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Bautista-Valle MV, Camacho-Vazquez C, Elizalde-Contreras JM, Monribot-Villanueva JL, Limón AMV, Bojórquez-Velázquez E, Zamora-Briseño JA, Jorrin-Novo JV, Ruiz-May E. Comparing and integrating TMT-SPS-MS3 and label-free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period. Proteomics 2024; 24:e2300239. [PMID: 37681534 DOI: 10.1002/pmic.202300239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Despite substantial advances in the use of proteomic technologies, their widespread application in fruit tissues of non-model and recalcitrant species remains limited. This hampers the understanding of critical molecular events during the postharvest period of fleshy tropical fruits. Therefore, we evaluated label-free quantitation (LFQ) and TMT-SPS-MS3 (TMT) approaches to analyse changes in the protein profile of mango peels during postharvest period. We compared two extraction methods (phenol and chloroform/methanol) and two peptide fractionation schemes (SCX and HPRP). We accurately identified 3065 proteins, of which, 1492 were differentially accumulated over at 6 days after harvesting (DAH). Both LFQ and TMT approaches share 210 differential proteins including cell wall proteins associated with fruit softening, as well as aroma and flavour-related proteins, which were increased during postharvest period. The phenolic protein extraction and the high-pH reverse-phase peptide fractionation was the most effective pipeline for relative quantification. Nevertheless, the information provided by the other tested strategies was significantly complementary. Besides, LFQ spectra allowed us to track down intact N-glycopeptides corroborating N-glycosylations on the surface of a desiccation-related protein. This work represents the largest proteomic comparison of mango peels during postharvest period made so far, shedding light on the molecular foundation of edible fruit during ripening.
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Affiliation(s)
- Mirna V Bautista-Valle
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Carolina Camacho-Vazquez
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Juan Luis Monribot-Villanueva
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Abraham M Vidal Limón
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Jesús V Jorrin-Novo
- Department of Biochemistry and Molecular Biology, ETSIAM, University of Cordoba, Cordoba, Spain
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
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2
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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3
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Zhang X, Wu R, Chelliappan B. Proteomic investigation and understanding on IgY purification and product development. Poult Sci 2023; 102:102843. [PMID: 37329629 PMCID: PMC10404759 DOI: 10.1016/j.psj.2023.102843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023] Open
Abstract
An increasing demand for the development of immunoglobin Y (IgY) illustrates the necessity of the component analysis in the process of conduction and quality control. This study investigated the proteomic changes in crude IgY extracts and purified IgY products obtained by sequential polyethylene glycol precipitation (PEG) of egg yolks followed by human mycoplasma protein-based affinity chromatography compared with intact egg yolks. After confirming the extraction efficiency and purity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, liquid chromatography tandem-mass spectrometry (LC-MS/MS) was performed with samples including fresh yolk, IgY extracted product and purified product. A total of 348 proteins were identified, with 36 proteins deleted and 209 newly detected proteins in the purified product compared to the intact egg yolk. The significantly decreased proteins mainly included phosvitin, albumin, and apolipoprotein B whereas the significantly increased proteins were mainly IgY-related proteins. GO analysis showed that the purified IgY product had ATPase activity and purine ribonucleoside triphosphate binding activity, and was mainly involved in purine and nucleic acid metabolism. This study will inevitably fasten the commercial application of IgY antibodies and is of greater significance for promotion, development and approval for new antibody derived drug products.
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Affiliation(s)
- Xiaoying Zhang
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, College of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China; Centre of Molecular & Environmental Biology, Department of Biology, University of Minho, Braga 4710-057, Portugal; Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| | - Rao Wu
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, College of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, China
| | - Brindha Chelliappan
- Department of Microbiology, PSG College of Arts & Science, Bharathiar University, Coimbatore, Tamilnadu 641014, India
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Abstract
Proteins are the key biological actors within cells, driving many biological processes integral to both healthy and diseased states. Understanding the depth of complexity represented within the proteome is crucial to our scientific understanding of cellular biology and to provide disease specific insights for clinical applications. Mass spectrometry-based proteomics is the premier method for proteome analysis, with the ability to both identify and quantify proteins. Although proteomics continues to grow as a robust field of bioanalytical chemistry, advances are still necessary to enable a more comprehensive view of the proteome. In this review, we provide a broad overview of mass spectrometry-based proteomics in general, and highlight four developing areas of bottom-up proteomics: (1) protein inference, (2) alternative proteases, (3) sample-specific databases and (4) post-translational modification discovery.
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Affiliation(s)
- Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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Skoraczyński G, Gambin A, Miasojedow B. Alignstein: Optimal transport for improved LC-MS retention time alignment. Gigascience 2022; 11:6795291. [PMID: 36329619 PMCID: PMC9633278 DOI: 10.1093/gigascience/giac101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/24/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Background Reproducibility of liquid chromatography separation is limited by retention time drift. As a result, measured signals lack correspondence over replicates of the liquid chromatography–mass spectrometry (LC-MS) experiments. Correction of these errors is named retention time alignment and needs to be performed before further quantitative analysis. Despite the availability of numerous alignment algorithms, their accuracy is limited (e.g., for retention time drift that swaps analytes’ elution order). Results We present the Alignstein, an algorithm for LC-MS retention time alignment. It correctly finds correspondence even for swapped signals. To achieve this, we implemented the generalization of the Wasserstein distance to compare multidimensional features without any reduction of the information or dimension of the analyzed data. Moreover, Alignstein by design requires neither a reference sample nor prior signal identification. We validate the algorithm on publicly available benchmark datasets obtaining competitive results. Finally, we show that it can detect the information contained in the tandem mass spectrum by the spatial properties of chromatograms. Conclusions We show that the use of optimal transport effectively overcomes the limitations of existing algorithms for statistical analysis of mass spectrometry datasets. The algorithm’s source code is available at https://github.com/grzsko/Alignstein.
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Affiliation(s)
- Grzegorz Skoraczyński
- Correspondence address. Grzegorz Skoraczyński, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097 Warsaw, Poland. E-mail:
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097 Warsaw, Poland
| | - Błażej Miasojedow
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Stefana Banacha 2, 02-097 Warsaw, Poland
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McKendry J, Stokes T, Mcleod JC, Phillips SM. Resistance Exercise, Aging, Disuse, and Muscle Protein Metabolism. Compr Physiol 2021; 11:2249-2278. [PMID: 34190341 DOI: 10.1002/cphy.c200029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Skeletal muscle is the organ of locomotion, its optimal function is critical for athletic performance, and is also important for health due to its contribution to resting metabolic rate and as a site for glucose uptake and storage. Numerous endogenous and exogenous factors influence muscle mass. Much of what is currently known regarding muscle protein turnover is owed to the development and use of stable isotope tracers. Skeletal muscle mass is determined by the meal- and contraction-induced alterations of muscle protein synthesis and muscle protein breakdown. Increased loading as resistance training is the most potent nonpharmacological strategy by which skeletal muscle mass can be increased. Conversely, aging (sarcopenia) and muscle disuse lead to the development of anabolic resistance and contribute to the loss of skeletal muscle mass. Nascent omics-based technologies have significantly improved our understanding surrounding the regulation of skeletal muscle mass at the gene, transcript, and protein levels. Despite significant advances surrounding the mechanistic intricacies that underpin changes in skeletal muscle mass, these processes are complex, and more work is certainly needed. In this article, we provide an overview of the importance of skeletal muscle, describe the influence that resistance training, aging, and disuse exert on muscle protein turnover and the molecular regulatory processes that contribute to changes in muscle protein abundance. © 2021 American Physiological Society. Compr Physiol 11:2249-2278, 2021.
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Affiliation(s)
- James McKendry
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Tanner Stokes
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan C Mcleod
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
| | - Stuart M Phillips
- Exercise Metabolism Research Group, Department of Kinesiology, McMaster University, Hamilton, Ontario, Canada
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Kalita B, Bano S, Vavachan VM, Taunk K, Seshadri V, Rapole S. Application of mass spectrometry based proteomics to understand diabetes: A special focus on interactomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140469. [DOI: 10.1016/j.bbapap.2020.140469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/07/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
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8
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LaFavers KA, Macedo E, Garimella PS, Lima C, Khan S, Myslinski J, McClintick J, Witzmann FA, Winfree S, Phillips CL, Hato T, Dagher PC, Wu XR, El-Achkar TM, Micanovic R. Circulating uromodulin inhibits systemic oxidative stress by inactivating the TRPM2 channel. Sci Transl Med 2020; 11:11/512/eaaw3639. [PMID: 31578243 DOI: 10.1126/scitranslmed.aaw3639] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/26/2019] [Accepted: 08/22/2019] [Indexed: 12/21/2022]
Abstract
High serum concentrations of kidney-derived protein uromodulin [Tamm-Horsfall protein (THP)] have recently been shown to be independently associated with low mortality in both older adults and cardiac patients, but the underlying mechanism remains unclear. Here, we show that THP inhibits the generation of reactive oxygen species (ROS) both in the kidney and systemically. Consistent with this experimental data, the concentration of circulating THP in patients with surgery-induced acute kidney injury (AKI) correlated with systemic oxidative damage. THP in the serum dropped after AKI and was associated with an increase in systemic ROS. The increase in oxidant injury correlated with postsurgical mortality and need for dialysis. Mechanistically, THP inhibited the activation of the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) channel. Furthermore, inhibition of TRPM2 in vivo in a mouse model mitigated the systemic increase in ROS during AKI and THP deficiency. Our results suggest that THP is a key regulator of systemic oxidative stress by suppressing TRPM2 activity, and our findings might help explain how circulating THP deficiency is linked with poor outcomes and increased mortality.
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Affiliation(s)
- Kaice A LaFavers
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Etienne Macedo
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Pranav S Garimella
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Camila Lima
- Division of Nephrology, Department of Medicine, University of Sao Paulo, Sao Paulo 05403, Brazil
| | - Shehnaz Khan
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jered Myslinski
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jeanette McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Frank A Witzmann
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Seth Winfree
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Carrie L Phillips
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Takashi Hato
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Pierre C Dagher
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Xue-Ru Wu
- Departments of Urology and Pathology, New York University School of Medicine and Veterans Affairs, New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010, USA
| | - Tarek M El-Achkar
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA. .,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA.,Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Radmila Micanovic
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Kalesh K, Denny PW. A BONCAT-iTRAQ method enables temporally resolved quantitative profiling of newly synthesised proteins in Leishmania mexicana parasites during starvation. PLoS Negl Trop Dis 2019; 13:e0007651. [PMID: 31856154 PMCID: PMC6939940 DOI: 10.1371/journal.pntd.0007651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/02/2020] [Accepted: 11/20/2019] [Indexed: 11/19/2022] Open
Abstract
Adaptation to starvation is integral to the Leishmania life cycle. The parasite can survive prolonged periods of nutrient deprivation both in vitro and in vivo. The identification of parasite proteins synthesised during starvation is key to unravelling the underlying molecular mechanisms facilitating adaptation to these conditions. Additionally, as stress adaptation mechanisms in Leishmania are linked to virulence as well as infectivity, profiling of the complete repertoire of Newly Synthesised Proteins (NSPs) under starvation is important for drug target discovery. However, differential identification and quantitation of low abundance, starvation-specific NSPs from the larger background of the pre-existing parasite proteome has proven difficult, as this demands a highly selective and sensitive methodology. Herein we introduce an integrated chemical proteomics method in L. mexicana promastigotes that involves a powerful combination of the BONCAT technique and iTRAQ quantitative proteomics Mass Spectrometry (MS), which enabled temporally resolved quantitative profiling of de novo protein synthesis in the starving parasite. Uniquely, this approach integrates the high specificity of the BONCAT technique for the NSPs, with the high sensitivity and multiplexed quantitation capability of the iTRAQ proteomics MS. Proof-of-concept experiments identified over 250 starvation-responsive NSPs in the parasite. Our results show a starvation-specific increased relative abundance of several translation regulating and stress-responsive proteins in the parasite. GO analysis of the identified NSPs for Biological Process revealed translation (enrichment P value 2.47e-35) and peptide biosynthetic process (enrichment P value 4.84e-35) as extremely significantly enriched terms indicating the high specificity of the NSP towards regulation of protein synthesis. We believe that this approach will find widespread use in the study of the developmental stages of Leishmania species and in the broader field of protozoan biology. Periodic nutrient scarcity plays crucial roles in the life cycle of the protozoan parasite Leishmania spp. Although adaptation to nutrient stress has a pivotal role in Leishmania biology, the underlying mechanisms remain poorly understood. In a period of nutrient starvation, the parasite responds by decreasing its protein production to conserve nutrient resources and to prevent formation of toxic proteins. However, even during severe starvation, the parasite generates certain essential quality control and rescue proteins. Differential identification of the complete repertoire of these proteins synthesised during starvation from the pre-existing proteins in the parasite holds the key to understanding the starvation adaptation mechanisms. This has been challenging to accomplish due to technical limitations. Using a combination of chemical labelling techniques and protein mass-spectrometry, we selectively identified and measured the proteins generated in the starving Leishmania parasite. Our results show a starvation time-dependent differential expression of important protein synthesis regulators in the parasite. This will serve as an important dataset for a holistic understanding of the starvation adaptation mechanisms in Leishmania. We also believe that this method will find widespread applications in the field of protozoa and other parasites causing Neglected Tropical Diseases.
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Affiliation(s)
- Karunakaran Kalesh
- Department of Chemistry, Durham University, Durham, United Kingdom
- * E-mail:
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
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Doyle LM, Wang MZ. Overview of Extracellular Vesicles, Their Origin, Composition, Purpose, and Methods for Exosome Isolation and Analysis. Cells 2019; 8:E727. [PMID: 31311206 PMCID: PMC6678302 DOI: 10.3390/cells8070727] [Citation(s) in RCA: 1622] [Impact Index Per Article: 324.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
The use of extracellular vesicles, specifically exosomes, as carriers of biomarkers in extracellular spaces has been well demonstrated. Despite their promising potential, the use of exosomes in the clinical setting is restricted due to the lack of standardization in exosome isolation and analysis methods. The purpose of this review is to not only introduce the different types of extracellular vesicles but also to summarize their differences and similarities, and discuss different methods of exosome isolation and analysis currently used. A thorough understanding of the isolation and analysis methods currently being used could lead to some standardization in the field of exosomal research, allowing the use of exosomes in the clinical setting to become a reality.
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Affiliation(s)
- Laura M Doyle
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA
| | - Michael Zhuo Wang
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66047, USA.
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11
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Nanaware PP, Jurewicz MM, Leszyk JD, Shaffer SA, Stern LJ. HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. Mol Cell Proteomics 2019; 18:490-503. [PMID: 30573663 PMCID: PMC6398211 DOI: 10.1074/mcp.ra118.000956] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
Presentation of antigenic peptides on MHC-II molecules is essential for tolerance to self and for initiation of immune responses against foreign antigens. DO (HLA-DO in humans, H2-O in mice) is a nonclassical MHC-II protein that has been implicated in control of autoimmunity and regulation of neutralizing antibody responses to viruses. These effects likely are related to a role of DO in selecting MHC-II epitopes, but previous studies examining the effect of DO on presentation of selected CD4 T cell epitopes have been contradictory. To understand how DO modulates MHC-II antigen presentation, we characterized the full spectrum of peptides presented by MHC-II molecules expressed by DO-sufficient and DO-deficient antigen-presenting cells in vivo and in vitro using quantitative mass spectrometry approaches. We found that DO controlled the diversity of the presented peptide repertoire, with a subset of peptides presented only when DO was expressed. Antigen-presenting cells express another nonclassical MHC-II protein, DM, which acts as a peptide editor by preferentially catalyzing the exchange of less stable MHC-II peptide complexes, and which is inhibited when bound to DO. Peptides presented uniquely in the presence of DO were sensitive to DM-mediated exchange, suggesting that decreased DM editing was responsible for the increased diversity. DO-deficient mice mounted CD4 T cell responses against wild-type antigen-presenting cells, but not vice versa, indicating that DO-dependent alterations in the MHC-II peptidome could be recognized by circulating T cells. These data suggest that cell-specific and regulated expression of HLA-DO serves to fine-tune MHC-II peptidomes, in order to enhance self-tolerance to a wide spectrum of epitopes while allowing focused presentation of immunodominant epitopes during an immune response.
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Affiliation(s)
- Padma P Nanaware
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Mollie M Jurewicz
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John D Leszyk
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Scott A Shaffer
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Lawrence J Stern
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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12
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Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci 2018; 5:90. [PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.
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Affiliation(s)
| | | | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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13
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Tutorial: Correction of shifts in single-stage LC-MS(/MS) data. Anal Chim Acta 2018; 999:37-53. [DOI: 10.1016/j.aca.2017.09.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 11/19/2022]
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Padrão AI, Ferreira R, Amado F, Vitorino R, Duarte JA. Uncovering the exercise-related proteome signature in skeletal muscle. Proteomics 2016; 16:816-30. [PMID: 26632760 DOI: 10.1002/pmic.201500382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 10/13/2015] [Accepted: 11/30/2015] [Indexed: 01/01/2023]
Abstract
Exercise training has been recommended as a nonpharmacological strategy for the prevention and attenuation of skeletal muscle atrophy in distinct pathophysiological conditions. Despite the well-established phenotypic alterations, the molecular mechanisms underlying exercise-induced skeletal muscle remodeling are poorly characterized. Proteomics based on mass spectrometry have been successfully applied for the characterization of skeletal muscle proteome, representing a pivotal approach for the wide characterization of the molecular networks that lead to skeletal muscle remodeling. Nevertheless, few studies were performed to characterize the exercise-induced proteome remodeling of skeletal muscle, with only six research papers focused on the cross-talk between exercise and pathophysiological conditions. In order to add new insights on the impact of distinct exercise programs on skeletal muscle proteome, molecular network analysis was performed with bioinformatics tools. This analysis highlighted an exercise-related proteome signature characterized by the up-regulation of the capacity for ATP generation, oxygen delivery, antioxidant capacity and regulation of mitochondrial protein synthesis. Chronic endurance training up-regulates the tricarboxylic acid cycle and oxidative phosphorylation system, whereas the release of calcium ion into cytosol and amino acid metabolism are the biological processes up-regulated by a single bout of exercise. Other issues as exercise intensity, load, mode and regimen as well as muscle type also influence the exercise-induced proteome signature. The comprehensive analysis of the molecular networks modulated by exercise training in health and disease, taking in consideration all these variables, might not only support the therapeutic effect of exercise but also highlight novel targets for the development of enhanced pharmacological strategies.
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Affiliation(s)
- Ana Isabel Padrão
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal.,CIAFEL, Faculty of Sports, University of Porto, Porto, Portugal
| | - Rita Ferreira
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- QOPNA, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Department of Medical Sciences and Institute for Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
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15
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Witzmann FA, Evan AP, Coe FL, Worcester EM, Lingeman JE, Williams JC. Label-free proteomic methodology for the analysis of human kidney stone matrix composition. Proteome Sci 2016; 14:4. [PMID: 26924944 PMCID: PMC4769560 DOI: 10.1186/s12953-016-0093-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Kidney stone matrix protein composition is an important yet poorly understood aspect of nephrolithiasis. We hypothesized that this proteome is considerably more complex than previous reports have indicated and that comprehensive proteomic profiling of the kidney stone matrix may demonstrate relevant constitutive differences between stones. We have analyzed the matrices of two unique human calcium oxalate stones (CaOx-Ia and CaOx-Id) using a simple but effective chaotropic reducing solution for extraction/solubilization combined with label-free quantitative mass spectrometry to generate a comprehensive profile of their proteomes, including physicochemical and bioinformatic analysis.` Results We identified and quantified 1,059 unique protein database entries in the two human kidney stone samples, revealing a more complex proteome than previously reported. Protein composition reflects a common range of proteins related to immune response, inflammation, injury, and tissue repair, along with a more diverse set of proteins unique to each stone. Conclusion The use of a simple chaotropic reducing solution and moderate sonication for extraction and solubilization of kidney stone powders combined with label-free quantitative mass spectrometry has yielded the most comprehensive list to date of the proteins that constitute the human kidney stone proteome. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0093-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frank A Witzmann
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Drive, Room 362A, Indianapolis, IN 46202-5120 USA
| | - Andrew P Evan
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Fredric L Coe
- Department of Medicine, Nephrology Section, University of Chicago, Chicago, IL USA
| | - Elaine M Worcester
- Department of Medicine, Nephrology Section, University of Chicago, Chicago, IL USA
| | - James E Lingeman
- International Kidney Stone Institute, Methodist Hospital, Indianapolis, IN USA
| | - James C Williams
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN USA
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16
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Yap HYY, Fung SY, Ng ST, Tan CS, Tan NH. Shotgun proteomic analysis of tiger milk mushroom (Lignosus rhinocerotis) and the isolation of a cytotoxic fungal serine protease from its sclerotium. JOURNAL OF ETHNOPHARMACOLOGY 2015; 174:437-451. [PMID: 26320692 DOI: 10.1016/j.jep.2015.08.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 06/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has been traditionally used as a complementary and alternative medicine for cancer treatment by the local communities of Southeast Asia. Despite the continuous research interest in its antiproliferative activity, the identity of the bioactive compound(s) responsible has yet to be determined. This study aims to bridge the gap in existing research literature by using proteomics approach for investigation of the nature of the anticancer substance of L. rhinocerotis. AIM OF THE STUDY To elucidate the proteome of L. rhinocerotis TM02 sclerotium by protein mass spectrometry and to further isolate and identify the cytotoxic component(s) bearing anticancer potential. MATERIALS AND METHODS The proteome of L. rhinocerotis sclerotium was analyzed by label-free quantitative shotgun proteomics, using 1D-SDS-PAGE coupled with nano-ESI-LC-MS/MS based on the availability of its genome-sequence database. The cytotoxicity of L. rhinocerotis sclerotial extracts against human breast adenocarcinoma cells (MCF7) were assessed by MTT cytotoxicity assay prior to successive purification steps by a combination of gel filtration chromatography, ammonium sulfate precipitation, and anion exchange chromatography. Bioactive compound(s) in the extracts was identified by shotgun proteomics and N-terminal protein sequencing. RESULTS Several proteins with interesting biological activities including lectins, fungal immunomodulatory proteins, and several antioxidant proteins were identified from the proteome of L. rhinocerotis. A cytotoxic protein fraction (termed F5) which was partially purified from its sclerotial cold water extract F5 shows two distinct bands of 31 and 36 kDa in reducing SDS-PAGE and exhibited potent selective cytotoxicity against MCF7 cells with IC50 value of 3.00 ± 1.01 μg/ml. Both bands were identified to be serine protease by LC-MS/MS analysis. Phenylmethylsulfonyl fluoride, a specific serine protease inhibitor, inhibited both the proteolytic activity and cytotoxicity of F5, suggesting that the cytotoxicity of F5 is related to its protease activity. CONCLUSIONS This study provides the first comprehensive and semi-quantitative profiling of the proteome of L. rhinocerotis sclerotium. Further investigation into its selective cytotoxicity shows that a serine protease-like protein, termed F5, may be targeted for new anticancer agent development.
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Affiliation(s)
- Hui-Yeng Y Yap
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Shin-Yee Fung
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Szu-Ting Ng
- Ligno Biotech Sdn Bhd, 43300 Balakong Jaya, Selangor, Malaysia
| | - Chon-Seng Tan
- Ligno Biotech Sdn Bhd, 43300 Balakong Jaya, Selangor, Malaysia
| | - Nget-Hong Tan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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17
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Skejic J, Steer DL, Dunstan N, Hodgson WC. Label-Free (XIC) Quantification of Venom Procoagulant and Neurotoxin Expression in Related Australian Elapid Snakes Gives Insight into Venom Toxicity Evolution. J Proteome Res 2015; 14:4896-906. [PMID: 26486890 DOI: 10.1021/acs.jproteome.5b00764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study demonstrates a direct role of venom protein expression alteration in the evolution of snake venom toxicity. Avian skeletal muscle contractile response to exogenously administered acetylcholine is completely inhibited upon exposure to South Australian and largely preserved following exposure to Queensland eastern brown snake Pseudonaja textilis venom, indicating potent postsynaptic neurotoxicity of the former and lack thereof of the latter venom. Label-free quantitative proteomics reveals extremely large differences in the expression of postsynaptic three-finger α-neurotoxins in these venoms, explaining the difference in the muscle contractile response and suggesting that the type of toxicity induced by venom can be modified by altered expression of venom proteins. Furthermore, the onset of neuromuscular paralysis in the rat phrenic nerve-diaphragm preparation occurs sooner upon exposure to the venom (10 μg/mL) with high expression of α-neurotoxins than the venoms containing predominately presynaptic β-neurotoxins. The study also finds that the onset of rat plasma coagulation is faster following exposure to the venoms with higher expression of venom prothrombin activator subunits. This is the first quantitative proteomic study that uses extracted ion chromatogram peak areas (MS1 XIC) of distinct homologous tryptic peptides to directly show the differences in the expression of venom proteins.
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Affiliation(s)
- Jure Skejic
- Department of Biochemistry and Molecular Biology, BIO21 Institute, University of Melbourne , 30 Flemington Road, Parkville, Victoria 3010, Australia.,Monash Venom Group, Department of Pharmacology, Monash University , 9 Ancora Imparo Way, Clayton, Victoria 3800, Australia
| | - David L Steer
- Monash Biomedical Proteomics Facility, Monash University , 23 Innovation Walk, Clayton, Victoria 3800, Australia
| | - Nathan Dunstan
- Venom Supplies Pty Ltd. , Stonewell Road, Tanunda, South Australia 5352, Australia
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Monash University , 9 Ancora Imparo Way, Clayton, Victoria 3800, Australia
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Arentz G, Weiland F, Oehler MK, Hoffmann P. State of the art of 2D DIGE. Proteomics Clin Appl 2015; 9:277-88. [DOI: 10.1002/prca.201400119] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/13/2014] [Accepted: 11/10/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Georgia Arentz
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Florian Weiland
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
| | - Martin K. Oehler
- School of Paediatrics and Reproductive Health; Research Centre for Reproductive Health; Robinson Institute; University of Adelaide; SA Australia
- Department of Gynaecological Oncology; Royal Adelaide Hospital; Adelaide SA Australia
| | - Peter Hoffmann
- School of Molecular and Biomedical Science; Adelaide Proteomics Centre; The University of Adelaide; Adelaide Australia
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19
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Li P, Lai X, Witzmann FA, Blazer-Yost BL. Bioinformatic Analysis of Differential Protein Expression in Calu-3 Cells Exposed to Carbon Nanotubes. Proteomes 2013; 1:219-239. [PMID: 25177543 PMCID: PMC4148817 DOI: 10.3390/proteomes1030219] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Carbon nanomaterials are widely produced and used in industry, medicine and scientific research. To examine the impact of exposure to nanoparticles on human health, the human airway epithelial cell line, Calu-3, was used to evaluate changes in the cellular proteome that could account for alterations in cellular function of airway epithelia after 24 hexposure to 10 μg/mL and 100 ng/mLof two common carbon nanoparticles, single- and multi-wall carbon nanotubes (SWCNT, MWCNT). After exposure to the nanoparticles, label-free quantitative mass spectrometry (LFQMS) was used to study the differential protein expression. Ingenuity Pathway Analysis (IPA) was used to conduct a bioinformaticanalysis of proteins identified in LFQMS. Interestingly, after exposure to ahigh concentration (10 μg/mL; 0.4 μg/cm2) of MWCNT or SWCNT, only 8 and 13 proteins, respectively, exhibited changes in abundance. In contrast, the abundance of hundreds of proteins was altered in response to a low concentration (100 ng/mL; 4 ng/cm2) of either CNT. Of the 281 and 282 proteins that were significantly altered in response to MWCNT or SWCNT respectively, 231 proteins were the same. Bioinformatic analyses found that the proteins in common to both nanotubes occurred within the cellular functions of cell death and survival, cell-to-cell signaling and interaction, cellular assembly and organization, cellular growth and proliferation, infectious disease, molecular transport and protein synthesis. The majority of the protein changes represent a decrease in amount suggesting a general stress response to protect cells. The STRING database was used to analyze the various functional protein networks. Interestingly, some proteins like cadherin 1 (CDH1), signal transducer and activator of transcription 1 (STAT1), junction plakoglobin (JUP), and apoptosis-associated speck-like protein containing a CARD (PYCARD), appear in several functional categories and tend to be in the center of the networks. This central positioning suggests they may play important roles in multiple cellular functions and activities that are altered in response to carbon nanotube exposure.
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Affiliation(s)
- Pin Li
- Department of Biology, Indiana University Purdue University, 723 West Michigan Street, Indianapolis, IN 46202, USA; E-Mail:
| | - Xianyin Lai
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 1345 West 16th Street, Indianapolis, IN 46202, USA; E-Mails: (X.L.); (F.A.W.)
| | - Frank A. Witzmann
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 1345 West 16th Street, Indianapolis, IN 46202, USA; E-Mails: (X.L.); (F.A.W.)
| | - Bonnie L. Blazer-Yost
- Department of Biology, Indiana University Purdue University, 723 West Michigan Street, Indianapolis, IN 46202, USA; E-Mail:
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 1345 West 16th Street, Indianapolis, IN 46202, USA; E-Mails: (X.L.); (F.A.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-317-278-1145; Fax: +1-317-274-2846
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