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Luo H, Ma Y, Bi J, Li Z, Wang Y, Su Z, Gerstweiler L, Ren Y, Zhang S. Experimental and molecular dynamics simulation studies on the physical properties of three HBc-VLP derivatives as nanoparticle protein vaccine candidates. Vaccine 2024:S0264-410X(24)00599-1. [PMID: 38811268 DOI: 10.1016/j.vaccine.2024.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Self-assembling virus-like particles (VLPs) are promising platforms for vaccine development. However, the unpredictability of the physical properties, such as self-assembly capability, hydrophobicity, and overall stability in engineered protein particles fused with antigens, presents substantial challenges in their downstream processing. We envision that these challenges can be addressed by combining more precise computer-aided molecular dynamics (MD) simulations with experimental studies on the modified products, with more to-date forcefield descriptions and larger models closely resembling real assemblies, realized by rapid advancement in computing technology. In this study, three chimeric designs based on the hepatitis B core (HBc) protein as model vaccine candidates were constructed to study and compare the influence of inserted epitopes as well as insertion strategy on HBc modifications. Large partial VLP models containing 17 chains for the HBc chimeric model vaccines were constructed based on the wild-type (wt) HBc assembly template. The findings from our simulation analysis have demonstrated good consistency with experimental results, pertaining to the surface hydrophobicity and overall stability of the chimeric vaccine candidates. Furthermore, the different impact of foreign antigen insertions on the HBc scaffold was investigated through simulations. It was found that separately inserting two epitopes into the HBc platform at the N-terminal and the major immunogenic regions (MIR) yields better results compared to a serial insertion at MIR in terms of protein structural stability. This study substantiates that an MD-guided design approach can facilitate vaccine development and improve its manufacturing efficiency by predicting products with extreme surface hydrophobicity or structural instability.
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Affiliation(s)
- Hong Luo
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia; State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Yanyan Ma
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Jingxiu Bi
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yingli Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong 030619, PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Lukas Gerstweiler
- School of Chemical Engineering, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide 5005, Australia.
| | - Ying Ren
- State Key Laboratory of Mesoscience and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS), Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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Lothert K, Harsy YMJ, Endres P, Müller E, Wolff MW. Evaluation of restricted access media for the purification of cell culture-derived Orf viruses. Eng Life Sci 2023; 23:e2300009. [PMID: 37664009 PMCID: PMC10472920 DOI: 10.1002/elsc.202300009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 09/05/2023] Open
Abstract
Recently, multimodal chromatography using restricted access media (RAM) for the purification of nanoparticles, such as viruses has regained increasing attention. These chromatography resins combine size exclusion on the particle shell and adsorptive interaction within the core. Accordingly, smaller process-related impurities, for example, DNA and proteins, can be retained, while larger product viruses can pass unhindered. We evaluated a range of currently available RAM, differing in the shells' pore cut-off and the core chemistry, for the purification of a cell culture-derived clarified model virus, namely the Orf virus (ORFV). We examined impurity depletion and product recovery as relevant criteria for the evaluation of column performance, as well as scale-up robustness and regeneration potential for evaluating a multiple use application. The results indicate that some columns, for example, the Capto Core, enable both a high DNA and protein removal, while others, for example, the Monomix Core 60 (MC60), are more suitable for DNA depletion. Furthermore, column regeneration is facilitated by using columns with larger shell pores (5000 vs. 700 kDa) and weaker binding interactions (anion exchange vs. multimodal). According to these findings, the choice of RAM resins should be selected according to the respective feed sample composition and the planned number of application cycles.
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Affiliation(s)
- Keven Lothert
- Institute of Bioprocess Engineering and Pharmaceutical TechnologyUniversity of Applied Sciences Mittelhessen (THM)GiessenGermany
| | - Yasmina M. J. Harsy
- Institute of Bioprocess Engineering and Pharmaceutical TechnologyUniversity of Applied Sciences Mittelhessen (THM)GiessenGermany
| | - Patrick Endres
- Tosoh Bioscience GmbH, Separations Business Unit ‐ EuropeGriesheimGermany
| | - Egbert Müller
- Tosoh Bioscience GmbH, Separations Business Unit ‐ EuropeGriesheimGermany
| | - Michael W. Wolff
- Institute of Bioprocess Engineering and Pharmaceutical TechnologyUniversity of Applied Sciences Mittelhessen (THM)GiessenGermany
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Lorenzo E, Miranda L, Gòdia F, Cervera L. Downstream process design for Gag HIV-1 based virus-like particles. Biotechnol Bioeng 2023; 120:2672-2684. [PMID: 37148527 DOI: 10.1002/bit.28419] [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: 11/24/2022] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/08/2023]
Abstract
Virus-like particles-based vaccines have been gaining interest in recent years. The manufacturing of these particles includes their production by cell culture followed by their purification to meet the requirements of its final use. The presence of host cell extracellular vesicles represents a challenge for better virus-like particles purification, because both share similar characteristics which hinders their separation. The present study aims to compare some of the most used downstream processing technologies for capture and purification of virus-like particles. Four steps of the purification process were studied, including a clarification step by depth filtration and filtration, an intermediate step by tangential flow filtration or multimodal chromatography, a capture step by ion exchange, heparin affinity and hydrophobic interaction chromatography and finally, a polishing step by size exclusion chromatography. In each step, the yields were evaluated by percentage of recovery of the particles of interest, purity, and elimination of main contaminants. Finally, a complete purification train was implemented using the best results obtained in each step. A final concentration of 1.40 × 1010 virus-like particles (VLPs)/mL with a purity of 64% after the polishing step was achieved, with host cell DNA and protein levels complaining with regulatory standards, and an overall recovery of 38%. This work has resulted in the development of a purification process for HIV-1 Gag-eGFP virus-like particles suitable for scale-up.
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Affiliation(s)
- Elianet Lorenzo
- Departament d'Enginyeria Química Biològica i Ambiental, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Laia Miranda
- Departament d'Enginyeria Química Biològica i Ambiental, Universitat Autònoma de Barcelona, Bellaterra, Spain
- University College London, London, UK
| | - Francesc Gòdia
- Departament d'Enginyeria Química Biològica i Ambiental, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Laura Cervera
- Departament d'Enginyeria Química Biològica i Ambiental, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Mi X, Wang SC, Winters MA, Carta G. Protein adsorption on core-shell resins for flow-through purifications: Effect of protein molecular size, shape, and salt concentration. Biotechnol Prog 2023; 39:e3300. [PMID: 36101005 DOI: 10.1002/btpr.3300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022]
Abstract
This work addresses the functional properties of the core-shell resins Capto Core 400 and 700 for a broad range of proteins spanning 66.5 to 660 kDa in molecular mass, including bovine serum albumin (BSA) in monomer and dimer form, fibronectin, thyroglobulin, and BSA conjugates with 10 and 30 kDa poly(ethylene glycol) chains. Negatively charged latex nanoparticles (NPs) with nominal diameters of 20, 40, and 100 nm are also studied as surrogates for bioparticles. Protein binding and its trends with respect to salt concentration depend on the protein size and are different for the two agarose-based multimodal resins. For the smaller proteins, the amount of protein bound over practical time scales is limited by the resin surface area and is larger for Capto Core 400 compared with Capto Core 700. For the larger proteins, diffusion is severely restricted in Capto Core 400, resulting in lower binding capacities than those observed for Capto Core 700 despite the larger surface area. Adding 500 mM NaCl reduces the local bound protein concentration and diffusional hindrance resulting in higher binding capacities for the large proteins in Capto Core 400 compared with low ionic strength conditions. The NPs are essentially completely excluded from the Capto Core 400 pores. However, 20 and 40 nm NPs bind significantly to Capto Core 700, further hindering protein diffusion. A model is provided to predict the dynamic binding capacities as a function of residence time.
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Affiliation(s)
- Xue Mi
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Sheng-Ching Wang
- Vaccine Process Research & Development, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Michael A Winters
- Vaccine Process Research & Development, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
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Fuks PE, Carta G. Preparation and characterization of agarose-encapsulated ceramic hydroxyapatite particles for flow-through chromatography. SEP SCI TECHNOL 2022. [DOI: 10.1080/01496395.2022.2026388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Preston E. Fuks
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia, USA
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Dhamane S, Patil U, Smith M, Adhikari M, Nazem A, Conrad JC, Kourentzi K, Willson RC. Isocratic reporter-exclusion immunoassay using restricted-access adsorbents. Analyst 2021; 146:4835-4840. [PMID: 34198311 PMCID: PMC9798887 DOI: 10.1039/d1an00396h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We introduce analyte-dependent exclusion of reporter reagents from restricted-access adsorbents as the basis of an isocratic reporter-exclusion immunoassay for viruses, proteins, and other analytes. Capto™ Core 700 and related resins possess a noninteracting size-selective outer layer surrounding a high-capacity nonspecific mixed-mode capture adsorbent core. In the absence of analyte, antibody-enzyme reporter conjugates can enter the adsorbent and be captured, and their signal is lost. In the presence of large or artificially-expanded analytes, reporter reagents bind to analyte species to form complexes large enough to be excluded from the adsorbent core, allowing their signal to be observed. This assay principle is demonstrated using M13 bacteriophage virus and human chorionic gonadotropin as model analytes. The simple isocratic detection approach described here allows a rapid implementation of immunoassay for detection of a wide range of analytes and uses inexpensive, generally-applicable, and stable column materials instead of costly analyte-specific immunoaffinity adsorbents.
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Affiliation(s)
- Sagar Dhamane
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Maxwell Smith
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Meena Adhikari
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA
| | - Ahmad Nazem
- Department of Biomedical Engineering, University of Houston, Houston, TX USA
| | - Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX USA
| | - Richard C. Willson
- Department of Biology and Biochemistry, University of Houston, Houston, TX USA,Department of Biomedical Engineering, University of Houston, Houston, TX USA,Department of Chemical and Biomolecular Engineering, University of Houston, TX USA,Escuela de Medicina y Ciencias de las Salud ITESM, Monterrey, Mexico,Corresponding author. (Richard C. Willson)
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Mi X, Fuks P, Wang SC, Winters MA, Carta G. Protein Adsorption on Core-shell Particles: Comparison of Capto™ Core 400 and 700 Resins. J Chromatogr A 2021; 1651:462314. [PMID: 34144396 DOI: 10.1016/j.chroma.2021.462314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 01/15/2023]
Abstract
Structural and functional characteristics of the two core-shell resins Capto™ Core 400 and 700, which are useful for the flow-through purification of bioparticles such as viruses, viral vectors, and vaccines, are compared using bovine serum albumin (BSA) and thyroglobulin (Tg) as models for small and large protein contaminants. Both resins are agarose-based and contain an adsorbing core surrounded by an inert shell. Although shell thicknesses are comparable (3.6 and 4.2 µm for Capto Core 400 and 700, respectively), the two resins differ substantially in pore size (pore radii of 19 and 50 nm, respectively). Because of the smaller pores and higher surface area, the BSA binding capacity of Capto Core 400 is approximately double that of Capto Core 700. However, for the much larger Tg, the attainable capacity is substantially larger for Capto Core 700. Mass transfer in both resins is affected by diffusional resistances through the shell and within the adsorbing core. For BSA, core and shell effective pore diffusivities are about 0.25 × 10-7 and 0.6 × 10-7 cm2/s, respectively, for Capto Core 400, and about 1.6 × 10-7 and 2.6 × 10-7 cm2/s, respectively, for Capto Core 700. These values decrease dramatically for Tg to 0.022 × 10-7 and 0.088 × 10-7 cm2/s and to 0.13 × 10-7 and 0.59 × 10-7 cm2/s for Capto Core 400 and 700, respectively. Adsorbed Tg further hinders diffusion of BSA in both resins. Column measurements show that, despite the higher static capacity of Capto Core 400 for BSA, the dynamic binding capacity is greater for Capto Core 700 as a result of its faster kinetics. However, some of this advantage is lost if the feed is a mixture of BSA and Tg since, in this case, Tg binding leads to greater diffusional hindrance for BSA.
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Affiliation(s)
- Xue Mi
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Preston Fuks
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sheng-Ching Wang
- Vaccine Process Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Michael A Winters
- Vaccine Process Research and Development, Merck & Co., Inc., West Point, PA, USA
| | - Giorgio Carta
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA.
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Folgueiras-González A, van den Braak R, Deijs M, van der Hoek L, de Groof A. A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA. Diagnostics (Basel) 2021; 11:diagnostics11050791. [PMID: 33925752 PMCID: PMC8145099 DOI: 10.3390/diagnostics11050791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
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Affiliation(s)
- Alba Folgueiras-González
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Robin van den Braak
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Correspondence:
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Gerstweiler L, Bi J, Middelberg APJ. Virus-like particle preparation is improved by control over capsomere-DNA interactions during chromatographic purification. Biotechnol Bioeng 2021; 118:1707-1720. [PMID: 33484156 DOI: 10.1002/bit.27687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022]
Abstract
Expression of viral capsomeres in bacterial systems and subsequent in vitro assembly into virus-like particles is a possible pathway for affordable future vaccines. However, purification is challenging as viral capsomeres show poor binding to chromatography media. In this study, the behavior of capsomeres in unfractionated bacterial lysate was compared with that for purified capsomeres, with or without added microbial DNA, to better understand reasons for poor bioprocess behavior. We show that aggregates or complexes form through the interaction between viral capsomeres and DNA, especially in bacterial lysates rich in contaminating DNA. The formation of these complexes prevents the target protein capsomeres from accessing the pores of chromatography media. We find that protein-DNA interactions can be modulated by controlling the ionic strength of the buffer and that at elevated ionic strengths the protein-DNA complexes dissociate. Capsomeres thus released show enhanced bind-elute behavior on salt-tolerant chromatography media. DNA could therefore be efficiently removed. We believe this is the first report of the use of an optimized salt concentration that dissociates capsomere-DNA complexes yet enables binding to salt-tolerant media. Post purification, assembly experiments indicate that DNA-protein interactions can play a negative role during in vitro assembly, as DNA-protein complexes could not be assembled into virus-like particles, but formed worm-like structures. This study reveals that the control over DNA-protein interaction is a critical consideration during downstream process development for viral vaccines.
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Affiliation(s)
- Lukas Gerstweiler
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia, Australia
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Sánchez-Trasviña C, Fuks P, Mushagasha C, Kimerer L, Mayolo-Deloisa K, Rito-Palomares M, Carta G. Structure and functional properties of Capto™ Core 700 core-shell particles. J Chromatogr A 2020; 1621:461079. [DOI: 10.1016/j.chroma.2020.461079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/13/2023]
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