The Experts below are selected from a list of 2392569 Experts worldwide ranked by ideXlab platform
Hsin-yiu Chou - One of the best experts on this subject based on the ideXlab platform.
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A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
BMC Bioinformatics, 2019Co-Authors: Tao-chuan Shih, Li-ping Ho, Jen-leih Wu, Hsin-yiu ChouAbstract:Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus , Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily Results The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of Antigenicity and cross Antigenicity. The conserved LEs for Iridoviridae family reflected high Antigenicity responses for the two subfamilies, while exclusive LEs reflected high Antigenicity responses only for the host-specific subfamily Conclusions Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
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A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
BMC Bioinformatics, 2019Co-Authors: Tao-chuan Shih, Hsin-yiu Chou, Tun-wen PaiAbstract:The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of Antigenicity and cross Antigenicity. The conserved LEs for Iridoviridae family reflected high Antigenicity responses for the two subfamilies, while exclusive LEs reflected high Antigenicity responses only for the host-specific subfamily Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
Tao-chuan Shih - One of the best experts on this subject based on the ideXlab platform.
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A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
BMC Bioinformatics, 2019Co-Authors: Tao-chuan Shih, Li-ping Ho, Jen-leih Wu, Hsin-yiu ChouAbstract:Background The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus , Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily Results The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of Antigenicity and cross Antigenicity. The conserved LEs for Iridoviridae family reflected high Antigenicity responses for the two subfamilies, while exclusive LEs reflected high Antigenicity responses only for the host-specific subfamily Conclusions Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
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A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
BMC Bioinformatics, 2019Co-Authors: Tao-chuan Shih, Hsin-yiu Chou, Tun-wen PaiAbstract:The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts and Betairidovirinae includes Iridovirus and Chloriridovirus, which infect invertebrate hosts. Clustered Iridoviridae subfamilies possess host-specific characteristics, which can be considered as exclusive features for in-silico prediction of effective epitopes for vaccine development. A voting mechanism-based linear epitope (LE) prediction system was applied to identify and endorse LE candidates with a minimum length requirement for each clustered subfamily The experimental results showed that four conserved epitopes among the Iridovirideae family, one exclusive epitope for invertebrate subfamily and two exclusive epitopes for vertebrate family were predicted. These predicted LE candidates were further validated by ELISA assays for evaluating the strength of Antigenicity and cross Antigenicity. The conserved LEs for Iridoviridae family reflected high Antigenicity responses for the two subfamilies, while exclusive LEs reflected high Antigenicity responses only for the host-specific subfamily Host-specific characteristics are important features and constraints for effective epitope prediction. Our proposed voting mechanism based system provides a novel approach for in silico LE prediction prior to vaccine development, and it is especially powerful for analyzing antigen sequences with exclusive features between two clustered groups.
Yingjun Kong - One of the best experts on this subject based on the ideXlab platform.
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aggregation and Antigenicity of virus like particle in salt solution a case study with hepatitis b surface antigen
Vaccine, 2015Co-Authors: Yi Chen, Yan Zhang, Can Quan, Yanli Yang, Mengran Yu, Yingjun Kong, Zhiguo SuAbstract:The phenomenon of aggregation of virus-like particles (VLPs) in salt solution and the corresponding effect upon Antigenicity was reported. Asymmetrical flow field-flow fractionation (AF4) combined with multi-angle laser light scattering (MALLS) was used to characterize the size and the aggregation behavior of hepatitis 13 surface antigen (HBsAg). The average diameter of HBsAg VLP was 22.8 +/- 0.4 nm and it tended to aggregate in salt solution to form large particles and the Antigenicity changed accordingly. In 0-4 M NaCl solution, part of HBsAg molecules aggregated rapidly into oligomeric particles (OP), whose diameter distributed from 25 to 40 nm, and the Antigenicity slightly decreased about 10%. The aggregation reaction is reversible. After removing NaCl, both size and Antigenicity could recover to normal level (92-96%). By contrast, the aggregation process is more complicated in (NH4)(2)SO4 solution. Most of HBsAg particles aggregated into OP and further aggregated into polymeric particles (PP). The diameter of the PP could reach 40 to 140 nm. The concentration of (NH4)(2)SO4 had remarkable influence upon the rate of aggregation. When concentration of (NH4)(2)SO4 was below 1 M, most of HBsAg aggregated only into OP in 1 h. While with concentration of (NH4)(2)SO4 above 1 M, most of particles formed PP within 1 h. The aggregation process to PP was irreversible. After removing (NH4)(2)SO4, the large aggregates could not recover to normal particles and the remaining Antigenicity was below 30%. (C) 2015 Elsevier Ltd. All rights reserved.
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aggregation and Antigenicity of virus like particle in salt solution a case study with hepatitis b surface antigen
Vaccine, 2015Co-Authors: Yi Chen, Yan Zhang, Can Quan, Yanli Yang, Jian Luo, Yingjun KongAbstract:The phenomenon of aggregation of virus-like particles (VLPs) in salt solution and the corresponding effect upon Antigenicity was reported. Asymmetrical flow field-flow fractionation (AF4) combined with multi-angle laser light scattering (MALLS) was used to characterize the size and the aggregation behavior of hepatitis 13 surface antigen (HBsAg). The average diameter of HBsAg VLP was 22.8 +/- 0.4 nm and it tended to aggregate in salt solution to form large particles and the Antigenicity changed accordingly. In 0-4 M NaCl solution, part of HBsAg molecules aggregated rapidly into oligomeric particles (OP), whose diameter distributed from 25 to 40 nm, and the Antigenicity slightly decreased about 10%. The aggregation reaction is reversible. After removing NaCl, both size and Antigenicity could recover to normal level (92-96%). By contrast, the aggregation process is more complicated in (NH4)(2)SO4 solution. Most of HBsAg particles aggregated into OP and further aggregated into polymeric particles (PP). The diameter of the PP could reach 40 to 140 nm. The concentration of (NH4)(2)SO4 had remarkable influence upon the rate of aggregation. When concentration of (NH4)(2)SO4 was below 1 M, most of HBsAg aggregated only into OP in 1 h. While with concentration of (NH4)(2)SO4 above 1 M, most of particles formed PP within 1 h. The aggregation process to PP was irreversible. After removing (NH4)(2)SO4, the large aggregates could not recover to normal particles and the remaining Antigenicity was below 30%. (C) 2015 Elsevier Ltd. All rights reserved.
Leigh G Griffiths - One of the best experts on this subject based on the ideXlab platform.
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flim guided raman imaging to study cross linking and calcification of bovine pericardium
Analytical Chemistry, 2020Co-Authors: Tanveer Ahmed Shaik, Leigh G Griffiths, Alba Alfonsogarcia, Xiangnan Zhou, Katherine M Arnold, Anne K Haudenschild, Christoph Krafft, Jurgen Popp, Laura MarcuAbstract:Bovine pericardium (BP) is a vascular biomaterial used in cardiovascular surgery that is typically cross-linked for masking Antigenicity and enhance stability. There is a need for biochemical evalu...
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stepwise solubilization based antigen removal for xenogeneic scaffold generation in tissue engineering
Acta Biomaterialia, 2013Co-Authors: Maelene L Wong, Kyriacos A Athanasiou, Janelle L Wong, Leigh G GriffithsAbstract:Abstract The ability of residual antigens on decellularized tissue to elicit the immune response upon implantation motivates development of a more rigorous antigen removal (AR) process for xenogeneic scaffold generation. Antigen removal strategies promoting solubilization of hydrophilic proteins (predominantly cytoplasmic) enhance the reduction of hydrophilic Antigenicity in bovine pericardium (BP); however, the diversity of protein antigens within a tissue necessitates development of AR strategies capable of addressing a spectrum of protein antigen solubilities. In the present study, methods for promoting solubilization of lipophilic proteins (predominantly membrane) were investigated for their ability to reduce lipophilic Antigenicity of BP when applied as a second AR step following our previously described hydrophilic AR method. Bovine pericardium following AR (BP-AR) was assessed for residual hydrophilic and lipophilic Antigenicity, removal of known lipophilic xenoantigens, tensile properties, and extracellular matrix structure and composition. Facilitating hydrophile solubilization (using dithiothreitol and potassium chloride) followed by lipophile solubilization (using amidosulfobetaine-14 (ASB-14)), in a two-step sequential, differential AR strategy, significantly reduces residual hydrophilic and lipophilic Antigenicity of BP-AR beyond that achieved with either one-step hydrophilic AR or decellularization using 1% (w/v) sodium dodecyl sulfate. Moreover, use of 1% (w/v) ASB-14 for lipophilic AR eliminates the two most critical known barriers to xenotransplantation (galactose-α(1,3)-galactose and major histocompatibility complex I)) from BP-AR without compromising the structure–function properties of the biomaterial. This study demonstrates the importance of a sequential, differential protein solubilization approach to reduce biomaterial Antigenicity in the production of a xenogeneic scaffold for heart valve tissue engineering.
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the role of protein solubilization in antigen removal from xenogeneic tissue for heart valve tissue engineering
Biomaterials, 2011Co-Authors: Maelene L Wong, Kent J Leach, Kyriacos A Athanasiou, Leigh G GriffithsAbstract:Decellularization techniques have been developed in an attempt to reduce the Antigenicity of xenogeneic biomaterials, a critical barrier in their use as tissue engineering scaffolds. However, numerous studies have demonstrated inadequate removal and subsequent persistence of antigens in the biomaterial following decellularization, resulting in an immune response upon implantation. Thus, methods to enhance antigen removal (AR) are critical for the use of xenogeneic biomaterials in tissue engineering and regenerative medicine. In the present study, AR methods incorporating protein solubilization principles were investigated for their ability to reduce Antigenicity of bovine pericardium (BP) for heart valve tissue engineering. Bovine pericardium following AR (BP-AR) was assessed for residual Antigenicity, tensile properties, and extracellular matrix composition. Increasing protein solubility during AR significantly decreased the residual Antigenicity of BP-AR-by an additional 80% compared to hypotonic solution or 60% compared to 0.1% (w/v) SDS decellularization methods. Moreover, solubilizing agents have a dominant effect on reducing the level of residual Antigenicity of BP-AR beyond that achieved by AR additives alone. Tested AR methods did not compromise the tensile properties of BP-AR compared to native BP. Furthermore, residual cell nuclei did not correlate to residual Antigenicity, demonstrating that residual nuclei counts may not be an appropriate indicator of successful AR. In conclusion, AR strategies promoting protein solubilization significantly reduced residual antigens compared to decellularization methods without compromising biomaterial functional properties. This study demonstrates the importance of solubilizing protein antigens for their removal in the generation of xenogeneic scaffolds.
Yi Chen - One of the best experts on this subject based on the ideXlab platform.
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aggregation and Antigenicity of virus like particle in salt solution a case study with hepatitis b surface antigen
Vaccine, 2015Co-Authors: Yi Chen, Yan Zhang, Can Quan, Yanli Yang, Mengran Yu, Yingjun Kong, Zhiguo SuAbstract:The phenomenon of aggregation of virus-like particles (VLPs) in salt solution and the corresponding effect upon Antigenicity was reported. Asymmetrical flow field-flow fractionation (AF4) combined with multi-angle laser light scattering (MALLS) was used to characterize the size and the aggregation behavior of hepatitis 13 surface antigen (HBsAg). The average diameter of HBsAg VLP was 22.8 +/- 0.4 nm and it tended to aggregate in salt solution to form large particles and the Antigenicity changed accordingly. In 0-4 M NaCl solution, part of HBsAg molecules aggregated rapidly into oligomeric particles (OP), whose diameter distributed from 25 to 40 nm, and the Antigenicity slightly decreased about 10%. The aggregation reaction is reversible. After removing NaCl, both size and Antigenicity could recover to normal level (92-96%). By contrast, the aggregation process is more complicated in (NH4)(2)SO4 solution. Most of HBsAg particles aggregated into OP and further aggregated into polymeric particles (PP). The diameter of the PP could reach 40 to 140 nm. The concentration of (NH4)(2)SO4 had remarkable influence upon the rate of aggregation. When concentration of (NH4)(2)SO4 was below 1 M, most of HBsAg aggregated only into OP in 1 h. While with concentration of (NH4)(2)SO4 above 1 M, most of particles formed PP within 1 h. The aggregation process to PP was irreversible. After removing (NH4)(2)SO4, the large aggregates could not recover to normal particles and the remaining Antigenicity was below 30%. (C) 2015 Elsevier Ltd. All rights reserved.
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aggregation and Antigenicity of virus like particle in salt solution a case study with hepatitis b surface antigen
Vaccine, 2015Co-Authors: Yi Chen, Yan Zhang, Can Quan, Yanli Yang, Jian Luo, Yingjun KongAbstract:The phenomenon of aggregation of virus-like particles (VLPs) in salt solution and the corresponding effect upon Antigenicity was reported. Asymmetrical flow field-flow fractionation (AF4) combined with multi-angle laser light scattering (MALLS) was used to characterize the size and the aggregation behavior of hepatitis 13 surface antigen (HBsAg). The average diameter of HBsAg VLP was 22.8 +/- 0.4 nm and it tended to aggregate in salt solution to form large particles and the Antigenicity changed accordingly. In 0-4 M NaCl solution, part of HBsAg molecules aggregated rapidly into oligomeric particles (OP), whose diameter distributed from 25 to 40 nm, and the Antigenicity slightly decreased about 10%. The aggregation reaction is reversible. After removing NaCl, both size and Antigenicity could recover to normal level (92-96%). By contrast, the aggregation process is more complicated in (NH4)(2)SO4 solution. Most of HBsAg particles aggregated into OP and further aggregated into polymeric particles (PP). The diameter of the PP could reach 40 to 140 nm. The concentration of (NH4)(2)SO4 had remarkable influence upon the rate of aggregation. When concentration of (NH4)(2)SO4 was below 1 M, most of HBsAg aggregated only into OP in 1 h. While with concentration of (NH4)(2)SO4 above 1 M, most of particles formed PP within 1 h. The aggregation process to PP was irreversible. After removing (NH4)(2)SO4, the large aggregates could not recover to normal particles and the remaining Antigenicity was below 30%. (C) 2015 Elsevier Ltd. All rights reserved.
