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Gao YC, Jiang NN, Qin XJ, Jiang H, Wei LB, Gao JR. High-throughput data on circular RNA reveal novel insights into chronic glomerulonephritis. Genes Genomics 2023; 45:475-490. [PMID: 36264417 DOI: 10.1007/s13258-022-01320-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs), a unique novel type of RNA, have been widely reported to be involved in physiologic and pathologic processes in humans. However, the exact molecular pathogenesis of circRNAs in chronic glomerulonephritis (CGN) is far from clear. OBJECTIVE This paper aims to evaluate the specific expression profile of circRNAs in renal cortex tissues from Adriamycin-induced CGN rats. METHODS CircRNAs were screened in renal cortex tissues from 3 CGN rats and 3 control rats by using high-throughput sequencing (HTS). Then, 4 circRNAs were selected randomly for verification by quantitative real-time polymerase chain reaction (qRT-PCR). In addition, the differentially expressed (DE) circRNAs were analyzed by bioinformatics methods. RESULTS In total, 31 significantly DE circRNAs were identified, which revealed their potential roles in CGN; in particular, we found that 4 confirmed altered circRNAs (rno-circ-RNAs 689, 3217, 1327, and 5001) might play important roles in the development of CGN. CONCLUSION This study reveals a cluster of circRNAs that are DE in Adriamycin-induced CGN rats, which brings us closer to understanding the pathogenic mechanisms and may provide new potential targets for clinical treatment.
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Affiliation(s)
- Ya-Chen Gao
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, China
| | - Nan-Nan Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, 103 Meishan Road, Hefei, China
| | - Xiu-Juan Qin
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Hui Jiang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Liang-Bing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Jia-Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China.
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Lichtenberg JY, Ling Y, Kim S. Non-Specific Adsorption Reduction Methods in Biosensing. SENSORS (BASEL, SWITZERLAND) 2019; 19:E2488. [PMID: 31159167 PMCID: PMC6603772 DOI: 10.3390/s19112488] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 01/05/2023]
Abstract
Non-specific adsorption (NSA) is a persistent problem that negatively affects biosensors, decreasing sensitivity, specificity, and reproducibility. Passive and active removal methods exist to remedy this issue, by coating the surface or generating surface forces to shear away weakly adhered biomolecules, respectively. However, many surface coatings are not compatible or effective for sensing, and thus active removal methods have been developed to combat this phenomenon. This review aims to provide an overview of methods of NSA reduction in biosensing, focusing on the shift from passive methods to active methods in the past decade. Attention is focused on protein NSA, due to their common use in biosensing for biomarker diagnostics. To our knowledge, this is the first review to comprehensively discuss active NSA removal methods. Lastly, the challenges and future perspectives of NSA reduction in biosensing are discussed.
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Affiliation(s)
- Jessanne Y Lichtenberg
- Department of Electrical and Computer Engineering, School of Engineering, Baylor University, Waco, TX 76798, USA.
| | - Yue Ling
- Department of Mechanical Engineering, School of Engineering, Baylor University, Waco, TX 76798, USA.
| | - Seunghyun Kim
- Department of Electrical and Computer Engineering, School of Engineering, Baylor University, Waco, TX 76798, USA.
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Zhou ZB, Niu YL, Huang GX, Lu JJ, Chen A, Zhu L. Silencing of circRNA.2837 Plays a Protective Role in Sciatic Nerve Injury by Sponging the miR-34 Family via Regulating Neuronal Autophagy. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:718-729. [PMID: 30098504 PMCID: PMC6088565 DOI: 10.1016/j.omtn.2018.07.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/22/2018] [Indexed: 12/15/2022]
Abstract
Circular RNAs (circRNAs) represent a class of non-coding RNAs that are involved in transcriptional and posttranscriptional gene expression regulation and associated with different kinds of human diseases. However, the characterization and function of circular RNAs in peripheral nerve injuries remain elusive. Here, we established a rat sciatic nerve injury model and identified at least 4,942 distinct circular RNA candidates and a series of circular RNAs that were differentially expressed in injured nerve tissues compared with matched normal tissues. We characterized one frequently downregulated circular RNA, circRNA.2837, and further investigated its function in sciatic nerve injury. We found that circRNA.2837 regulated autophagy in neurons in vitro and in vivo, and downregulation of circRNA.2837 alleviated sciatic nerve injury via inducing autophagy in vivo. Mechanistically, knockdown of circRNA.2837 may protect neurons against neurological injury by acting as a sponge for members of miR-34 family. Our findings suggested that differentially expressed circular RNAs were involved in the pathogenesis of sciatic nerve injury, and circular RNAs exerted regulatory functions in sciatic nerve injury and might be used as potential targets in sciatic nerve injury therapy.
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Affiliation(s)
- Zhi-Bin Zhou
- Orthopaedic Trauma and Reconstruction Surgery Center, Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yu-Long Niu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China
| | - Gao-Xiang Huang
- Department of Pathology, No.181 Hospital of PLA, Guilin, Guangxi, 541002, China
| | - Jia-Jia Lu
- Orthopaedic Trauma and Reconstruction Surgery Center, Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Aimin Chen
- Orthopaedic Trauma and Reconstruction Surgery Center, Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
| | - Lei Zhu
- Orthopaedic Trauma and Reconstruction Surgery Center, Department of Orthopaedics, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China.
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Zhou Z, Du D, Chen A, Zhu L. Circular RNA expression profile of articular chondrocytes in an IL-1β-induced mouse model of osteoarthritis. Gene 2018; 644:20-26. [DOI: 10.1016/j.gene.2017.12.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/11/2017] [Indexed: 12/16/2022]
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Hinrichs K, Eichhorn KJ. Adsorption of Proteins at Solid Surfaces. ELLIPSOMETRY OF FUNCTIONAL ORGANIC SURFACES AND FILMS 2018. [PMCID: PMC7121624 DOI: 10.1007/978-3-319-75895-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karsten Hinrichs
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Berlin, Germany
| | - Klaus-Jochen Eichhorn
- Abteilung Analytik, Leibniz-Institut für Polymerforschung Dresden e.V., Dresden, Sachsen Germany
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Nador J, Kalas B, Saftics A, Agocs E, Kozma P, Korosi L, Szekacs I, Fried M, Horvath R, Petrik P. Plasmon-enhanced two-channel in situ Kretschmann ellipsometry of protein adsorption, cellular adhesion and polyelectrolyte deposition on titania nanostructures. OPTICS EXPRESS 2016; 24:4812-4823. [PMID: 29092309 DOI: 10.1364/oe.24.004812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plasmon-enhanced in situ spectroscopic ellipsometry was realized using the Kretschmann geometry. A 10-μL flow cell was designed for multi-channel measurements using a semi-cylindrical lens. Dual-channel monitoring of the layer formation of different organic structures has been demonstrated on titania nanoparticle thin films supported by gold. Complex modeling capabilities as well as a sensitivity of ~40 pg/mm2 with a time resolution of 1 s was achieved. The surface adsorption was enhanced by the titania nanoparticles due to the larger specific surface and nanoroughness, which is consistent with our previous results on titanate nanotubes.
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Kanyong P, Sun G, Rösicke F, Syritski V, Panne U, Hinrichs K, Rappich J. Maleimide functionalized silicon surfaces for biosensing investigated by in-situ IRSE and EQCM. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2014.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Petrik P, Kumar N, Juhasz G, Major C, Fodor B, Agocs E, Lohner T, Pereira SF, Urbach HP, Fried M. Optical characterization of macro-, micro- and nanostructures using polarized light. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/558/1/012008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Oliveira ON, Iost RM, Siqueira JR, Crespilho FN, Caseli L. Nanomaterials for diagnosis: challenges and applications in smart devices based on molecular recognition. ACS APPLIED MATERIALS & INTERFACES 2014; 6:14745-66. [PMID: 24968359 DOI: 10.1021/am5015056] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Clinical diagnosis has always been dependent on the efficient immobilization of biomolecules in solid matrices with preserved activity, but significant developments have taken place in recent years with the increasing control of molecular architecture in organized films. Of particular importance is the synergy achieved with distinct materials such as nanoparticles, antibodies, enzymes, and other nanostructures, forming structures organized on the nanoscale. In this review, emphasis will be placed on nanomaterials for biosensing based on molecular recognition, where the recognition element may be an enzyme, DNA, RNA, catalytic antibody, aptamer, and labeled biomolecule. All of these elements may be assembled in nanostructured films, whose layer-by-layer nature is essential for combining different properties in the same device. Sensing can be done with a number of optical, electrical, and electrochemical methods, which may also rely on nanostructures for enhanced performance, as is the case of reporting nanoparticles in bioelectronics devices. The successful design of such devices requires investigation of interface properties of functionalized surfaces, for which a variety of experimental and theoretical methods have been used. Because diagnosis involves the acquisition of large amounts of data, statistical and computational methods are now in widespread use, and one may envisage an integrated expert system where information from different sources may be mined to generate the diagnostics.
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Affiliation(s)
- Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo , CP 369, 13560-970 São Carlos, São Paulo, Brazil
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Hinrichs K, Eichhorn KJ. Adsorption of Proteins at Solid Surfaces. ELLIPSOMETRY OF FUNCTIONAL ORGANIC SURFACES AND FILMS 2014. [PMCID: PMC7121270 DOI: 10.1007/978-3-642-40128-2_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ellipsometry has a very high thin film sensitivity and can resolve sub-nm changes in the thickness of a protein film on a solid substrates. Being a technique based on photons in and photons out it can also be applied at solid-liquid interfaces. Ellipsometry has therefore found many in situ applications on protein layer dynamics but studies of protein layer structure are also frequent. Numerous ex situ applications on detection and quantification of protein layers are found and several biosensing concepts have been proposed. In this chapter, the use of ellipsometry in the above mentioned areas is reviewed and experimental methodology including cell design is briefly discussed. The classical ellipsometric challenge to determine both thickness and refractive index of a thin film is addressed and an overview of strategies to determine surface mass density is given. Included is also a discussion about spectral representations of optical properties of a protein layer in terms of a model dielectric function concept and its use for analysis of protein layer structure.
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Affiliation(s)
- Karsten Hinrichs
- Leibniz Institute for Analytical Sciences - ISAS - e. V., Berlin, Germany
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Zhang X, Tretjakov A, Hovestaedt M, Sun G, Syritski V, Reut J, Volkmer R, Hinrichs K, Rappich J. Electrochemical functionalization of gold and silicon surfaces by a maleimide group as a biosensor for immunological application. Acta Biomater 2013; 9:5838-44. [PMID: 23117146 DOI: 10.1016/j.actbio.2012.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/11/2012] [Accepted: 10/18/2012] [Indexed: 11/25/2022]
Abstract
In the present study we investigated the preparation of biofunctionalized surfaces using the direct electrochemical grafting of maleimidophenyl molecules with subsequent covalent immobilization of specific peptide to detect target antibody, thereby extending the application of the biosensing systems towards immunodiagnostics. Para-maleimidophenyl (p-MP) functional groups were electrochemically grafted on gold and silicon surfaces from solutions of the corresponding diazonium salt. A specially synthesized peptide modified with cysteine (Cys-peptide) was then immobilized on the p-MP grafted substrates by cross-linking between the maleimide groups and the sulfhydryl group of the cysteine residues. Accordingly, the Cys-peptide worked as an antigen that was able to bind specifically the target antibody (anti-GST antibody), while it was non-sensitive to a negative contrast antibody (i.e. anti-Flag β). The immobilization of both specific and non-specific antibodies on the Cys-peptide-modified surfaces was monitored by infrared spectroscopic ellipsometry, a quartz crystal microbalance integrated in flow injection analysis system and potentiometric response. The results obtained clearly demonstrated that the direct modification of a surface with maleimidophenyl provides a very simple and reliable way of preparing biofunctionalized surfaces suitable for the construction of immunological biosensors.
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Zhang X, Sun G, Hovestädt M, Syritski V, Esser N, Volkmer R, Janietz S, Rappich J, Hinrichs K. A new strategy for the preparation of maleimide-functionalised gold surfaces. Electrochem commun 2010. [DOI: 10.1016/j.elecom.2010.07.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Zhang X, Sun G, Hinrichs K, Janietz S, Rappich J. Infrared spectroscopic study of the amidation reaction of aminophenyl modified Au surfaces and p-nitrobenzoic acid as model system. Phys Chem Chem Phys 2010; 12:12427-9. [DOI: 10.1039/c0cp00058b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nikonenko NA, Bushnak IA, Keddie JL. Spectroscopic ellipsometry of mucin layers on an amphiphilic diblock copolymer surface. APPLIED SPECTROSCOPY 2009; 63:889-98. [PMID: 19678985 DOI: 10.1366/000370209788964449] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Both visible and infrared (IR) spectroscopic ellipsometry have been employed to study the structure of thin layers of bovine submaxillary mucin (BSM) adsorbed on poly(acrylic acid-block-methyl methacrylate) (PAA-b-PMMA) copolymer and poly(methyl methacrylate) (PMMA) surfaces at three pH values (3, 7, and 10). The adsorbed mucin layer on the copolymer surface had the greatest thickness (17 nm) when adsorbed from a mucin solution at a pH of 3. For the first time, IR ellipsometry was used to identify adhesive interactions and conformational changes in mucin/polymer double layers. After applying the regularized method of deconvolution in the analysis, the formation of hydrogen bonds between the carboxyl groups of the BSM and PAA-b-PMMA copolymer in double layers has been found. The IR ellipsometry data, in agreement with the visible ellipsometry analysis, indicate the pH dependence of adhesion of mucin to the copolymer surface. There is an increase in the amount of hydrogen-bonded carboxyl groups in mucin deposited at a pH of 3. There is no evidence that the amide groups of the mucin participate in this bonding. At the lower pH, the IR ellipsometry spectra after deconvolution reveal an increase in the proportion of beta-sheets in the BSM upon adsorption on the copolymer surface, indicating a more unfolded, aggregated structure. The IR ellipsometry data also indicated some changes in the conformational states of the side groups in the copolymer induced by entanglements and bonding interactions with the mucin macromolecules. Deconvolution provides an unprecedented level of information from the IR ellipsometry spectra and yields important insights.
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Affiliation(s)
- Nataliya A Nikonenko
- B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, Nezalezhnasti Ave. 68, 220072 Minsk, Belarus.
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