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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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2
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Pan L, Chen J, Fu H, Wang N, Zhou J, Zhang S, Lu S, Dong J, Wang Q, Yan H. Effects of fabrication of conjugates between different polyphenols and bovine bone proteins on their structural and functional properties. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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3
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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4
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Faraldi M, Mangiavini L, Conte C, Banfi G, Napoli N, Lombardi G. A novel methodological approach to simultaneously extract high-quality total RNA and proteins from cortical and trabecular bone. Open Biol 2022; 12:210387. [PMID: 35506206 PMCID: PMC9065961 DOI: 10.1098/rsob.210387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Molecular differences between cortical and trabecular bone, of relevance to understanding the pathophysiological basis of bone diseases, can be determined only through effective isolation methods for RNA and proteins. Here we present a TRIzol-based method, which combines bone pulverization and homogenization to extract simultaneously total RNA and proteins from human cortical and trabecular bone from the same carrot. RNA integrity and purity were determined as the 260/280 nm and 260/230 nm absorbance ratios and the 28S/18S rRNA ratio. Protein integrity and quality were evaluated by Coomassie blue staining. Reverse transcription quantitative polymerase chain reaction and immunoblotting for bone-specific genes and proteins were performed to verify the suitability of the isolated material in downstream applications. The 260/280 nm and 260/230 nm absorbance ratios were, on average, less than or equal to 1.8. Bands on agarose gel were consistent with intact RNA, with mean 28S/18S ratios of 1.68 ± 0.35 and 1.88 ± 0.10 for cortical and trabecular bone, respectively. Band patterns after Coomassie blue staining confirmed protein integrity. Successful gene and protein expression analysis, with relevant differences between the two compartments, highlighted the suitability of the material in downstream applications. The method presented here is appropriate and effective for the study of human bone.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Laura Mangiavini
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Caterina Conte
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy,Department of Endocrinology, Nutrition and Metabolic Diseases, IRCCS MultiMedica, Milan, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Vita-Salute San Raffaele University, Milan, Italy
| | - Nicola Napoli
- Unit of Endocrinology and Diabetes, Departmental Faculty of Medicine and Surgery, Campus Bio-Medico University of Rome, Rome, Italy,Division of Bone and Mineral Diseases, Washington University in St Louis, St Louis, MO, USA
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milan, Italy,Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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5
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Yuen JWM, Li KK, Lam TC. Preparation of Hard Tissues Like Bone or Cartilage for Shotgun Mass Spectrometry Analysis of the Proteome. Curr Protoc 2021; 1:e282. [PMID: 34679255 DOI: 10.1002/cpz1.282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Proteomic analyses of intervertebral discs (IVDs) reveal information for understanding the fundamentals of biological processes and pathogenesis but also provide insights for novel pharmaceutical development. Sensitive mass spectrometry techniques and bioinformatics have advanced the detection and identification of proteins from any sample. Due to the challenges of catastrophic sample-loss artifacts during hard-tissue extraction, however, many researchers have omitted the cartilage endplates of IVDs for protein extraction, analyzing only the cellular components of the annulus fibrosus and/or nucleus pulposus. The full proteomic picture of IVDs is compromised without extracting proteins from intact IVDs. Here, we describe a novel preparation method using snap-freeze grinding, which allows for mechanical disruption and customized chemical lysis of hard tissues such as bone or cartilage. This method replaces the time-consuming and insufficient conventional tissue homogenization methods. Sample loss and contamination could be minimized during proteolysis by using an in-solution protein digestion and desalting procedure. We demonstrate excellent proteome coverage with intact mouse IVDs by analyzing samples in a hybrid quadrupole time-of-flight tandem mass spectrometer. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- John W M Yuen
- School of Nursing, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - K K Li
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Thomas C Lam
- School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,Centre for Eye and Vision Research, Hong Kong Science Park, Pak Shek Kok, Hong Kong
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Pramualkijja T, Pirak T, Euston SR. Valorization of chicken slaughterhouse by-products: Production and properties of chicken trachea hydrolysates using commercial proteases. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2021. [DOI: 10.1080/10942912.2021.1986522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Teeda Pramualkijja
- Department of Product Development, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Tantawan Pirak
- Department of Product Development, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Stephen R. Euston
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, UK
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7
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Cleland TP, Wang Z, Wang B, Picu CR, Vashishth D. Mechano-chemical regulation of bat wing bones for flight. J Mech Behav Biomed Mater 2021; 124:104809. [PMID: 34517171 DOI: 10.1016/j.jmbbm.2021.104809] [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: 05/17/2020] [Revised: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 11/15/2022]
Abstract
Distal phalanges in bat wings have been hypothesized to be cartilaginous to allow for flight. We provide new evidence on how bat wing development might facilitate flight though protein-based regulation of bone mineralization and lead to more deflection at phalanx than humerus. Between Pteropus poliocephalus and Pteropus hypomelanus, two large bat species, we detected 112 proteins including 11 associated with mineralization and analyzed their distribution between the wing bones. Here, in contrast to previous reports, we found no cartilage-specific proteins and demonstrate that distal phalanges in bat wings are in fact low density bone that contain collagen I (the main constituent of bone's organic matrix) and proteins associated with mineralization in bone such as osteomodulin, bone-specific protein osteocalcin. The functional relevance of these changes was explored by measuring changes in mineral (crystal sizes, packing and density), material (Young's modulus and hardness) and structural characteristics. Consistent with changes in proteins associated with mineralization, mineral crystal thickness and alignment decreased from humerus to phalanges, and the mineral platelets were less densely packed along the wing length. Crystal thickness was negatively correlated with proteins associated with inhibition of mineralization as well as with two types of small leucine-rich proteoglycans, indicating the mineral growth and maturity is down regulated by these proteins independent of mineral quantity. The Young's modulus decreased across the wing and was significantly correlated with bone mineral density. Thus, the results from two bat species, studied here, demonstrate progressive alterations in bone mineralization occur in concert with the changes in secretion of bone regulatory proteins along the wing length. This altered mineralization together with structural changes serve to lighten the limb bone and optimize biomechanical properties conducive to flight.
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Affiliation(s)
- Timothy P Cleland
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Zehai Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Bowen Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catalin R Picu
- Department of Mechanical, Aerospace, and Nuclear Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Deepak Vashishth
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA; Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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8
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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9
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Early CM, Morhardt AC, Cleland TP, Milensky CM, Kavich GM, James HF. Chemical effects of diceCT staining protocols on fluid-preserved avian specimens. PLoS One 2020; 15:e0238783. [PMID: 32946473 PMCID: PMC7500670 DOI: 10.1371/journal.pone.0238783] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/31/2020] [Indexed: 01/05/2023] Open
Abstract
Diffusible iodine-based contrast-enhanced computed tomography (diceCT) techniques allow visualization of soft tissues of fluid-preserved specimens in three dimensions without dissection or histology. Two popular diceCT stains, iodine-potassium iodide (I2KI) dissolved in water and elemental iodine (I2) dissolved in 100% ethanol (EtOH), yield striking results. Despite the widespread use of these stains in clinical and biological fields, the molecular mechanisms that result in color change and radiopacity attributed to iodine staining are poorly understood. Requests to apply these stains to anatomical specimens preserved in natural history museums are increasing, yet curators have little information about the potential for degradation of treated specimens. To assess the molecular effects of iodine staining on typical museum specimens, we compared the two popular stains and two relatively unexplored stains (I2KI in 70% EtOH, I2 in 70% EtOH). House sparrows (Passer domesticus) were collected and preserved under uniform conditions following standard museum protocols, and each was then subjected to one of the stains. Results show that the three ethanol-based stains worked equally well (producing fully stained, life-like, publication quality scans) but in different timeframes (five, six, or eight weeks). The specimen in I2KI in water became degraded in physical condition, including developing flexible, demineralized bones. The ethanol-based methods also resulted in some demineralization but less than the water-based stain. The pH of the water-based stain was notably acidic compared to the water used as solvent in the stain. Our molecular analyses indicate that whereas none of the stains resulted in unacceptable levels of protein degradation, the bones of a specimen stained with I2KI in water demineralized throughout the staining process. We conclude that staining with I2KI or elemental I2 in 70% EtOH can yield high-quality soft-tissue visualization in a timeframe that is similar to that of better-known iodine-based stains, with lower risk of negative impacts on specimen condition.
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Affiliation(s)
- Catherine M. Early
- Biology Department, Science Museum of Minnesota, Saint Paul, MN, United States of America
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- Department of Biological Sciences, Ohio University, Athens, OH, United States of America
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
| | - Ashley C. Morhardt
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO, United States of America
| | - Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher M. Milensky
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Gwénaëlle M. Kavich
- Museum Conservation Institute, Smithsonian Institution, Washington, D.C., United States of America
| | - Helen F. James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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Licini C, Montalbano G, Ciapetti G, Cerqueni G, Vitale-Brovarone C, Mattioli-Belmonte M. Analysis of multiple protein detection methods in human osteoporotic bone extracellular matrix: From literature to practice. Bone 2020; 137:115363. [PMID: 32298836 DOI: 10.1016/j.bone.2020.115363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/15/2022]
Abstract
The punctual analysis of bone Extracellular Matrix (ECM) proteins represents a pivotal point for medical research in bone diseases like osteoporosis. Studies in this field, historically done to appreciate bone biology, were mainly conducted on animal samples and, up to today, only a few studies on protein detection in human bone are present. The challenges in bone ECM protein extraction and quantitation protocols are related to both the separation of proteins from the mineral content (i.e. hydroxyapatite) and the difficulty of avoiding protein denaturation during the extraction processes. The aim of the present work was to define appropriate protocol(s) for bone ECM protein extraction that could be applied to investigate both normal and pathological conditions. We compared and optimised some of the most used protocols present in the literature, modifying the protein precipitation method, the buffer used for resuspension and/or the volume of reagent used. Bradford and BCA assays and Western Blotting were used to evaluate the variations in the total protein recovery and the amount of selected proteins (Type I Collagen, TGF-β, IGF-1, Decorin, Osteopontin, Bone Sialoprotein-2 and Osteocalcin). Collectively, we were capable to draw-up two single-extract protocols with optimal recovery and ideal protein content, that can be used for a detailed analysis of ECM proteins in pathological bone samples. Time-consuming multi-extract procedures, optimised in their precipitation methods, are however crucial for a precise detection of specific proteins, like osteocalcin. As the matter of fact, also the demineralization processes, commonly suggested and performed in several protocols, could hinder an accurate protein detection, thus inherently affecting the study of a pathological bone ECM. This study represents a starting point for the definition of appropriate strategies in the study of bone extracellular matrix proteins involved in the onset and maintenance of bone diseases, as well as a tool for the development of customized scaffolds capable to modulate a proper feedback loop in bone remodelling, altered in case of diseases like osteoporosis.
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Affiliation(s)
- Caterina Licini
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Giorgia Montalbano
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Gabriela Ciapetti
- Laboratorio di Fisiopatologia Ortopedica e Medicina Rigenerativa, Istituto Ortopedico Rizzoli, IRCCS, Via di Barbiano 1/10, 40136 Bologna, Italy
| | - Giorgia Cerqueni
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
| | - Chiara Vitale-Brovarone
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Monica Mattioli-Belmonte
- Department of Clinical and Molecular Sciences (DISCLIMO), Università Politecnica delle Marche, Via Tronto 10/A, 60126 Ancona, Italy
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11
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Díaz-Martín RD, Ambrosio JR, Flores RM, Gonzáles-Pozos S, Valencia-Caballero L. Cytoskeletal and extracellular matrix proteins resist the burning of bones. Forensic Sci Int 2019; 305:110027. [PMID: 31704515 DOI: 10.1016/j.forsciint.2019.110027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/07/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Due the proteins from bone remains are highly resistant to pass of time and environmental conditions, they could tell us about the events that probably happened in the past. In the forensic and physical anthropology context, burnt bone remains are one of the most common pieces of recovered evidence and, generally, they are associated with funerary practices, criminal scenes or massive catastrophic events. In the present study, bone pieces of pigs were calcined at different calcination temperatures, and proteins were searched using biochemical, immunochemical and ultrastructure visualization under these experimentally conditions. For this purpose, it was successfully developed a non-demineralizing protein extraction method from burnt bone remains and the use of specific antibodies permitted the identification of different extracellular matrix and intracellular proteins. While collagen proteins type I and IV were identified and detected under middle and high calcination temperatures (300°C and 600°C); cytoskeletal proteins as actin, tubulin and, the microtubule associated protein Tau, were found under calcination process, even up high calcination temperatures. Under ultrastructural analysis, fibrous materials with a classical disposition of collagens were observed even at high calcination temperatures of the burnt bone remains. The protein identification and characterization in burnt bones as performed in present studies, is clearly demonstrating that using specific strategies for protein characterizations it is possible to found protein biomarkers in burnt bone remains and this strategy could be useful for forensic and anthropological purposes.
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Affiliation(s)
- Rubén Darío Díaz-Martín
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México; Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Javier R Ambrosio
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Ricardo Mondragón Flores
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), México
| | | | - Lorena Valencia-Caballero
- Departamento de Innovación en Material Biológico Humano (DIMBIH), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México.
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12
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Guss JD, Taylor E, Rouse Z, Roubert S, Higgins CH, Thomas CJ, Baker SP, Vashishth D, Donnelly E, Shea MK, Booth SL, Bicalho RC, Hernandez CJ. The microbial metagenome and bone tissue composition in mice with microbiome-induced reductions in bone strength. Bone 2019; 127:146-154. [PMID: 31207357 PMCID: PMC6708759 DOI: 10.1016/j.bone.2019.06.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 01/10/2023]
Abstract
The genetic components of microbial species that inhabit the body are known collectively as the microbiome. Modifications to the microbiome have been implicated in disease processes throughout the body and have recently been shown to influence bone. Prior work has associated changes in the microbial taxonomy (phyla, class, species, etc.) in the gut with bone phenotypes but has provided limited information regarding mechanisms. With the goal of achieving a more mechanistic understanding of the effects of the microbiome on bone, we perform a metagenomic analysis of the gut microbiome that provides information on the functional capacity of the microbes (all microbial genes present) rather than only characterizing the microbial taxa. Male C57Bl/6 mice were subjected to disruption of the gut microbiota (ΔMicrobiome) using oral antibiotics (from 4 to 16 weeks of age) or remained untreated (n = 6-7/group). Disruption of the gut microbiome in this manner has been shown to lead to reductions in tissue mechanical properties and whole bone strength in adulthood with only minor changes in bone geometry and density. ΔMicrobiome led to modifications in the abundance of microbial genes responsible for the synthesis of the bacterial cell wall and capsule; bacterially synthesized carbohydrates; and bacterially synthesized vitamins (B and K) (p < 0.01). Follow up analysis focused on vitamin K, a factor that has previously been associated with bone health. The vitamin K content of the cecum, liver and kidneys was primarily microbe-derived forms of vitamin K (menaquinones) and was decreased by 32-66% in ∆Microbiome mice compared to untreated animals (p < 0.01). Bone mineral crystallinity determined using Raman spectroscopy was decreased in ∆Microbiome mice (p = 0.01). This study illustrates the use of metagenomic analysis to link the microbiome to bone phenotypes and provides preliminary findings implicating microbially synthesized vitamin-K as a regulator of bone matrix quality.
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Affiliation(s)
- Jason D Guss
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Erik Taylor
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Zach Rouse
- Material Science and Engineering, Cornell University, New York, NY, USA
| | - Sebastian Roubert
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | | | - Corinne J Thomas
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Shefford P Baker
- Material Science and Engineering, Cornell University, New York, NY, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Eve Donnelly
- Material Science and Engineering, Cornell University, New York, NY, USA; Hospital for Special Surgery, New York, NY, USA
| | - M Kyla Shea
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | | | - Christopher J Hernandez
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA; Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA; Hospital for Special Surgery, New York, NY, USA.
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13
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Schroeter ER, Blackburn K, Goshe MB, Schweitzer MH. Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181433. [PMID: 31598217 PMCID: PMC6731700 DOI: 10.1098/rsos.181433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800-1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
| | - Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
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14
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Schweitzer MH, Schroeter ER, Cleland TP, Zheng W. Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils. Proteomics 2019; 19:e1800251. [PMID: 31172628 DOI: 10.1002/pmic.201800251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC.,North Carolina Museum of Natural Sciences, Raleigh, NC.,Museum of the Rockies, Montana State University, Bozeman, MT.,Department of Geology, Lund University, Sölvegatan 12, SE-223 62, Lund, Sweden
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, 20746, MD
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
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15
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Mueller C, Gambarotti M, Benini S, Picci P, Righi A, Stevanin M, Hombach-Klonisch S, Henderson D, Liotta L, Espina V. Unlocking bone for proteomic analysis and FISH. J Transl Med 2019; 99:708-721. [PMID: 30659273 PMCID: PMC10752433 DOI: 10.1038/s41374-018-0168-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/04/2018] [Accepted: 09/14/2018] [Indexed: 11/08/2022] Open
Abstract
Bone tissue is critically lagging behind soft tissues and biofluids in our effort to advance precision medicine. The main challenges have been accessibility and the requirement for deleterious decalcification processes that impact the fidelity of diagnostic histomorphology and hinder downstream analyses such as fluorescence in-situ hybridization (FISH). We have developed an alternative fixation chemistry that simultaneously fixes and decalcifies bone tissue. We compared tissue morphology, immunohistochemistry (IHC), cell signal phosphoprotein analysis, and FISH in 50 patient matched primary bone cancer cases that were either formalin fixed and decalcified, or theralin fixed with and without decalcification. Use of theralin improved tissue histomorphology, whereas overall IHC was comparable to formalin fixed, decalcified samples. Theralin-fixed samples showed a significant increase in protein and DNA extractability, supporting technologies such as laser-capture microdissection and reverse phase protein microarrays. Formalin-fixed bone samples suffered from a fixation artifact where protein quantification of β-actin directly correlated with fixation time. Theralin-fixed samples were not affected by this artifact. Moreover, theralin fixation enabled standard FISH staining in bone cancer samples, whereas no FISH staining was observed in formalin-fixed samples. We conclude that the use of theralin fixation unlocks the molecular archive within bone tissue allowing bone to enter the standard tissue analysis pipeline. This will have significant implications for bone cancer patients, in whom personalized medicine has yet to be implemented.
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Affiliation(s)
- Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Marco Gambarotti
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Stefania Benini
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Piero Picci
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Righi
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Monica Stevanin
- Department of Pathology, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Dana Henderson
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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16
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Cleland TP, Newsome GA, Hollinger RE. Proteomic and direct analysis in real time mass spectrometry analysis of a Native American ceremonial hat. Analyst 2019; 144:7437-7446. [DOI: 10.1039/c9an01557d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Complementary mass spectrometry analyses were performed to study a broken ceremonial hat of the Tlingit in the collection of the Smithsonian Institution National Museum of Natural History.
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Affiliation(s)
| | | | - R. Eric Hollinger
- Smithsonian Institution
- National Museum of Natural History
- Washington
- USA
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17
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Sroga GE, Vashishth D. Phosphorylation of Extracellular Bone Matrix Proteins and Its Contribution to Bone Fragility. J Bone Miner Res 2018; 33:2214-2229. [PMID: 30001467 DOI: 10.1002/jbmr.3552] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 07/05/2018] [Accepted: 07/08/2018] [Indexed: 01/22/2023]
Abstract
Phosphorylation of bone matrix proteins is of fundamental importance to all vertebrates including humans. However, it is currently unknown whether increase or decline of total protein phosphorylation levels, particularly in hypophosphatemia-related osteoporosis, osteomalacia, and rickets, contribute to bone fracture. To address this gap, we combined biochemical measurements with mechanical evaluation of bone to discern fracture characteristics associated with age-related development of skeletal fragility in relation to total phosphorylation levels of bone matrix proteins and one of the key representatives of bone matrix phosphoproteins, osteopontin (OPN). Here for the first time, we report that as people age the total phosphorylation level declines by approximately 20% for bone matrix proteins and approximately 30% for OPN in the ninth decade of human life. Moreover, our results suggest that the decline of total protein phosphorylation of extracellular matrix (ECM) contributes to bone fragility, but less pronouncedly than glycation. We theorize that the separation of two sources of OPN negative charges, acidic backbone amino acids and phosphorylation, would be nature's means of assuring that OPN functions in both energy dissipation and biomineralization. We propose that total phosphorylation decline could be an important contributor to the development of osteoporosis, increased fracture risk and skeletal fragility. Targeting the enzymes kinase FamC20 and bone alkaline phosphatase involved in the regulation of matrix proteins' phosphorylation could be a means for the development of suitable therapeutic treatments. © 2018 American Society for Bone and Mineral Research.
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Affiliation(s)
- Grażyna E Sroga
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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18
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Cleland TP. Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics. J Proteome Res 2018; 17:3976-3983. [DOI: 10.1021/acs.jproteome.8b00637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
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19
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Li S, He Z, Li H. Effect of nano-scaled rabbit bone powder on physicochemical properties of rabbit meat batter. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:4533-4541. [PMID: 29485183 DOI: 10.1002/jsfa.8981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND To explore a new method of deep processing and to improve the value of rabbit bone, we prepared a nano-scaled rabbit bone powder by dry ball milling and compared the effect of different particle sizes of rabbit bone powder [fine-scaled (236.01 ± 5.99 μm), superfine-scaled (65.92 ± 1.71 μm), nano-scaled (502.52 ± 11.72 nm)] on the nutritional characteristics, pH, color, water-holding capacity, textural and rheological attributes of rabbit meat batter. RESULTS The rabbit bone powder significantly affected nutritional characteristics of meat batters; in particular, the contents of calcium were increased, regardless of particle size. Additionally, the rabbit meat batter, which contained 20 g kg-1 nano-scaled rabbit bone, had the lowest centrifugal and cooking losses among the treatments. CONCLUSION Based on the textural and rheological attributes of the rabbit meat batters, the addition of 20 g kg-1 nano-scaled rabbit bone was the best treatment. This represents an important finding with respect to the deep processing of rabbit bone in the rabbit meat industry. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Shaobo Li
- College of Food Science, Southwest University, Chongqing, PR China
| | - Zhifei He
- College of Food Science, Southwest University, Chongqing, PR China
- Chongqing Engineering Research Center of Regional Food, Chongqing, PR China
| | - Hongjun Li
- College of Food Science, Southwest University, Chongqing, PR China
- Chongqing Engineering Research Center of Regional Food, Chongqing, PR China
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20
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Nikolaev AL, Gopin AV, Severin AV, Rudin VN, Mironov MA, Dezhkunov NV. Ultrasonic synthesis of hydroxyapatite in non-cavitation and cavitation modes. ULTRASONICS SONOCHEMISTRY 2018; 44:390-397. [PMID: 29680625 DOI: 10.1016/j.ultsonch.2018.02.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/22/2018] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
The size control of materials is of great importance in research and technology because materials of different size and shape have different properties and applications. This paper focuses on the synthesis of hydroxyapatite in ultrasound fields of different frequencies and intensities with the aim to find the conditions which allow control of the particles size. The results are evaluated by X-ray diffraction, Transmission Electron Microscopy, morphological and sedimentation analyses. It is shown that the hydroxyapatite particles synthesized at low intensity non-cavitation regime of ultrasound have smaller size than those prepared at high intensity cavitation regime. The explanation of observed results is based on the idea of formation of vortices at the interface between phosphoric acid and calcium hydroxide solution where the nucleation of hydroxyapatite particles is taken place. Smaller vortices formed at high frequency non-cavitation ultrasound regime provide smaller nucleation sites and smaller resulting particles, compared to vortices and particles obtained without ultrasound. Discovered method has a potential of industrial application of ultrasound for the controlled synthesis of nanoparticles.
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Affiliation(s)
- A L Nikolaev
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - A V Gopin
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A V Severin
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - V N Rudin
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - M A Mironov
- N.N. Andreev Acoustic Institute, Shvernika Street, 4, Moscow, 117036, Russia
| | - N V Dezhkunov
- Belarusian State University of Informatics and Radioelectronics, 6 P. Brovki Street, Minsk, 220013, Belarus
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21
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Thomas CJ, Cleland TP, Sroga GE, Vashishth D. Accumulation of carboxymethyl-lysine (CML) in human cortical bone. Bone 2018; 110:128-133. [PMID: 29408699 PMCID: PMC5878737 DOI: 10.1016/j.bone.2018.01.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 01/22/2023]
Abstract
Advanced glycation end-products (AGEs) are a category of post translational modification associated with the degradation of the structural properties of multiple different types of tissues. Typically, AGEs are the result of a series of post-translational modification reactions between sugars and proteins through a process known as non-enzymatic glycation (NEG). Increases in the rate of NEG of bone tissue are associated with type 2 diabetes and skeletal fragility. Current methods of assessing NEG and its impact on bone fracture risk involve measurement of pentosidine or total fluorescent AGEs (fAGEs). However, pentosidine represents only a small fraction of possible fAGEs present in bone, and neither pentosidine nor total fAGE measurement accounts for non-fluorescent AGEs, which are known to form in significant amounts in skin and other collagenous tissues. Carboxymethyl-lysine (CML) is a non-fluorescent AGE that is often measured and has been shown to accumulate in tissues such as skin, heart, arteries, and intervertebral disks, but is currently not assessed in bone. Here we show the localization of CML to collagen I using mass spectrometry for the first time in human bone. We then present a new method using demineralization followed by heating and trypsin digestion to measure CML content in human bone and demonstrate that CML in bone is 40-100 times greater than pentosidine (the current most commonly used marker of AGEs in bone). We then establish the viability of CML as a measurable AGE in bone by showing that levels of CML, obtained from bone using this technique, increase with age (p<0.05) and are correlated with previously reported measures of bone toughness. Thus, CML is a viable non-fluorescent AGE target to assess AGE accumulation and fragility in bone. The method developed here to extract and measure CML from human bone could facilitate the development of a new diagnostic assay to evaluate fracture risk and potentially lead to new therapeutic approaches to address bone fragility.
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Affiliation(s)
- Corinne J Thomas
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Grazyna E Sroga
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA.
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22
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Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci 2017; 283:rspb.2016.0593. [PMID: 27306052 DOI: 10.1098/rspb.2016.0593] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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23
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Cleland TP. Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications. J Proteome Res 2017; 17:536-542. [DOI: 10.1021/acs.jproteome.7b00670] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Timothy P. Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
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Abstract
Bone metastasis from primary cancer sites creates diagnostic and therapeutic challenges. Calcified bone is difficult to biopsy due to tissue hardness and patient discomfort, thus limiting the frequency and availability of bone/bone marrow biopsy material for molecular profiling. In addition, bony tissue must be demineralized (decalcified) prior to histomorphologic analysis. Decalcification processes rely on three main principles: (a) solubility of calcium salts in an acid, such as formic or nitric acid; (b) calcium chelation with ethylenediaminetetraacetic acid (EDTA); or (c) ion-exchange resins in a weak acid. A major roadblock in molecular profiling of bony tissue has been the lack of a suitable demineralization process that preserves histomorphology of calcified and soft tissue elements while also preserving phosphoproteins and nucleic acids. In this chapter, we describe general issues relevant to specimen collection and preservation of osseous tissue for molecular profiling. We provide two protocols: (a) one-step preservation of tissue histomorphology and proteins and posttranslational modifications, with simultaneous decalcification of bony tissue, and (b) ethanol-based tissue processing for TheraLin-fixed bony tissue.
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25
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Schroeter ER, DeHart CJ, Schweitzer MH, Thomas PM, Kelleher NL. Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ 2016; 4:e2603. [PMID: 27812413 PMCID: PMC5088622 DOI: 10.7717/peerj.2603] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 11/22/2022] Open
Abstract
Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Caroline J DeHart
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Paul M Thomas
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Neil L Kelleher
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
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26
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Cleland TP, Thomas CJ, Gundberg CM, Vashishth D. Influence of carboxylation on osteocalcin detection by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2109-15. [PMID: 27470908 PMCID: PMC5014568 DOI: 10.1002/rcm.7692] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Osteocalcin is a small, abundant bone protein that is difficult to detect using high-throughput tandem mass spectrometry (MS/MS) proteomic approaches from bone protein extracts, and is predominantly detected by non-MS immunological methods. Here, we analyze bovine osteocalcin and its post-translational modifications to determine why a protein of this size goes undetected. METHODS Osteocalcin was purified from cow bone using well-established methods. Intact osteocalcin or trypsin-digested osteocalcin were separated using an Agilent 1200 series high-performance liquid chromatography (HPLC) system and analyzed using a ThermoScientific LTQ-Orbitrap XL after fragmentation with higher-energy collision dissociation. Data were analyzed using Mascot or Prosight Lite. RESULTS Our results support previous findings that the cow osteocalcin has up to three carboxylations using both intact osteocalcin and digested forms. Using Mascot, we were able to detect osteocalcin peptides, but no fragments that localized the carboxylations. Full annotation using Prosight Lite of the intact (three carboxylations), N-terminal peptide (one carboxylation), and middle peptide (two carboxylations) showed complete fragmentation was present, but complete neutral loss was observed. CONCLUSIONS Osteocalcin carboxylation, and its associated neutral losses, makes high-throughput detection of this protein challenging; however, alternative fragmentation or limited purification can overcome these challenges. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA
| | - Corinne J Thomas
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA
| | - Caren M Gundberg
- Department of Orthopedics and Rehabilitation, Yale University, New Haven, CT, 06520, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA.
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27
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Allam K, El Bouari A, Belhorma B, Bih L. Removal of Methylene Blue from Water Using Hydroxyapatite Submitted to Microwave Irradiation. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jwarp.2016.83030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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