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Xu Y, Wu C, Jin J, Tang W, Chen Y, Chang AK, Ying X. Transcriptome Analysis and Identification of Cadmium-Induced Oxidative Stress Response Genes in Different Meretrix meretrix Developmental Stages. Animals (Basel) 2024; 14:352. [PMID: 38275810 PMCID: PMC10812554 DOI: 10.3390/ani14020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Cadmium (Cd) is one of the major pollutants in the aquatic environment, and it can easily accumulate in aquatic animals and result in toxic effects by changing the metabolism of the body, causing a serious impact on the immune system, reproductive system, and the development of offspring. The clam Meretrix meretrix is one of the commercially important species that is cultivated in large-scale aquaculture in China. To elucidate the underlying molecular mechanisms of Cd2+ in the developmental processes, fertilized eggs and larvae of M. meretrix at different developmental stages were exposed to Cd2+ (27.2 mg L-1 in natural seawater) or just natural seawater without Cd2+ (control), and high-throughput transcriptome sequencing and immunohistochemistry techniques were used to analyze the toxic effects of Cd on larvae at different early developmental stages. The results revealed 31,914 genes were differentially expressed in the different stages of M. meretrix development upon treatment with Cd2+. Ten of these genes were differentially expressed in all stages of development examined, but they comprised only six unigenes (CCO, Ndh, HPX, A2M, STF, and pro-C3), all of which were related to the oxidative stress response. Under Cd exposure, the expression levels of CCO and Ndh were significantly upregulated in D-shaped and pediveliger larvae, while pro-C3 expression was significantly upregulated in the fertilized egg, D-shaped larva, and pediveliger. Moreover, HPX, A2M, and STF expression levels in the fertilized egg and pediveliger larvae were also significantly upregulated. In contrast, CCO, Ndh, HPX, A2M, STF, and pro-C3 expression levels in the postlarva were all downregulated under Cd exposure. Besides the genes with changes in expression identified by the transcriptome, the expression of two other oxidative stress-related genes (MT and Nfr2) was also found to change significantly in the different developmental stages of M. meretrix upon Cd exposure, confirming their roles in combating oxidative stress. Overall, the findings of this study indicated that Cd would interfere with cellular respiration, ion transport, and immune response through inducing oxidative stress, and changes in the expression of oxidative stress-related genes might be an important step for M. meretrix to deal with the adverse effects of Cd at different stages of its development.
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Affiliation(s)
- Yiyuan Xu
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Chenghui Wu
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Jianyu Jin
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Wenhan Tang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Yuting Chen
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Alan Kueichieh Chang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
| | - Xueping Ying
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China; (Y.X.)
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou 325035, China
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2
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Janisse SE, Fernandez RL, Heffern MC. Characterizing metal-biomolecule interactions by mass spectrometry. Trends Biochem Sci 2023; 48:815-825. [PMID: 37433704 DOI: 10.1016/j.tibs.2023.06.006] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/13/2023]
Abstract
Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism's health. The labile nature of metal-biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal-biomolecule interactions.
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Affiliation(s)
- Samuel E Janisse
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Rebeca L Fernandez
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA
| | - Marie C Heffern
- Department of Chemistry, University of California, Davis, One Shields Drive, Davis, CA 95616, USA.
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3
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Sachko AM, Goryainova OS, Ivanova TI, Nikolaeva IY, Tarnopolskaia ME, Bychkov AY, Gaas MY, Vorob'ev NV, Kaprin AD, Shegay PV, Tillib SV. Analysis of Transferrin in the Urine of Patients with Bladder Cancer Using Nanobodies. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1105-1115. [PMID: 37758310 DOI: 10.1134/s0006297923080059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/14/2023] [Accepted: 07/03/2023] [Indexed: 10/03/2023]
Abstract
It is known that the saturation ratio of transferrin (Tf) with iron in human blood is an important clinical parameter. Specific antibodies can be used to analyze subtle changes in the relative abundance of different forms of transferrin potentially associated with a pathological process. Recently, the authors of this study were able to obtain and characterize highly specific single-domain antibodies (nanobodies) that predominantly recognize the iron-saturated (holo-Tf) or iron-unsaturated (apo-Tf) form of transferrin. In this work, under conditions closer to physiological than in the previous experiments, we further demonstrated that these unique nanobodies have extremely high differential binding specificity for different forms of Tf in different human biological fluids. Using these nanobodies, we were able to analyze for the first time relative abundance of the transferrin forms in urine samples from the patients with bladder cancer (BC). We have shown that increase in the concentration of total Tf in the urine samples normalized for creatinine is associated with the degree of progress and growth of malignancy of BC. In the samples of healthy donors and in the early stages of BC (G1), Tf is detected in much smaller amounts (compared to the later stages) and only with additional concentration of the studied samples. For most of the studied urine samples from the BC patients, it is expected (as previously shown in the case of Tf in the blood of terminal ovarian cancer patients) that the concentration of apo-Tf is clearly higher than holo-Tf, especially in the case of the most advanced muscle-invasive BC. It was a surprise for us that approximately equal amounts of apo-Tf and holo-Tf were found in the urine samples of some patients with BC. We hypothesized that the holo-Tf fraction in this case could be largely represented by the "secondary complexes" formed by apo-Tf in combination with ions other than Fe3+, which accumulate in the urine of some cancer patients and are able to bind to apo-Tf, changing its conformation towards holo-Tf. By using inductively coupled plasma mass spectroscopy (ICP-MS), we obtained first results confirming our hypothesis. Preparation of the holo-Tf in these urine samples was found to be highly enriched in zinc and nickel. Also, relative enrichment in cadmium has been observed in this preparation, but at much lower concentrations. The obtained data indicate that the used nanobody, while recognizing predominantly the iron-saturated form of transferrin (holo-Tf), is also capable of binding transferrin in association with other metal ions that are different from iron. This ability could potentially open up new possibilities for investigation of relative abundance of various metal ions in association with transferrin in human biological fluids in normal and pathological conditions.
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Affiliation(s)
- Anastasiya M Sachko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Oksana S Goryainova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Tatiana I Ivanova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Tsyb Medical Radiological Research Centre, Branch of the National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Obninsk, 249036, Russia
| | - Irina Yu Nikolaeva
- Faculty of Geology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Andrew Y Bychkov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Margarita Ya Gaas
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Nikolay V Vorob'ev
- Hertsen Moscow Oncology Research Institute, Branch of the National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
- Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, Moscow, 119991, Russia
| | - Andrey D Kaprin
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | - Petr V Shegay
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
- National Medical Research Radiological Centre, Ministry of Health of the Russian Federation, Moscow, 125284, Russia
| | - Sergei V Tillib
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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An Efficient and Economical N-Glycome Sample Preparation Using Acetone Precipitation. Metabolites 2022; 12:metabo12121285. [PMID: 36557323 PMCID: PMC9786591 DOI: 10.3390/metabo12121285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Due to the critical role of the glycome in organisms and its close connections with various diseases, much time and effort have been dedicated to glycomics-related studies in the past decade. To achieve accurate and reliable identification and quantification of glycans extracted from biological samples, several analysis methods have been well-developed. One commonly used methodology for the sample preparation of N-glycomics usually involves enzymatic cleavage by PNGase F, followed by sample purification using C18 cartridges to remove proteins. PNGase F and C18 cartridges are very efficient both for cleaving N-glycans and for protein removal. However, this method is most suitable for a limited quantity of samples. In this study, we developed a sample preparation method focusing on N-glycome extraction and purification from large-scale biological samples using acetone precipitation. The N-glycan yield was first tested on standard glycoprotein samples, bovine fetuin and complex biological samples, and human serum. Compared to C18 cartridges, most of the sialylated N-glycans from human serum were detected with higher abundance after acetone precipitation. However, C18 showed a slightly higher efficiency for protein removal. Using the unfiltered human serum as the baseline, around 97.7% of the proteins were removed by acetone precipitation, while more than 99.9% of the proteins were removed by C18 cartridges. Lastly, the acetone precipitation was applied to N-glycome extraction from egg yolks to demonstrate large-scale glycomics sample preparation.
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Janisse SE, Sharma VA, Caceres A, Medici V, Heffern MC. Systematic Evaluation of Copper(II)-Loaded Immobilized Metal Affinity Chromatography For Selective Enrichment of Copper-Binding Species in Human Serum and Plasma. Metallomics 2022; 14:6656374. [PMID: 35929804 PMCID: PMC9434637 DOI: 10.1093/mtomcs/mfac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/20/2022] [Indexed: 11/12/2022]
Abstract
Copper is essential in a host of biological processes, and disruption of its homeostasis is associated with diseases including neurodegeneration and metabolic disorders. Extracellular copper shifts in its speciation between healthy and disease states, and identifying molecular components involved in these perturbations could widen the panel of biomarkers for copper status. While there have been exciting advances in approaches for studying the extracellular proteome with mass-spectrometry-based methods, the typical workflows disrupt metal-protein interactions due to the lability of these bonds either during sample preparation or in gas-phase environments. We sought to develop and apply a workflow to enrich for and identify protein populations with copper-binding propensities in extracellular fluids using an immobilized metal affinity chromatography (IMAC) resin. The strategy was optimized using human serum to allow for maximum quantity and diversity of protein enrichment. Protein populations could be differentiated based on protein load on the resin, likely on account of differences in abundance and affinity. The enrichment workflow was applied to plasma samples from patients with Wilson disease (WD) and protein IDs and differential abundancies compared to healthy subjects were compared to those yielded from a traditional proteomic workflow. While the IMAC workflow preserved differential abundance and protein ID information from the traditional workflow, it identified several additional proteins being differentially abundant including those involved in lipid metabolism, immune system, and antioxidant pathways. Our results suggest the potential for this IMAC workflow to identify new proteins as potential biomarkers in copper-associated disease states.
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Affiliation(s)
- Samuel E Janisse
- Department of Chemistry, University of California Davis, One Shields Drive, Davis, CA 95616, USA
| | - Vibha A Sharma
- Department of Chemistry, University of California Davis, One Shields Drive, Davis, CA 95616, USA
| | - Amanda Caceres
- Department of Chemistry, University of California Davis, One Shields Drive, Davis, CA 95616, USA
| | - Valentina Medici
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of California Davis, 4150 V Street, PSSB Suite 3500, Sacramento, CA 95817, USA
| | - Marie C Heffern
- Department of Chemistry, University of California Davis, One Shields Drive, Davis, CA 95616, USA
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6
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Abolghasemi-Dehaghani S, Gharanfoli M, Habibi-Rezaei M, Khavari-Nejad RA. Enhanced recovery yield by utilizing an improved purification method for recombinant human follicle-stimulating hormone expressed in CHO cells: Applying CaptureSelect™-FSH affinity matrix. J LIQ CHROMATOGR R T 2021. [DOI: 10.1080/10826076.2021.1960857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Mohsen Gharanfoli
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mehran Habibi-Rezaei
- Protein Biotechnology Research Lab (PBRL), School of Biology, College of Science, University of Tehran, Tehran, Iran
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7
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Yamauchi K. Evolution of thyroid hormone distributor proteins in fish. Gen Comp Endocrinol 2021; 305:113735. [PMID: 33549607 DOI: 10.1016/j.ygcen.2021.113735] [Citation(s) in RCA: 4] [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: 07/16/2020] [Revised: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022]
Abstract
In plasma, thyroid hormone (TH) is bound to several TH distributor proteins (THDPs), constituting a TH delivery/distribution network. Extensive studies of THDPs from tetrapods has proposed an evolutionary scenario concerning structural and functional changes in THDPs, especially for transthyretin (TTR). When assessing, in an evolutionary context, the roles of THDPs as a component constituting part of the vertebrate thyroid system, the data from fish THDPs are critical. In this review the phylogenetic distributions, spatiotemporal expression patterns and binding properties of THDPs in fish are described, and the question of whether the evolutionary hypotheses proposed in tetrapod THDPs can be applied to fish THDPs is assessed. The phylogenetic distributions of THDPs are highly variable among fish groups. Analysis in this review reveals that the evolutionary hypotheses proposed in tetrapod THDPs cannot be applied to fish THDPs, and that the role of plasma lipoproteins as THDPs grows in importance in fish groups. In primitive fish, zinc is an import factor in TH binding to TTR, and high zinc content may facilitate the acquisition of high TH binding activity during the early evolution of TTR. Finally, the possible roles of THDPs in the vertebrate thyroid system are discussed.
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Affiliation(s)
- Kiyoshi Yamauchi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan.
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Yamauchi K. The interaction of zinc with the multi-functional plasma thyroid hormone distributor protein, transthyretin: evolutionary and cross-species comparative aspects. Biometals 2021; 34:423-437. [PMID: 33686575 DOI: 10.1007/s10534-021-00294-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022]
Abstract
A considerable body of evidence has been accumulated showing the interrelationship between zinc and the plasma thyroid hormone (TH) distributor protein, transthyretin (TTR). TTR is a multi-functional protein, which emerged from 5-hydroxyisourate hydrolase (HIUHase) by neo-functionalization after gene duplication during early chordate evolution. HIUHase is also a zinc-binding protein. Most biochemical and molecular biological findings have been obtained from mammalian studies. However, in the past two decades, it has become clear that fish TTR displays zinc-dependent TH binding. After a brief introduction on plasma zinc, THs and their binding proteins, this review will focus on the role of zinc in TTR functions of various vertebrates. In particular primitive fish TTR has an extremely high zinc content, with an increased number of histidine residues which are involved in TH binding. However, zinc-dependent TH binding may have been gradually lost from TTRs during higher vertebrate evolution. Although human TTR has a low zinc content, zinc plays an essential role in TTR functions other than TH binding: the stability of TTR-holo retinol binding protein 4 (holoRBP4) complex, TTR amyloidogenesis, the sequestration of amyloid β (Aβ) fibrils and cryptic proteolytic activity. The interaction of TTR with metallothioneins may be a critical step in the exertion of some of these functions. Evolutionary and physiological insights on zinc-dependent functions of TTRs are also discussed.
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Affiliation(s)
- Kiyoshi Yamauchi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, 422-8529, Japan.
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Hameed O, Ozcan F, Ertul S, Cagil EM. Preparation of Immobilized Metal Affinity Nanofiber for Globulin Depletion. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Rodriguez EL, Poddar S, Iftekhar S, Suh K, Woolfork AG, Ovbude S, Pekarek A, Walters M, Lott S, Hage DS. Affinity chromatography: A review of trends and developments over the past 50 years. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1157:122332. [PMID: 32871378 PMCID: PMC7584770 DOI: 10.1016/j.jchromb.2020.122332] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022]
Abstract
The field of affinity chromatography, which employs a biologically-related agent as the stationary phase, has seen significant growth since the modern era of this method began in 1968. This review examines the major developments and trends that have occurred in this technique over the past five decades. The basic principles and history of this area are first discussed. This is followed by an overview of the various supports, immobilization strategies, and types of binding agents that have been used in this field. The general types of applications and fields of use that have appeared for affinity chromatography are also considered. A survey of the literature is used to identify major trends in these topics and important areas of use for affinity chromatography in the separation, analysis, or characterization of chemicals and biochemicals.
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Affiliation(s)
| | - Saumen Poddar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Sazia Iftekhar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyungah Suh
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Ashley G Woolfork
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Susan Ovbude
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Allegra Pekarek
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Morgan Walters
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Shae Lott
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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11
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Linking molecular targets of Cd in the bloodstream to organ-based adverse health effects. J Inorg Biochem 2020; 216:111279. [PMID: 33413916 DOI: 10.1016/j.jinorgbio.2020.111279] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022]
Abstract
The chronic exposure of human populations to toxic metals remains a global public health concern. Although chronic Cd exposure is linked to kidney damage, osteoporosis and cancer, the underlying biomolecular mechanisms remain incompletely understood. Since other diseases could also be causally linked to chronic Cd exposure, a systems toxicology-based approach is needed to gain new insight into the underlying exposure-disease relationship. This approach requires one to integrate the cascade of dynamic bioinorganic chemistry events that unfold in the bloodstream after Cd enters with toxicological events that unfold in target organs over time. To this end, we have conducted a systematic literature search to identify all molecular targets of Cd in plasma and in red blood cells (RBCs). Based on this information it is impossible to describe the metabolism of Cd and the toxicological relevance of it binding to molecular targets in/on RBCs is elusive. Perhaps most importantly, the role that peptides, amino acids and inorganic ions, including HCO3-, Cl- and HSeO3- play in terms of mediating the translocation of Cd to target organs and its detoxification is poorly understood. Causally linking human exposure to this metal with diseases requires a much better integration of the bioinorganic chemistry of Cd that unfolds in the bloodstream with target organs. This from a public health point of view important goal will require collaborations between scientists from different disciplines to untangle the complex mechanisms which causally link Cd exposure to disease.
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Horta S, Qu JH, Dekimpe C, Bonnez Q, Vandenbulcke A, Tellier E, Kaplanski G, Delport F, Geukens N, Lammertyn J, Vanhoorelbeke K. Co(III)-NTA Mediated Antigen Immobilization on a Fiber Optic-SPR Biosensor for Detection of Autoantibodies in Autoimmune Diseases: Application in Immune-Mediated Thrombotic Thrombocytopenic Purpura. Anal Chem 2020; 92:13880-13887. [DOI: 10.1021/acs.analchem.0c02586] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Jia-Huan Qu
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Charlotte Dekimpe
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Quintijn Bonnez
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Aline Vandenbulcke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
| | - Edwige Tellier
- INSERM, INRAE, C2VN, Jardin du Pharo, Aix Marseille Univ, 58 Boulevard Charles Livon, 13007 Marseille , France
| | - Gilles Kaplanski
- INSERM, INRAE, C2VN, Jardin du Pharo, Aix Marseille Univ, 58 Boulevard Charles Livon, 13007 Marseille , France
- APHM, INSERM, INRAE, C2VN, Hôpital de la Conception, Service de médecine interne, Aix Marseille Univ, 147 Boulevard Baille, 13005 Marseille, France
| | - Filip Delport
- FOx Biosystems NV, Bioville, Agoralaan Abis, Diepenbeek 3590, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem De Croylaan 42, Heverlee B-3001, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Herestraat 49, Leuven 3000, Belgium
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Mahdian S, Zarrabi M, Moini A, Movahedi M, Shahhoseini M. In silico identification of new inhibitors for βeta-2-glycoprotein I as a major antigen in antiphospholipid antibody syndrome. J Mol Model 2020; 26:156. [PMID: 32458176 DOI: 10.1007/s00894-020-04406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
Abstract
Beta 2 glycoprotein I (β2GPI) is a major antigen for autoantibodies present in antiphospholipid antibody syndrome (APS). β2GPI is a single polypeptide with five repeated domains and different conformations. The activated J-shaped conformation of β2GPI binds to negatively charged phospholipids in the membrane via the fifth domain and causes blood clotting reactions. We applied a drug repurposing strategy using virtual screening and molecular dynamics to find the best FDA drugs against the fifth domain of β2GPI. In the first phase, FDA drugs that had the most favorable ΔG with the fifth domain of β2GPI were selected by virtual screening. Among these drugs that had the most favorable ΔG, Vorapaxar and Antrafenine were selected for molecular dynamics (MD) simulation studies. MD simulation was performed to evaluate the stability of Vorapaxar and Antrafenine complexes and the effect of the two drugs on protein conformation. Also, MD simulation was done to investigate the effect of Antrafenine and Vorapaxar on the binding of β2GPI to the platelet model membrane. According to the results, Vorapaxar and Antrafenine were bound to the protein with the favorable binding energy (Vorapaxar and Antrafenine binding energies are - 49.641 and - 38.803 kcal/mol, respectively). In this study, it was shown that unlike protein alone and protein in the Antrafenine complex, the protein in the Vorapaxar complex was completely separated from the model membrane after 350 ns. Moreover, Vorapaxar led to more changes in the activated J-shape of β2GPI. Thus, Vorapaxar can be a suitable candidate for further investigations on the treatment of APS.
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Affiliation(s)
- Soodeh Mahdian
- Department of Biochemistry, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mahboobeh Zarrabi
- Department of Biotechnology, Biological Faculty, Alzahra University, Tehran, Iran
| | - Ashraf Moini
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Disease Research Center (BDRC), Tehran University of Medical Sciences, Tehran, Iran.,Department of Gynecology and Obstetrics, Arash Women's Hospital, Tehran, University of Medical Sciences, Tehran, Iran
| | - Monireh Movahedi
- Department of Biochemistry, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran.
| | - Maryam Shahhoseini
- Reproductive Epidemiology Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. .,Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
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14
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Simplification of affinity macroporous monolith microfluidic column synthesis and its ability for protein separation. J Pharm Biomed Anal 2020; 181:113099. [DOI: 10.1016/j.jpba.2020.113099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 01/10/2023]
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15
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Li Y, Huang YS, He B, Liu R, Qu G, Yin Y, Shi J, Hu L, Jiang G. Cadmium-binding proteins in human blood plasma. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 188:109896. [PMID: 31704329 DOI: 10.1016/j.ecoenv.2019.109896] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Blood is the transmission medium for metal contaminants to and from bodily organs; as such, it can provide useful and reliable information about their bio-kinetics as they're distributed throughout the body. Metals can interact with endogenous proteins present in the blood, and these metal-protein complexes often dictate the fates of the introduced metals. The aim of this study was to investigate cadmium-binding protein characteristics in normal human plasma. Cadmium-binding plasma proteins in two different groups: normal human plasma (n = 29), and normal paired maternal and fetal umbilical cord plasmas (n = 3), were analyzed. In order to detect cadmium-binding plasma proteins present in low concentrations, blood plasma samples were first depleted of their two most abundant proteins - albumin and immunoglobulin G. Both the crude and depleted plasma samples were analyzed using column gel electrophoresis in conjunction with Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). One cadmium-binding protein was detected in 11 of 29 normal plasma samples and all three paired maternal and cord plasma samples. This protein was further identified as apolipoprotein A-I by high-resolution mass spectrometry. To the best of our knowledge, this is the first study to reveal cadmium-binding proteins in real human blood plasma, which is extremely critical to our understanding of cadmium transportation and accumulation in human blood.
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Affiliation(s)
- Yiling Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yong-Shun Huang
- Department of Occupational Medicine, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, Guangdong, 510300, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Runzeng Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Institute of Environment and Health, Jianghan University, Wuhan, 430056, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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16
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Coverdale JPC, Barnett JP, Adamu AH, Griffiths EJ, Stewart AJ, Blindauer CA. A metalloproteomic analysis of interactions between plasma proteins and zinc: elevated fatty acid levels affect zinc distribution. Metallomics 2019; 11:1805-1819. [PMID: 31612889 DOI: 10.1039/c9mt00177h] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Serum albumin is a highly abundant plasma protein associated with the transport of metal ions, pharmaceuticals, fatty acids and a variety of small molecules in the blood. Once thought of as a molecular 'sponge', mounting evidence suggests that the albumin-facilitated transport of chemically diverse entities is not independent. One such example is the transport of Zn2+ ions and non-esterified 'free' fatty acids (FFAs) by albumin, both of which bind at high affinity sites located in close proximity. Our previous research suggests that their transport in blood plasma is linked via an allosteric mechanism on serum albumin. In direct competition, albumin-bound FFAs significantly decrease the binding capacity of albumin for Zn2+, with one of the predicted consequences being a change in plasma/serum zinc speciation. Using liquid chromatography (LC), ICP-MS and fluorescence assays, our work provides a quantitative assessment of this phenomenon, and finds that in the presence of high FFA concentrations encountered in various physiological conditions, a significant proportion of albumin-bound Zn2+ is re-distributed amongst plasma/serum proteins. Using peptide mass fingerprinting and immunodetection, we identify candidate acceptor proteins for Zn2+ liberated from albumin. These include histidine-rich glycoprotein (HRG), a multifunctional protein associated with the regulation of blood coagulation, and members of the complement system involved in the innate immune response. Our findings highlight how FFA-mediated changes in extracellular metal speciation might contribute to the progression of certain pathological conditions.
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Affiliation(s)
| | - James P Barnett
- Department of Life Sciences, Birmingham City University, Edgbaston, B15 3TN, UK
| | - Adamu H Adamu
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Ellie J Griffiths
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK
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17
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Abstract
Abstract
Nickel-binding proteins play an important role in the biological processes and can also be utilized in several fields of biotechnology. This study was focused on analysing the nickel-binding proteins from the blood sera of humans (Homo sapiens), cattle (Bos taurus), sheep (Ovis aries), red deer (Cervus elaphus), mouflon (Ovis orientalis), fallow deer (Dama dama), horses (Equus ferus caballus), pigs (Sus scrofa domesticus), wildboars (Sus scrofa), brown bears (Ursus arctos) and pheasants (Phasianus colchicus). The presence of higher abundance proteins in the blood serum, such as albumins, may mask the detection of lower abundance proteins. The samples were depleted from these higher abundance proteins to facilitate the detection of those with lower abundance. For the characterization of these proteins, nickel cations bound to tetradentate ligand nitrilotriacetic acid(Ni-NTA)immobilized on agarose beads were incubated with animal sera to capture nickel-binding proteins and subsequently the proteins were eluted and fractionated on sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The results showed a set of nickel-binding proteins with various molecular weights within different animal species. A unique ~42 kDa nickel-binding protein in the brown bear serum, which was not present in any of the other species, was further characterized and identified by matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF/MS). This protein was identified as ahaptoglobin-like protein. This result may provide some valuable clue for the physiological difference in the metal binding proteins in the serum of Ursus arctos and other animals.
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18
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Zhang S, Cao Y, Cheng H. Expression of Aspergillus niger N5-5 in E. coli and purification and identification of products. Saudi J Biol Sci 2018; 24:1842-1848. [PMID: 29551933 PMCID: PMC5851913 DOI: 10.1016/j.sjbs.2017.11.025] [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] [Received: 10/13/2017] [Revised: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 12/02/2022] Open
Abstract
Due to the feature of high hydrolysis, tannase is widely used in food, beverage, brewing and other fields. However, high cost in producing natural tannase makes it difficult to apply tannase to industry in a large-scale. Microbial expression systems can be used for preparing numerous amount of enzyme at low cost, so in this paper Aspergillus niger N5-5 was expressed using E. coli system. Specific primers were designed based on the Aspergillus niger N5-5 sequence N3 (GenBank, No.: KP677552), and tannase gene tan was promoted to carry 6 His tag and enzyme cutting site which contains NdeI/HindIII using PCR amplification. Then, tannase gene tan was connected to expression vector by NdeI/HindIII enzyme cutting. In this way, recombinant expression vector tan-pET43.1a was formed. Then, the expression vector pET43.1a by NdeI/HindIII enzyme cutting was transformed into E. coli BL21 (DE3) to induce expression of Aspergillus niger N5-5. When the induced fungi were disrupted by the ultrasonic wave, the crude enzyme was extracted and purified by using the IMAC, and then the activity of the crude enzyme and pure enzyme was determined. According to the results of determination of the tannase activity, the tannase activity of the crude enzyme was greatly improved after the crude enzyme was purified, and the specific activity of the pure enzyme was about 8 times of that of the crude enzyme. The results of SDS-PAGE of the pure enzyme showed that the molecular mass of the pure enzyme was about 65 kDa/64–65 kDa, which was consistent with the expected result (64.2 kDa), It can be concluded that the crude enzyme solution was purified successfully. The results of pure enzyme’s protein identification by Western Blotting showed that clear protein bands pro-3 were observed. Molecular mass of clear protein bands pro-3 was about 65 kDa, which was in line with the expected results (64.2 kDa). It can be seen that the aforementioned expression protein could be specifically combined with His tag. It proved expression protein to be a recombinant fusion protein with 6 His tag.
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Affiliation(s)
- Shuai Zhang
- School of Food & Pharmaceutical Engineering, Zhaoqing University, Zhaoqing, Guangdong 526061, China.,College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Yong Cao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Cheng
- College of Biological & Chemical Engineering, Guangxi University of Science and Technology, Liuzhou 545006, China.,Collaborative Innovation Center of Sugarcane Industry of Guangxi, Nanning 530004, China
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19
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Zhang Z, Li L. Efficient synthesis of molecularly imprinted polymers with bio-recognition sites for the selective separation of bovine hemoglobin. J Sep Sci 2018; 41:2479-2487. [DOI: 10.1002/jssc.201701479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Zulei Zhang
- School of Biology and Chemical Engineering; Jiaxing University; Jiaxing China
| | - Lei Li
- School of Biology and Chemical Engineering; Jiaxing University; Jiaxing China
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20
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Zhang Z, Wang H, Wang H, Wu C, Li M, Li L. Fabrication and evaluation of molecularly imprinted magnetic nanoparticles for selective recognition and magnetic separation of lysozyme in human urine. Analyst 2018; 143:5849-5856. [DOI: 10.1039/c8an01746h] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Lyz-MMIPs displayed a uniform core–shell structure, favorable magnetic properties, good accessibility, and good stability and had a good affinity and excellent binding selectivity to Lyz.
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Affiliation(s)
- Zulei Zhang
- School of Biology and Chemical Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Hongmei Wang
- School of Biology and Chemical Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Hailong Wang
- School of Biology and Chemical Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Cuichen Wu
- Attribute Sciences
- Amgen Inc
- One Amgen Center Drive
- Thousand Oaks
- USA
| | - Mengli Li
- School of Biology and Chemical Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Lei Li
- School of Biology and Chemical Engineering
- Jiaxing University
- Jiaxing 314001
- China
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21
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Detection of histidine-rich glycoprotein and fibrinogen with nickel-enzyme conjugates: Purification of rabbit HRG. Anal Biochem 2017; 525:67-72. [DOI: 10.1016/j.ab.2017.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 02/06/2017] [Accepted: 02/18/2017] [Indexed: 11/19/2022]
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22
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Zhang Z, Zhang X, Niu D, Li Y, Shi J. Large-pore, silica particles with antibody-like, biorecognition sites for efficient protein separation. J Mater Chem B 2017; 5:4214-4220. [DOI: 10.1039/c7tb00886d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The MI-LPSPs, with antibody-like, bio-recognition sites, displayed good affinity and excellent binding selectivity to BSA.
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Affiliation(s)
- Zulei Zhang
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Xingdi Zhang
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Dechao Niu
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Yongsheng Li
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
| | - Jianlin Shi
- Lab of Low-Dimensional Materials Chemistry
- Key Laboratory for Ultrafine Materials of Ministry of Education
- School of Materials Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
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23
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Remelli M, Nurchi VM, Lachowicz JI, Medici S, Zoroddu MA, Peana M. Competition between Cd(II) and other divalent transition metal ions during complex formation with amino acids, peptides, and chelating agents. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Huang Z, Ma L, Huang C, Li Q, Nice EC. Proteomic profiling of human plasma for cancer biomarker discovery. Proteomics 2016; 17. [PMID: 27550791 DOI: 10.1002/pmic.201600240] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/03/2016] [Accepted: 08/18/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Zhao Huang
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou P. R. China
- Criminal police detachment of Guang'an City Public Security Bureau; P. R. China
| | - Linguang Ma
- Criminal police detachment of Guang'an City Public Security Bureau; P. R. China
| | - Canhua Huang
- State Key Laboratory for Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center of Biotherapy; Chengdu P. R. China
| | - Qifu Li
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou P. R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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25
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Gladilovich V, Greifenhagen U, Sukhodolov N, Selyutin A, Singer D, Thieme D, Majovsky P, Shirkin A, Hoehenwarter W, Bonitenko E, Podolskaya E, Frolov A. Immobilized metal affinity chromatography on collapsed Langmuir-Blodgett iron(III) stearate films and iron(III) oxide nanoparticles for bottom-up phosphoproteomics. J Chromatogr A 2016; 1443:181-90. [PMID: 27016113 DOI: 10.1016/j.chroma.2016.03.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 01/27/2023]
Abstract
Phosphorylation is the enzymatic reaction of site-specific phosphate transfer from energy-rich donors to the side chains of serine, threonine, tyrosine, and histidine residues in proteins. In living cells, reversible phosphorylation underlies a universal mechanism of intracellular signal transduction. In this context, analysis of the phosphoproteome is a prerequisite to better understand the cellular regulatory networks. Conventionally, due to the low contents of signaling proteins, selective enrichment of proteolytic phosphopeptides by immobilized metal affinity chromatography (IMAC) is performed prior to their LC-MS or -MS/MS analysis. Unfortunately, this technique still suffers from low selectivity and compromised analyte recoveries. To overcome these limitations, we propose IMAC systems comprising stationary phases based on collapsed Langmuir-Blodgett films of iron(III) stearate (FF) or iron(III) oxide nanoparticles (FO) and mobile phases relying on ammonia, piperidine and heptadecafluorooctanesulfonic acid (PFOS). Experiments with model phosphopeptides and phosphoprotein tryptic digests showed superior binding capacity, selectivity and recovery for both systems in comparison to the existing commercial analogs. As evidenced by LC-MS/MS analysis of the HeLa phosphoproteome, these features of the phases resulted in increased phosphoproteome coverage in comparison to the analogous commercially available phases, indicating that our IMAC protocol is a promising chromatographic tool for in-depth phosphoproteomic research.
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Affiliation(s)
- Vladimir Gladilovich
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia
| | - Uta Greifenhagen
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany
| | | | | | - David Singer
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany
| | - Domenika Thieme
- Leibniz Institute of Plant Biochemistry, Proteome Analytics Research Group, Germany
| | - Petra Majovsky
- Leibniz Institute of Plant Biochemistry, Proteome Analytics Research Group, Germany
| | - Alexey Shirkin
- Institute of Analytical Instrumentation, Russian Academy of Science, Russia
| | | | - Evgeny Bonitenko
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia
| | - Ekaterina Podolskaya
- Institute of Toxicology, Russian Federal Agency for Biology and Medicine, Russia; Institute of Analytical Instrumentation, Russian Academy of Science, Russia
| | - Andrej Frolov
- Universität Leipzig, Faculty of Chemistry and Mineralogy, Germany; Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Germany.
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26
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Min L, Zheng N, Zhao S, Cheng J, Yang Y, Zhang Y, Yang H, Wang J. Long-term heat stress induces the inflammatory response in dairy cows revealed by plasma proteome analysis. Biochem Biophys Res Commun 2016; 471:296-302. [PMID: 26851364 DOI: 10.1016/j.bbrc.2016.01.185] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 01/31/2016] [Indexed: 11/18/2022]
Abstract
In this work we employed a comparative proteomic approach to evaluate seasonal heat stress and investigate proteomic alterations in plasma of dairy cows. Twelve lactating Holstein dairy cows were used and the treatments were: heat stress (n = 6) in hot summer (at the beginning of the moderate heat stress) and no heat stress (n = 6) in spring natural ambient environment, respectively. Subsequently, heat stress treatment lasted 23 days (at the end of the moderate heat stress) to investigate the alterations of plasma proteins, which might be employed as long-term moderate heat stress response in dairy cows. Changes in plasma proteins were analyzed by two-dimensional electrophoresis (2-DE) combined with mass spectrometry. Analysis of the properties of the identified proteins revealed that the alterations of plasma proteins were related to inflammation in long-term moderate heat stress. Furthermore, the increase in plasma tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) directly demonstrated that long-term moderate heat stress caused an inflammatory response in dairy cows.
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Affiliation(s)
- Li Min
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jianbo Cheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Yongxin Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yangdong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Hongjian Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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27
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Gao R, Zhao S, Hao Y, Zhang L, Cui X, Liu D, Zhang M, Tang Y. Synthesis of magnetic dual-template molecularly imprinted nanoparticles for the specific removal of two high-abundance proteins simultaneously in blood plasma. J Sep Sci 2015; 38:3914-3920. [DOI: 10.1002/jssc.201500882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 08/29/2015] [Accepted: 08/31/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Ruixia Gao
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
| | - Siqi Zhao
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
| | - Yi Hao
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Lili Zhang
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Xihui Cui
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Dechun Liu
- Department of Hepatobiliary Surgery; First Hospital of Xi'an Jiaotong University; Xi'an China
| | - Min Zhang
- College of Chemistry and Chemical Engineering; Shanghai University of Engineering Science; Shanghai China
| | - Yuhai Tang
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
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28
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Gao R, Zhang L, Hao Y, Cui X, Liu D, Zhang M, Tang Y. One-step preparation of magnetic imprinted nanoparticles adopting dopamine-cupric ion as a co-monomer for the specific recognition of bovine hemoglobin. J Sep Sci 2015; 38:3568-74. [DOI: 10.1002/jssc.201500677] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Ruixia Gao
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
| | - Lili Zhang
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Yi Hao
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Xihui Cui
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
| | - Dechun Liu
- Department of Hepatobiliary Surgery; First Hospital of Xi'an Jiaotong University; Xi'an China
| | - Min Zhang
- College of Chemistry and Chemical Engineering; Shanghai University of Engineering Science; Shanghai China
| | - Yuhai Tang
- Institute of Analytical Science, School of Science; Xi'an Jiaotong University; Xi'an China
- College of Pharmacy; Xi'an Jiaotong University; Xi'an China
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29
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Suzuki S, Kasai K, Yamauchi K. Characterization of little skate (Leucoraja erinacea) recombinant transthyretin: Zinc-dependent 3,3',5-triiodo-l-thyronine binding. Gen Comp Endocrinol 2015; 217-218:43-53. [PMID: 25863347 DOI: 10.1016/j.ygcen.2015.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 12/13/2022]
Abstract
Transthyretin (TTR) diverged from an ancestral 5-hydroxyisourate hydrolase (HIUHase) by gene duplication at some early stage of chordate evolution. To clarify how TTR had participated in the thyroid system as an extracellular thyroid hormone (TH) binding protein, TH binding properties of recombinant little skate Leucoraja erinacea TTR was investigated. At the amino acid level, skate TTR showed 37-46% identities with the other vertebrate TTRs. Because the skate TTR had a unique histidine-rich segment in the N-terminal region, it could be purified by Ni-affinity chromatography. The skate TTR was a 46-kDa homotetramer of 14.5kDa subunits, and had one order of magnitude higher affinity for 3,3',5-triiodo-l-thyronine (T3) and some halogenated phenols than for l-thyroxine. However, the skate TTR had no HIUHase activity. Ethylenediaminetetraacetic acid (EDTA) treatment inhibited [(125)I]T3 binding activity whereas the addition of Zn(2+) to the EDTA-treated TTR recovered [(125)I]T3 binding activity in a Zn(2+) concentration-dependent manner. Scatchard analysis revealed the presence of two classes of binding site for T3, with dissociation constants of 0.24 and 17nM. However, the high-affinity sites were completely abolished with 1mM EDTA, whereas the remaining low-affinity sites decreased binding capacity. The number of zinc per TTR was quantified to be 4.5-6.3. Our results suggest that skate TTR has tight Zn(2+)-binding sites, which are essential for T3 binding to at least the high-affinity sites. Zn(2+) binding to the N-terminal histidine-rich segment may play an important role in acquisition or reinforcement of TH binding ability during early evolution of TTR.
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Affiliation(s)
- Shunsuke Suzuki
- Department of Biological Science, Graduate School of Science, Shizuoka University, Shizuoka 422-8529, Japan.
| | - Kentaro Kasai
- Department of Biological Science, Graduate School of Science, Shizuoka University, Shizuoka 422-8529, Japan.
| | - Kiyoshi Yamauchi
- Department of Biological Science, Graduate School of Science, Shizuoka University, Shizuoka 422-8529, Japan; Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan.
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30
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Perçin I, Karakoç V, Ergün B, Denizli A. Metal-immobilized magnetic nanoparticles for cytochrome C purification from rat liver. Biotechnol Appl Biochem 2015; 63:31-40. [DOI: 10.1002/bab.1347] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 01/14/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Işık Perçin
- Department of Biology; Molecular Biology Division; Hacettepe University; Beytepe Ankara Turkey
| | - Veyis Karakoç
- Department of Chemistry; Biochemistry Division; Hacettepe University; Beytepe Ankara Turkey
| | - Bahar Ergün
- Department of Chemistry; Biochemistry Division; Hacettepe University; Beytepe Ankara Turkey
| | - Adil Denizli
- Department of Chemistry; Biochemistry Division; Hacettepe University; Beytepe Ankara Turkey
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31
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Ferreira CMH, Pinto ISS, Soares EV, Soares HMVM. (Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review. RSC Adv 2015. [DOI: 10.1039/c4ra15453c] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. Additionally, their impact on the biological systems is also presented and discussed.
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Affiliation(s)
- Carlos M. H. Ferreira
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Isabel S. S. Pinto
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Eduardo V. Soares
- Bioengineering Laboratory
- Chemical Engineering Department
- ISEP-School of Engineering of Polytechnic Institute of Porto
- Porto
- Portugal
| | - Helena M. V. M. Soares
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
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32
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Pei X, Kang W, Yue W, Bange A, Heineman W, Papautsky I. Disposable copper-based electrochemical sensor for anodic stripping voltammetry. Anal Chem 2014; 86:4893-900. [PMID: 24773513 PMCID: PMC4030804 DOI: 10.1021/ac500277j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/14/2014] [Indexed: 11/28/2022]
Abstract
In this work, we report the first copper-based point-of-care sensor for electrochemical measurements demonstrated by zinc determination in blood serum. Heavy metals require careful monitoring, yet current methods are too complex for a point-of-care system. Electrochemistry offers a simple approach to metal detection on the microscale, but traditional carbon, gold (Au), or platinum (Pt) electrodes are difficult or expensive to microfabricate, preventing widespread use. Our sensor features a new low-cost electrode material, copper, which offers simple fabrication and compatibility with microfabrication and PCB processing, while maintaining competitive performance in electrochemical detection. Anodic stripping voltammetry of zinc using our new copper-based sensors exhibited a 140 nM (9.0 ppb) limit of detection (calculated) and sensitivity greater than 1 μA/μM in the acetate buffer. The sensor was also able to determine zinc in a bovine serum extract, and the results were verified with independent sensor measurements. These results demonstrate the advantageous qualities of this lab-on-a-chip electrochemical sensor for clinical applications, which include a small sample volume (μL scale), reduced cost, short response time, and high accuracy at low concentrations of analyte.
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Affiliation(s)
- Xing Pei
- BioMicroSystems
Lab, Department of Electrical Engineering and Computing
Systems, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States
| | - Wenjing Kang
- BioMicroSystems
Lab, Department of Electrical Engineering and Computing
Systems, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States
| | - Wei Yue
- Department
of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Adam Bange
- Department
of Chemistry, Xavier University, Cincinnati, Ohio 45207-4221, United States
| | - William
R. Heineman
- Department
of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, United States
| | - Ian Papautsky
- BioMicroSystems
Lab, Department of Electrical Engineering and Computing
Systems, University of Cincinnati, Cincinnati, Ohio 45221-0030, United States
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33
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Gao R, Mu X, Hao Y, Zhang L, Zhang J, Tang Y. Combination of surface imprinting and immobilized template techniques for preparation of core-shell molecularly imprinted polymers based on directly amino-modified Fe 3O 4 nanoparticles for specific recognition of bovine hemoglobin. J Mater Chem B 2014; 2:1733-1741. [PMID: 32261403 DOI: 10.1039/c3tb21684e] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this work, the core-shell bovine hemoglobin (BHb)-imprinted superparamagnetic nanoparticles (Fe3O4@BHb-MIPs) were synthesized by combining for the first time a surface imprinting technique and a two-step immobilized template strategy. Initially, amino-functionalized Fe3O4 nanoparticles (Fe3O4@NH2) were synthesized directly through a facile one-pot hydrothermal method. Next, BHb was immobilized on the surface of Fe3O4@NH2 through non-covalent interactions. Then, siloxane co-polymerization on the Fe3O4@NH2-protein complex surface resulted in a polymeric network molded around BHb which then became further immobilized. Finally, a thin polymer layer with specific recognition cavities for BHb was formed on the surface of Fe3O4@NH2 after the removal of the template protein. The morphology and structure property of the prepared magnetic nanoparticles were characterized by transmission electronic microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffractometer (XRD), and vibrating sample magnetometer (VSM). To obtain the best selectivity and binding performance, the polymerization and adsorption conditions were investigated in detail. Under the optimized conditions, the Fe3O4@BHb-MIPs exhibited fast adsorption kinetics, large binding capacity, significant selectivity, and favorable reproducibility. The resultant Fe3O4@BHb-MIPs could not only specifically extract BHb from a mixed standard protein mixture, but also selectively enriched BHb from a real bovine blood sample. In addition, the synthetic process was quite simple and the stability and regeneration of the Fe3O4@BHb-MIPs were also satisfactory.
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Affiliation(s)
- Ruixia Gao
- Institute of Analytical Science, Faculty of Science, Xi'an Jiaotong University, Xi'an 710049, P. R. China. tyh57@ mail.xjtu.edu.cn
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34
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Identification of differentially expressed serum proteins in infectious purpura fulminans. DISEASE MARKERS 2014; 2014:698383. [PMID: 24659849 PMCID: PMC3934775 DOI: 10.1155/2014/698383] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/26/2013] [Accepted: 01/01/2014] [Indexed: 12/19/2022]
Abstract
Purpura fulminans (PF) is a life-threatening hemorrhagic condition. Because of the rarity and randomness of the disease, no improvement in treatment has been made for a long time. In this study, we assessed the serum proteome response to PF by comparing serum proteins between healthy controls and PF patient. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) approach was used after depleting 6 abundant proteins of serum. In total, 262 proteins were confidently identified with 2 unique peptides, and 38 proteins were identified significantly up- (≥2) or downregulated (≤0.5) based on spectral counting ratios (SpCPF/N). In the 38 proteins with significant abundance changes, 11 proteins were previously known to be associated with burn or sepsis response, but 27 potentially novel proteins may be specifically associated with PF process. Two differentially expressed proteins, alpha-1-antitrypsin (SERPINA1) and alpha-2 antiplasmin (SERPINF2), were validated by Western blot. This is the first study where PF patient and healthy controls are compared in a proteomic study to elucidate proteins involved in the response to PF. This study provides an initial basis for future studies of PF, and the differentially expressed proteins might provide new therapeutic targets to decrease the mortality of PF.
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35
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Gao R, Zhang L, Hao Y, Cui X, Tang Y. Specific removal of protein using protein imprinted polydopamine shells on modified amino-functionalized magnetic nanoparticles. RSC Adv 2014. [DOI: 10.1039/c4ra07965e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A simple approach for the specific removal of protein using polydopamine imprinted shells on modified amino-functionalized magnetic nanoparticles was developed.
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Affiliation(s)
- Ruixia Gao
- Institute of Analytical Science
- School of Science
- Xi’an Jiaotong University
- Xi’an 710049, P. R. China
| | - Lili Zhang
- College of Pharmacy
- Xi’an Jiaotong University
- Xi’an 710061, P. R. China
| | - Yi Hao
- College of Pharmacy
- Xi’an Jiaotong University
- Xi’an 710061, P. R. China
| | - Xihui Cui
- College of Pharmacy
- Xi’an Jiaotong University
- Xi’an 710061, P. R. China
| | - Yuhai Tang
- Institute of Analytical Science
- School of Science
- Xi’an Jiaotong University
- Xi’an 710049, P. R. China
- College of Pharmacy
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