID: 31381354 DOI: 10.1021/acs.nanolett.9b01323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The analysis of biosamples, e.g., blood, is a ubiquitous task of proteomics, genomics, and biosensing fields; yet, it still faces multiple challenges, one of the greatest being the selective separation and detection of target proteins from these complex biosamples. Here, we demonstrate the development of an on-chip light-triggered reusable nanostructured selective and quantitative protein separation and preconcentration platform for the direct analysis of complex biosamples. The on-chip selective separation of required protein analytes from raw biosamples is performed using antibody-photoacid-modified Si nanopillars vertical arrays (SiNPs) of ultralarge binding surface area and enormously high binding affinity, followed by the light-controlled rapid release of the tightly bound target proteins in a controlled liquid media. Two important experimental observations are presented: (1) the first demonstration on the control of biological reaction binding affinity by the nanostructuring of the capturing surface, leading to highly efficient protein collection capabilities, and (2) the light-triggered switching of the highly sticky binding surfaces into highly reflective nonbinding surfaces, leading to the rapid and quantitative release of the originally tightly bound protein species. Both of these two novel behaviors were theoretically and experimentally investigated. Importantly, this is the first demonstration of a three-dimensional (3D) SiNPs on-chip filter with ultralarge binding surface area and reversible light-controlled quantitative release of adsorbed biomolecules for direct purification of blood samples, able to selectively collect and separate specific low abundant proteins, while easily removing unwanted blood components (proteins, cells) and achieving desalting results, without the requirement of time-consuming centrifugation steps, the use of desalting membranes, or affinity columns.
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Affiliation(s)
- Ella Borberg
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Marina Zverzhinetsky
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Adva Krivitsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
| | - Alon Kosloff
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Omri Heifler
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv University , Tel Aviv 69978 , Israel
| | - Gal Degabli
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Hagit Peretz Soroka
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Ronit Satchi Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine , Tel Aviv University , Tel Aviv 69978 , Israel
| | - Larisa Burstein
- The Wolfson Applied Materials Research Centre , Tel-Aviv University , Tel-Aviv 69978 , Israel
| | - Shlomi Reuveni
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Haim Diamant
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Vadim Krivitsky
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
| | - Fernando Patolsky
- School of Chemistry, Faculty of Exact Sciences , Tel Aviv University , Tel Aviv , 69978 , Israel
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering , Tel Aviv University , Tel Aviv 69978 , Israel
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He C, Jia C, Zhang Y, Xu P. Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae. J Proteome Res 2018; 17:2335-2344. [DOI: 10.1021/acs.jproteome.8b00032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Cuitong He
- Anhui Medical University, Hefei 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chenxi Jia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ping Xu
- Anhui Medical University, Hefei 230032, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, P. R. China
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17
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Stewart JL, Mercadante VR, Dias NW, Canisso IF, Yau P, Imai B, Lima FS. Nerve Growth Factor-Beta, purified from bull seminal plasma, enhances corpus luteum formation and conceptus development in Bos taurus cows. Theriogenology 2018; 106:30-38. [DOI: 10.1016/j.theriogenology.2017.10.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/25/2017] [Accepted: 10/04/2017] [Indexed: 01/09/2023]
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18
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Fractionation of Soluble Proteins Using DEAE-Sepharose, SP-Sepharose, and Phenyl Sepharose Chromatographies for Proteomics. Methods Mol Biol 2017; 1788:157-164. [PMID: 29196897 DOI: 10.1007/7651_2017_91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
In order to simplify a complex mixture of soluble proteins from tissues, a protocol to fractionate samples prior to two-dimensional (2D) gel electrophoresis has been developed. These methods involve the use of DEAE-Sepharose, SP-Sepharose, and phenyl Sepharose chromatographic columns and the fractionation of the protein mixtures based on differential anionic, cationic, and hydrophobic properties of the proteins, respectively. Fractionation of the soluble proteins with DEAE-Sepharose can result in an increase in the number of detectable 2D gel spots. These gel spots are amenable to protein identification by using in-gel trypsin digestions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and peptide mass fingerprinting. The DEAE-Sepharose column fractionation acts to partition soluble proteins from cell extracts. Similarly, a SP-Sepharose column can fractionate soluble proteins and increase the number of detectable gel spots. Lastly, fractionation of cell extract with a phenyl Sepharose column can also result in an increase in the number of detectable 2D gel spots. This chapter describes an easy, inexpensive way to fractionate soluble proteins and a way to better profile proteomes.
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19
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Ma G, Pan J, Han J, Gao L, Zhang S, Li R. Identification of M. tuberculosis antigens in the sera of tuberculosis patients using biomimetic affinity chromatography in conjunction with ESI-CID-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1061-1062:452-458. [PMID: 28820984 DOI: 10.1016/j.jchromb.2017.07.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Accepted: 07/28/2017] [Indexed: 11/16/2022]
Abstract
The profiling of abnormally-expressed proteins in host cells using mass spectrometry (MS) analysis is a classical approach for screening disease-associated biomarkers in clinical diagnosis. However, few pathogen-specific antigens can currently be detected in serum using this proteomic approach, since these are very low-abundant proteins that are easily masked by host high-abundant proteins. Identification of pathogen-specific antigens in the sera of tuberculosis patients is crucial for the clinical diagnosis of this infectious disease, especially in immune-compromised patients. In the present study, two biomimetic affinity chromatography (BiAC) media, At-23 and A115-94, were selected from a library of BiAC media and used to selectively fractionate Albumin and Immunoglobulin from sera, respectively, prior to MS analyses. Each fraction was collected and screened against the proteomic database of M. tuberculosis complex. Three antigens, FbpA, FbpB and BfrB, were identified with two distinct peptides in BiAC-fractionated sera from tuberculosis patients, which were confirmed by Western blotting. Moreover, the identification of pathogen-specific antigens in sera by BiAC in conjunction with ESI-CID-MS/MS represents a promising strategy for the discovery of disease-associated biomarkers in other diseases.
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Affiliation(s)
- Guorong Ma
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinting Pan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jincheng Han
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lina Gao
- Clinical Laboratory of the Second Affiliated Hospital, Lanzhou University, Lanzhou 730030, China
| | - Shulin Zhang
- Department of Immunology and Microbiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China.
| | - Rongxiu Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Engineering Research Center of Cells & Therapeutic Antibodies, Ministry of Education, Shanghai, China.
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20
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21
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A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
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22
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Montaño-Gutierrez LF, Ohta S, Kustatscher G, Earnshaw WC, Rappsilber J. Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data. Mol Biol Cell 2017; 28:673-680. [PMID: 28057767 PMCID: PMC5328625 DOI: 10.1091/mbc.e16-06-0370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 11/30/2022] Open
Abstract
Nano Random Forests is a machine learning-based approach to extract valuable information about multiprotein complexes in collections of proteomics experiments. In mitotic chromosome data, it retrieves known relationships among kinetochore substructures and provides highly specific predictions about uncharacterized protein function. Ever-increasing numbers of quantitative proteomics data sets constitute an underexploited resource for investigating protein function. Multiprotein complexes often follow consistent trends in these experiments, which could provide insights about their biology. Yet, as more experiments are considered, a complex’s signature may become conditional and less identifiable. Previously we successfully distinguished the general proteomic signature of genuine chromosomal proteins from hitchhikers using the Random Forests (RF) machine learning algorithm. Here we test whether small protein complexes can define distinguishable signatures of their own, despite the assumption that machine learning needs large training sets. We show, with simulated and real proteomics data, that RF can detect small protein complexes and relationships between them. We identify several complexes in quantitative proteomics results of wild-type and knockout mitotic chromosomes. Other proteins covary strongly with these complexes, suggesting novel functional links for later study. Integrating the RF analysis for several complexes reveals known interdependences among kinetochore subunits and a novel dependence between the inner kinetochore and condensin. Ribosomal proteins, although identified, remained independent of kinetochore subcomplexes. Together these results show that this complex-oriented RF (NanoRF) approach can integrate proteomics data to uncover subtle protein relationships. Our NanoRF pipeline is available online.
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Affiliation(s)
- Luis F Montaño-Gutierrez
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Shinya Ohta
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.,Center for Innovative and Translational Medicine, Medical School, Kochi University, Kochi 783-8505, Japan
| | - Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom .,Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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23
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Lepedda AJ, Lobina O, Rocchiccioli S, Nieddu G, Ucciferri N, De Muro P, Idini M, Nguyen HQT, Guarino A, Spirito R, Formato M. Identification of differentially expressed plasma proteins in atherosclerotic patients with type 2 diabetes. J Diabetes Complications 2016; 30:880-6. [PMID: 27037039 DOI: 10.1016/j.jdiacomp.2016.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
Abstract
Besides hyperglycaemia and insulin resistance, several factors are associated with a higher cardiovascular risk in type 2 diabetes mellitus (T2DM), many of them being closely related to each other owing to common origins or pathways. The pathophysiological mechanisms underlying vascular dysfunctions in diabetes include reduced bioavailability of nitric oxide, increased ROS and prothrombotic factors production, as well as activation of receptors for advanced glycation end-products. These alterations contribute to create a pro-inflammatory/thrombotic state that ultimately leads to plaque formation and complication. This study aimed at identifying differentially expressed plasma proteins between T2DM and non-diabetic patients undergoing carotid endarterectomy, by means of two-dimensional electrophoresis coupled with LC-MS/MS. Before analysis, plasma samples were enriched in low-expression proteins through combinatorial hexapeptide ligand libraries. Both mono- and two-dimensional western blotting were performed for data validation. Differentially expressed proteins were mapped onto STRING v10 to build a protein-protein interaction network. Sixteen differentially expressed spots were identified with a high score. Among them, there were fibrinogen beta and gamma chains, complement C1r, C3 and C4-B subcomponents, alpha-1-antitrypsin (AAT), vitronectin and CD5 antigen-like. Protein-Protein interaction analysis evidenced a network among differentially expressed proteins in which vitronectin seems to represent a potentially pivotal node among fibrinolysis, complement dependent immune responses and inflammation in accordance with a number of in vitro and in vivo evidences for a contributory role of these proteins to the development of diabetic atherosclerosis.
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Affiliation(s)
| | - Omar Lobina
- Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | | | - Gabriele Nieddu
- Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | - Nadia Ucciferri
- Istituto di Fisiologia Clinica, National Research Council, Pisa, Italy
| | - Pierina De Muro
- Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | - Michela Idini
- Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | | | - Anna Guarino
- Centro Cardiologico "F. Monzino," IRCCS, Milan, Italy
| | - Rita Spirito
- Centro Cardiologico "F. Monzino," IRCCS, Milan, Italy
| | - Marilena Formato
- Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy.
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24
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Herrera-Chalé F, Ruiz-Ruiz JC, Betancur-Ancona D, Segura-Campos MR. Potential Therapeutic Applications of Mucuna pruriens Peptide Fractions Purified by High-Performance Liquid Chromatography as Angiotensin-Converting Enzyme Inhibitors, Antioxidants, Antithrombotic and Hypocholesterolemic Agents. J Med Food 2016; 19:187-95. [DOI: 10.1089/jmf.2015.0098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Jorge Carlos Ruiz-Ruiz
- Department of Chemical-Biochemical Engineering, Institute of Technology of Merida, Merida, Yucatan, Mexico
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25
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Brown P, Bromberg L, Rial-Hermida MI, Wasbrough M, Hatton TA, Alvarez-Lorenzo C. Magnetic Surfactants and Polymers with Gadolinium Counterions for Protein Separations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:699-705. [PMID: 26725503 DOI: 10.1021/acs.langmuir.5b04146] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
New magnetic surfactants, (cationic hexadecyltrimethlyammonium bromotrichlorogadolinate (CTAG), decyltrimethylammonium bromotrichlorogadolinate (DTAG), and a magnetic polymer (poly(3-acrylamidopropyl)trimethylammonium tetrachlorogadolinate (APTAG)) have been synthesized by the simple mixing of the corresponding surfactants and polymer with gadolinium metal ions. A magnetic anionic surfactant, gadolinium tri(1,4-bis(2-ethylhexoxy)-1,4-dioxobutane-2-sulfonate) (Gd(AOT)3), was synthesized via metathesis. Both routes enable facile preparation of magnetically responsive magnetic polymers and surfactants without the need to rely on nanocomposites or organic frameworks with polyradicals. Electrical conductivity, surface tensiometry, SQUID magnetometry, and small-angle neutron scattering (SANS) demonstrate surface activity and self-aggregation behavior of the magnetic surfactants similar to their magnetically inert parent analogues but with added magnetic properties. The binding of the magnetic surfactants to proteins enables efficient separations under low-strength (0.33 T) magnetic fields in a new, nanoparticle-free approach to magnetophoretic protein separations and extractions. Importantly, the toxicity of the magnetic surfactants and polymers is, in some cases, lower than that of their halide analogues.
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Affiliation(s)
- Paul Brown
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Lev Bromberg
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - M Isabel Rial-Hermida
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidade de Santiago de Compostela , 15782-Santiago de Compostela, Spain
| | - Matthew Wasbrough
- NIST Centre for Neutron Research, National Institute of Standards and Technology , 100 Bureau Drive, MS 6100, Gaithersburg, Maryland 20899-6100, United States
| | - T Alan Hatton
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacia y Tecnología Farmacéutica, Facultad de Farmacia, Universidade de Santiago de Compostela , 15782-Santiago de Compostela, Spain
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26
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Aasebø E, Forthun RB, Berven F, Selheim F, Hernandez-Valladares M. Global Cell Proteome Profiling, Phospho-signaling and Quantitative Proteomics for Identification of New Biomarkers in Acute Myeloid Leukemia Patients. Curr Pharm Biotechnol 2016; 17:52-70. [PMID: 26306748 PMCID: PMC5388801 DOI: 10.2174/1389201016666150826115626] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/29/2015] [Accepted: 07/23/2015] [Indexed: 12/31/2022]
Abstract
The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low resolution mass spectrometers. However, most of the studies did not follow up, confirm or validate their candidates with more patient samples. Current proteomics methods, new high resolution and fast mass spectrometers allow the identification and quantification of several thousands of proteins obtained from few tens of μg of AML cell lysate. Enrichment methods for posttranslational modifications (PTM), such as phosphorylation, can isolate several thousands of site-specific phosphorylated peptides from AML patient samples, which subsequently can be quantified with high confidence in new mass spectrometers. While recent reports aiming to propose proteomic or phosphoproteomic biomarkers on the studied AML patient samples have taken advantage of the technological progress, the access to large cohorts of AML patients to sample from and the availability of appropriate control samples still remain challenging.
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Affiliation(s)
| | | | | | | | - Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine, Building for Basic Biology, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.
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A Review: Proteomics in Nasopharyngeal Carcinoma. Int J Mol Sci 2015; 16:15497-530. [PMID: 26184160 PMCID: PMC4519910 DOI: 10.3390/ijms160715497] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 06/08/2015] [Accepted: 07/01/2015] [Indexed: 12/24/2022] Open
Abstract
Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies.
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28
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Parray HA, Yun JW. Proteomic Identification of Target Proteins of Thiodigalactoside in White Adipose Tissue from Diet-Induced Obese Rats. Int J Mol Sci 2015; 16:14441-63. [PMID: 26121299 PMCID: PMC4519851 DOI: 10.3390/ijms160714441] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 12/11/2022] Open
Abstract
Previously, galectin-1 (GAL1) was found to be up-regulated in obesity-prone subjects, suggesting that use of a GAL1 inhibitor could be a novel therapeutic approach for treatment of obesity. We evaluated thiodigalactoside (TDG) as a potent inhibitor of GAL1 and identified target proteins of TDG by performing comparative proteome analysis of white adipose tissue (WAT) from control and TDG-treated rats fed a high fat diet (HFD) using two dimensional gel electrophoresis (2-DE) combined with MALDI-TOF-MS. Thirty-two spots from a total of 356 matched spots showed differential expression between control and TDG-treated rats, as identified by peptide mass fingerprinting. These proteins were categorized into groups such as carbohydrate metabolism, tricarboxylic acid (TCA) cycle, signal transduction, cytoskeletal, and mitochondrial proteins based on functional analysis using Protein Annotation Through Evolutionary Relationship (PANTHER) and Database for Annotation, Visualization, Integrated Discovery (DAVID) classification. One of the most striking findings of this study was significant changes in Carbonic anhydrase 3 (CA3), Voltage-dependent anion channel 1 (VDAC1), phosphatidylethanolamine-binding protein 1 (PEBP1), annexin A2 (ANXA2) and lactate dehydrogenase A chain (LDHA) protein levels between WAT from control and TDG-treated groups. In addition, we confirmed increased expression of thermogenic proteins as well as reduced expression of lipogenic proteins in response to TDG treatment. These results suggest that TDG may effectively prevent obesity, and TDG-responsive proteins can be used as novel target proteins for obesity treatment.
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Affiliation(s)
- Hilal Ahmad Parray
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk 712-714, Korea.
| | - Jong Won Yun
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk 712-714, Korea.
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29
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de Castro RJS, Sato HH. Biologically active peptides: Processes for their generation, purification and identification and applications as natural additives in the food and pharmaceutical industries. Food Res Int 2015; 74:185-198. [PMID: 28411983 DOI: 10.1016/j.foodres.2015.05.013] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/01/2015] [Accepted: 05/08/2015] [Indexed: 12/01/2022]
Abstract
Recent technological advances have created great interest in the use of biologically active peptides. Bioactive peptides can be defined as specific portions of proteins with 2 to 20 amino acids that have desirable biological activities, including antioxidant, anti-hypertensive, antithrombotic, anti-adipogenic, antimicrobial and anti-inflammatory effects. Specific characteristics, including low toxicity and high specificity, make these molecules of particular interest to the food and pharmaceutical industries. This review focuses on the production of bioactive peptides, with special emphasis on fermentation and enzymatic hydrolysis. The combination of different technologies and the use of auxiliary processes are also addressed. A survey of isolation, purification and peptide characterization methods was conducted to identify the major techniques used to determine the structures of bioactive peptides. Finally, the antioxidant, antimicrobial, anti-hypertensive, anti-adipogenic activities and probiotic-bacterial growth-promoting aspects of various peptides are discussed.
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Affiliation(s)
- Ruann Janser Soares de Castro
- Department of Food Science, School of Food Engineering, University of Campinas, 80 Rua Monteiro Lobato, Campinas, SP, Brazil.
| | - Hélia Harumi Sato
- Department of Food Science, School of Food Engineering, University of Campinas, 80 Rua Monteiro Lobato, Campinas, SP, Brazil
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30
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Ortiz-Martinez M, Winkler R, García-Lara S. Preventive and therapeutic potential of peptides from cereals against cancer. J Proteomics 2014; 111:165-83. [PMID: 24727098 DOI: 10.1016/j.jprot.2014.03.044] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/13/2014] [Accepted: 03/31/2014] [Indexed: 01/08/2023]
Abstract
Epidemiological studies have shown that regular consumption of food based on whole-grain cereals and their products is associated with reduced risks of various types of degenerative chronic diseases. Food proteins are considered an important source of nutraceutical peptides and amino acids that can exert biological functions to promote health and prevent disease, including cancer. There have been several reports on peptides with anti-tumour activity in recent years. Plant-derived peptides, such as rapeseed, amaranth and soybean lunasin have received main attention. In this review, we extend this vision to analyse the evidence of current advances in peptides in cereals such as wheat, maize, rice, barley, rye and pseudocereals compared with soybean. We also show evidence of several mechanisms through which bioactive peptide exerts anti-tumour activity. Finally, we report the current status of major strategies for the fractionation, isolation and characterisation of bioactive peptides in cereals. BIOLOGICAL SIGNIFICANCE In recent reports, it has been shown that peptides are an interesting alternative in the search for new treatments for cancer. One of the most studied sources of these peptides is food proteins; however, a review that includes more recent findings for cereals as a potential source of bioactive peptides in the treatment of cancer, the techniques for their isolation and characterisation and the assays used to prove their bioactivity is not available. This review can be used as a tool in the search for new sources of anti-cancer peptides. The authors have no conflicts of interest, financial or otherwise.
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Affiliation(s)
| | - Robert Winkler
- Dep. of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato Gto., Mexico
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MIĘKUS NATALIA, OLĘDZKA ILONA, PLENIS ALINA, WOŹNIAK ZOFIA, LEWCZUK ANNA, KOSZAŁKA PATRYCJA, SEROCZYŃSKA BARBARA, BĄCZEK TOMASZ. Gel electrophoretic separation of proteins from cultured neuroendocrine tumor cell lines. Mol Med Rep 2014; 11:1407-15. [DOI: 10.3892/mmr.2014.2864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/05/2014] [Indexed: 11/05/2022] Open
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Johnson D, Boyes B, Orlando R. The use of ammonium formate as a mobile-phase modifier for LC-MS/MS analysis of tryptic digests. J Biomol Tech 2014; 24:187-97. [PMID: 24294112 DOI: 10.7171/jbt.13-2404-005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A major challenge facing current mass spectrometry (MS)-based proteomics research is the large concentration range displayed in biological systems, which far exceeds the dynamic range of commonly available mass spectrometers. One approach to overcome this limitation is to improve online reversed-phase liquid chromatography (RP-LC) separation methodologies. LC mobile-phase modifiers are used to improve peak shape and increase sample load tolerance. Trifluoroacetic acid (TFA) is a commonly used mobile-phase modifier, as it produces peptide separations that are far superior to other additives. However, TFA leads to signal suppression when incorporated with electrospray ionization (ESI), and thus, other modifiers, such as formic acid (FA), are used for LC-MS applications. FA exhibits significantly less signal suppression, but is not as effective of a modifier as TFA. An alternative mobile-phase modifier is the combination of FA and ammonium formate (AF), which has been shown to improve peptide separations. The ESI-MS compatibility of this modifier has not been investigated, particularly for proteomic applications. This work compares the separation metrics of mobile phases modified with FA and FA/AF and explores the use of FA/AF for the LC-MS analysis of tryptic digests. Standard tryptic-digest peptides were used for comparative analysis of peak capacity and sample load tolerance. The compatibility of FA/AF in proteomic applications was examined with the analysis of soluble proteins from canine prostate carcinoma tissue. Overall, the use of FA/AF improved online RP-LC separations and led to significant increases in peptide identifications with improved protein sequence coverage.
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Affiliation(s)
- Darryl Johnson
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA; and
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33
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Radhakrishnan D, Yamashita C, Gillio-Meina C, Fraser DD. Translational research in pediatrics III: bronchoalveolar lavage. Pediatrics 2014; 134:135-54. [PMID: 24982109 DOI: 10.1542/peds.2013-1911] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The role of flexible bronchoscopy and bronchoalveolar lavage (BAL) for the care of children with airway and pulmonary diseases is well established, with collected BAL fluid most often used clinically for microbiologic pathogen identification and cellular analyses. More recently, powerful analytic research methods have been used to investigate BAL samples to better understand the pathophysiological basis of pediatric respiratory disease. Investigations have focused on the cellular components contained in BAL fluid, such as macrophages, lymphocytes, neutrophils, eosinophils, and mast cells, as well as the noncellular components such as serum molecules, inflammatory proteins, and surfactant. Molecular techniques are frequently used to investigate BAL fluid for the presence of infectious pathologies and for cellular gene expression. Recent advances in proteomics allow identification of multiple protein expression patterns linked to specific respiratory diseases, whereas newer analytic techniques allow for investigations on surfactant quantification and function. These translational research studies on BAL fluid have aided our understanding of pulmonary inflammation and the injury/repair responses in children. We review the ethics and practices for the execution of BAL in children for translational research purposes, with an emphasis on the optimal handling and processing of BAL samples.
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Affiliation(s)
- Dhenuka Radhakrishnan
- Departments of Pediatrics,Children's Health Research Institute, London, Ontario, Canada
| | - Cory Yamashita
- Medicine,Centre for Critical Illness Research, Western University, London, Ontario, Canada; andPhysiology and Pharmacology, and
| | | | - Douglas D Fraser
- Departments of Pediatrics,Children's Health Research Institute, London, Ontario, Canada;Centre for Critical Illness Research, Western University, London, Ontario, Canada; andPhysiology and Pharmacology, andClinical Neurologic Sciences, Western University, London, Ontario, Canada;Translational Research Centre, London, Ontario, Canada
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34
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Umar A, Jaremko M, Burgers PC, Luider TM, Foekens JA, Paša-Tolic L. High-throughput proteomics of breast carcinoma cells: a focus on FTICR-MS. Expert Rev Proteomics 2014; 5:445-55. [DOI: 10.1586/14789450.5.3.445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Qoronfleh MW. Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective. Expert Rev Proteomics 2014; 3:179-95. [PMID: 16608432 DOI: 10.1586/14789450.3.2.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Contemporary proteomics, currently in its exponential growth phase, is a bewildering array of tools. Proteomic methods are the result of a convergence of rapidly improving mass spectrometry technologies, protein chemistry and separation sciences, genomics and bioinformatics. Strides in improving proteomics technologies to map and measure proteomes and subproteomes are being made. However, no single proteomic platform appears ideally suited to address all research needs or accomplish ambitious goals satisfactorily. However, proteomics is in a unique position to contribute to protein discovery and to public health in terms of better biomarkers, diagnostics and treatment of disease. While the potential is great, many challenges and issues remain to be solved. Fundamental issues, such as biological variability, pre-analytic factors and analytical reproducibility, remain to be resolved. Neither an all-genetic approach nor an all-proteomic approach will solve biological complexity. Proteomics will be the foundation for constructing and extracting useful knowledge to pharma and biotech depicted in the following path: data --> structured data --> information --> information architecture --> knowledge --> useful knowledge.
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Affiliation(s)
- M Walid Qoronfleh
- Core Technology Alliance CTA, University of Michigan, Ann Arbor, MI 48109-1274, USA.
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Klein J, Buffin-Meyer B, Mullen W, Carty DM, Delles C, Vlahou A, Mischak H, Decramer S, Bascands JL, Schanstra JP. Clinical proteomics in obstetrics and neonatology. Expert Rev Proteomics 2014; 11:75-89. [PMID: 24404900 DOI: 10.1586/14789450.2014.872564] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clinical proteomics has been applied to the identification of biomarkers of obstetric and neonatal disease. We will discuss a number of encouraging studies that have led to potentially valid biomarkers in the context of Down's syndrome, preterm birth, amniotic infections, preeclampsia, intrauterine growth restriction and obstructive uropathies. Obtaining noninvasive biomarkers (e.g., from the maternal circulation, urine or cervicovaginal fluid) may be more feasible for obstetric diseases than for diseases of the fetus, for which invasive methods are required (e.g., amniotic fluid, fetal urine). However, studies providing validated proteomics-identified biomarkers are limited. Efforts should be made to save well-characterized samples of these invasive body fluids so that many valid biomarkers of pregnancy-related diseases will be identified in the coming years using proteomics based analysis upon adoption of 'clinical proteomics guidelines'.
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Affiliation(s)
- Julie Klein
- Mosaiques diagnostics & therapeutics, Hannover, Germany
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Weston LA, Bauer KM, Hummon AB. Comparison of bottom-up proteomic approaches for LC-MS analysis of complex proteomes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2013; 5:10.1039/C3AY40853A. [PMID: 24288579 PMCID: PMC3839868 DOI: 10.1039/c3ay40853a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Discovery-based proteomic studies aim to answer important biological questions by identifying as many proteins as possible. In order to accomplish this lofty goal, an effort must be placed on determining an optimal workflow that maximizes protein identifications. In this study, we compare protein extraction, digestion and fractionation methods for bottom-up proteomics using a human colon cancer cell line as our model system. Four different buffers for protein extraction, two digestion approaches, as well as three sample fractionation methods were evaluated in order to determine an accessible workflow that gives maximal protein identifications. Samples comparing these workflows were analyzed via UPLC paired with tandem MS on a Q-Exactive mass spectrometer. Our goal is to determine an optimal workflow to enable users to maximize protein identifications. Our results show that an increased number of confident protein identifications are attained with a filter-aided digestion approach as compared to an in-solution digestion. Overall SDS-PAGE fractionation leads to higher numbers of identifications than SCX SpinTip and reverse phased cartridge platforms. The novel aspect of this work is the comparison of two readily available, offline platforms for fractionation in reference to a traditional technique, SDS-PAGE.
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Affiliation(s)
| | | | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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38
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Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
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39
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Lim UM, Yap MGS, Lim YP, Goh LT, Ng SK. Identification of autocrine growth factors secreted by CHO cells for applications in single-cell cloning media. J Proteome Res 2013; 12:3496-510. [PMID: 23763710 DOI: 10.1021/pr400352n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Chinese hamster ovary (CHO) cell lines are widely used for the expression of therapeutic recombinant proteins, including monoclonal antibodies and other biologics. For manufacturing, cells derived from a single-cell clone are typically used to ensure product consistency. Presently, fetal bovine serum (FBS) is commonly used to support low cell density cultures to obtain clonal cell populations because cells grow slowly, or even do not survive at low cell densities in protein-free media. However, regulatory authorities have discouraged the use of FBS to reduce the risk of contamination by adventitious agents from animal-derived components. In this study, we demonstrated how a complementary mass spectrometry-based shotgun proteomics strategy enabled the identification of autocrine growth factors in CHO cell-conditioned media, which has led to the development of a fully defined single-cell cloning media that is serum and animal component-free. Out of 290 secreted proteins that were identified, eight secreted growth factors were reported for the first time from CHO cell cultures. By supplementing a combination of these growth factors to protein-free basal media, single cell growth of CHO cells was improved with cloning efficiencies of up to 30%, a 2-fold improvement compared to unsupplemented basal media. Complementary effects of these autocrine growth factors with other paracrine growth factors were also demonstrated when the mixture improved cloning efficiency to 42%, similar to that for the conditioned medium.
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Affiliation(s)
- U Ming Lim
- Bioprocessing Technology Institute , Agency for Science, Technology and Research-A*STAR, 20 Biopolis Way 06-01, Singapore 138668, Republic of Singapore
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40
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Zürbig P, Jahn H. Use of proteomic methods in the analysis of human body fluids in Alzheimer research. Electrophoresis 2013; 33:3617-30. [PMID: 23160951 DOI: 10.1002/elps.201200360] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/27/2012] [Accepted: 09/27/2012] [Indexed: 01/23/2023]
Abstract
Proteomics is the study of the entire population of proteins and peptides in an organism or a part of it, such as a cell, tissue, or fluids like cerebrospinal fluid, plasma, serum, urine, or saliva. It is widely assumed that changes in the composition of the proteome may reflect disease states and provide clues to its origin, eventually leading to targets for new treatments. The ability to perform large-scale proteomic studies now is based jointly on recent advances in our analytical methods. Separation techniques like CE and 2DE have developed and matured. Detection methods like MS have also improved greatly in the last 5 years. These developments have also driven the fields of bioinformatics, needed to deal with the increased data production and systems biology. All these developing methods offer specific advantages but also come with certain limitations. This review describes the different proteomic methods used in the field, their limitations, and their possible pitfalls. Based on a literature search in PubMed, we identified 112 studies that applied proteomic techniques to identify biomarkers for Alzheimer disease. This review describes the results of these studies on proteome changes in human body fluids of Alzheimer patients reviewing the most important studies. We extracted a list of 366 proteins and peptides that were identified by these studies as potential targets in Alzheimer research.
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41
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Chan KC, Issaq HJ. Fractionation of peptides by strong cation-exchange liquid chromatography. Methods Mol Biol 2013; 1002:311-315. [PMID: 23625412 DOI: 10.1007/978-1-62703-360-2_23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chromatography in all its formats plays an important role in proteomics research. The search for protein biomarkers for different diseases has been an active area of research. The dynamic concentration range and the large number of proteins in a proteome require the development of multidimensional separation strategies to allow for the identification of the largest number of proteins. Strong cation-exchange chromatography (SCX) has been used extensively for the fractionation of proteins and peptides. This chapter provides a detailed description for the SCX fractionation of complex proteome samples.
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Affiliation(s)
- King C Chan
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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42
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Al Asmari A, Khan HA, Manthiri RA. Rapid profiling of crude scorpion venom using liquid chromatography and its relevance to species identification. ACTA CHROMATOGR 2012. [DOI: 10.1556/achrom.24.2012.3.12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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43
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Wright P, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 2012; 77:738-765.e52. [DOI: 10.1016/j.theriogenology.2011.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 12/27/2022]
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Petriz BA, Gomes CP, Rocha LAO, Rezende TMB, Franco OL. Proteomics applied to exercise physiology: A cutting-edge technology. J Cell Physiol 2011; 227:885-98. [DOI: 10.1002/jcp.22809] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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45
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Issaq HJ, Fox SD, Chan KC, Veenstra TD. Global proteomics and metabolomics in cancer biomarker discovery. J Sep Sci 2011; 34:3484-92. [PMID: 22102289 DOI: 10.1002/jssc.201100528] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 10/06/2011] [Indexed: 12/15/2022]
Abstract
Chromatography and electrophoresis have been used for the last half-century to separate small and large molecules. Advances in MS instrumentation and techniques for sample introduction into the mass analyzer (i.e. matrix-assisted laser desorption/ionization and electrospray ionization), chromatography in all its formats and modes and two-dimensional gel electrophoresis, including two-dimensional difference gel electrophoresis, enabled the separation of complex biological mixtures, such as the proteome and the metabolome, in a biological sample. These advances have made it possible to identify compounds that can be used to discriminate between two samples taken from healthy and diseased individuals. The objective is to find proteins or metabolites that can be used as a clinical test for the early diagnosis, prognosis and monitoring of the disease and the outcome of therapy. In this manuscript, we present an overview of what has been achieved in the search for biomarkers, with emphasis on cancer, using separation science and MS.
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Affiliation(s)
- Haleem J Issaq
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA.
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46
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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48
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Chan KC, Veenstra TD, Issaq HJ. Comparison of Fluorescence, Laser-Induced Fluorescence, and Ultraviolet Absorbance Detection for Measuring HPLC Fractionated Protein/Peptide Mixtures. Anal Chem 2011; 83:2394-6. [DOI: 10.1021/ac1032462] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- King C. Chan
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, P.O. Box B, Frederick, Maryland 21702, United States
| | - Timothy D. Veenstra
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, P.O. Box B, Frederick, Maryland 21702, United States
| | - Haleem J. Issaq
- Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, P.O. Box B, Frederick, Maryland 21702, United States
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49
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The Combination of Lectin Affinity Chromatography, Gel Electrophoresis and Mass Spectrometry in the Study of Plant Glycoproteome: Preliminary Insights. Chromatographia 2011. [DOI: 10.1007/s10337-010-1846-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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50
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Ly L, Wasinger VC. Protein and peptide fractionation, enrichment and depletion: Tools for the complex proteome. Proteomics 2011; 11:513-34. [DOI: 10.1002/pmic.201000394] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 10/03/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022]
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