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Spontaneous and Electrically Induced Anisotropy of Composite Agarose Gels. Gels 2022; 8:gels8110753. [DOI: 10.3390/gels8110753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/22/2022] Open
Abstract
Agarose gels containing and not bacteriorhodopsin purple membranes (incorporated before gelling) manifest spontaneous optical anisotropy. The dependencies of the anisotropy on the agarose concentration and time have been studied. The rise in the anisotropy is explained by the predominant orientation of the agarose fibers during the gelling and subsequent deformation of the gel net. In the electric field, additional optical anisotropy rises, which is caused by the orientation of the membranes. A procedure has been developed to separate electrically induced and spontaneous anisotropy in composite gels. The isoelectric points and surface electric potential of bacteriorhodopsin trimer and purple membranes are calculated by the method of protein electrostatics to explain their electric asymmetry, which leads to perpendicular orientation in the direct electric field and longitudinal in the kilohertz sinusoidal field. The results allow for an increase in the separation capability of composite gels of electrophoresis for macromolecules with different sizes by applying an appropriate electric field to modulate the effective pore size.
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Fatimi A, Okoro OV, Podstawczyk D, Siminska-Stanny J, Shavandi A. Natural Hydrogel-Based Bio-Inks for 3D Bioprinting in Tissue Engineering: A Review. Gels 2022; 8:179. [PMID: 35323292 PMCID: PMC8948717 DOI: 10.3390/gels8030179] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Three-dimensional (3D) printing is well acknowledged to constitute an important technology in tissue engineering, largely due to the increasing global demand for organ replacement and tissue regeneration. In 3D bioprinting, which is a step ahead of 3D biomaterial printing, the ink employed is impregnated with cells, without compromising ink printability. This allows for immediate scaffold cellularization and generation of complex structures. The use of cell-laden inks or bio-inks provides the opportunity for enhanced cell differentiation for organ fabrication and regeneration. Recognizing the importance of such bio-inks, the current study comprehensively explores the state of the art of the utilization of bio-inks based on natural polymers (biopolymers), such as cellulose, agarose, alginate, decellularized matrix, in 3D bioprinting. Discussions regarding progress in bioprinting, techniques and approaches employed in the bioprinting of natural polymers, and limitations and prospects concerning future trends in human-scale tissue and organ fabrication are also presented.
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Affiliation(s)
- Ahmed Fatimi
- Department of Chemistry, Polydisciplinary Faculty, Sultan Moulay Slimane University, P.O. Box 592 Mghila, Beni-Mellal 23000, Morocco
- ERSIC, Polydisciplinary Faculty, Sultan Moulay Slimane University, P.O. Box 592 Mghila, Beni-Mellal 23000, Morocco
| | - Oseweuba Valentine Okoro
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050 Brussels, Belgium; (O.V.O.); (J.S.-S.)
| | - Daria Podstawczyk
- Department of Process Engineering and Technology of Polymer and Carbon Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373 Wroclaw, Poland;
| | - Julia Siminska-Stanny
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050 Brussels, Belgium; (O.V.O.); (J.S.-S.)
- Department of Process Engineering and Technology of Polymer and Carbon Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Norwida 4/6, 50-373 Wroclaw, Poland;
| | - Amin Shavandi
- 3BIO-BioMatter, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050 Brussels, Belgium; (O.V.O.); (J.S.-S.)
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3
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Ross ML, Kunkel J, Long S, Asuri P. Combined Effects of Confinement and Macromolecular Crowding on Protein Stability. Int J Mol Sci 2020; 21:ijms21228516. [PMID: 33198190 PMCID: PMC7697604 DOI: 10.3390/ijms21228516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/18/2023] Open
Abstract
Confinement and crowding have been shown to affect protein fates, including folding, functional stability, and their interactions with self and other proteins. Using both theoretical and experimental studies, researchers have established the independent effects of confinement or crowding, but only a few studies have explored their effects in combination; therefore, their combined impact on protein fates is still relatively unknown. Here, we investigated the combined effects of confinement and crowding on protein stability using the pores of agarose hydrogels as a confining agent and the biopolymer, dextran, as a crowding agent. The addition of dextran further stabilized the enzymes encapsulated in agarose; moreover, the observed increases in enhancements (due to the addition of dextran) exceeded the sum of the individual enhancements due to confinement and crowding. These results suggest that even though confinement and crowding may behave differently in how they influence protein fates, these conditions may be combined to provide synergistic benefits for protein stabilization. In summary, our study demonstrated the successful use of polymer-based platforms to advance our understanding of how in vivo like environments impact protein function and structure.
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4
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Change of network structure in agarose gels by aging during storage studied by NMR and electrophoresis. Carbohydr Polym 2020; 245:116497. [DOI: 10.1016/j.carbpol.2020.116497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/20/2022]
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5
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Saccharomyces cerevisiae and Candida albicans Yeast Cells Labeled with Fe(III) Complexes as MRI Probes. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6030041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of MRI probes is of interest for labeling antibiotic-resistant fungal infections based on yeast. Our work showed that yeast cells can be labeled with high-spin Fe(III) complexes to produce enhanced T2 water proton relaxation. These Fe(III)-based macrocyclic complexes contained a 1,4,7-triazacyclononane framework, two pendant alcohol groups, and either a non-coordinating ancillary group and a bound water molecule or a third coordinating pendant. The Fe(III) complexes that had an open coordination site associated strongly with Saccharomyces cerevisiae upon incubation, as shown by screening using Z-spectra analysis. The incubation of one Fe(III) complex with either Saccharomyces cerevisiae or Candida albicans yeast led to an interaction with the β-glucan-based cell wall, as shown by the ready retrieval of the complex by the bidentate chelator called maltol. Other conditions, such as a heat shock treatment of the complexes, produced Fe(III) complex uptake that could not be reversed by the addition of maltol. Appending a fluorescence dye to Fe(TOB) led to uptake through secretory pathways, as shown by confocal fluorescence microscopy and by the incomplete retrieval of the Fe(III) complex by the maltol treatment. Yeast cells that were labeled with these Fe(III) complexes displayed enhanced water proton T2 relaxation, both for S. cerevisiae and for yeast and hyphal forms of C. albicans.
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Latreille PL, Adibnia V, Nour A, Rabanel JM, Lalloz A, Arlt J, Poon WCK, Hildgen P, Martinez VA, Banquy X. Spontaneous shrinking of soft nanoparticles boosts their diffusion in confined media. Nat Commun 2019; 10:4294. [PMID: 31541104 PMCID: PMC6754464 DOI: 10.1038/s41467-019-12246-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
Improving nanoparticles (NPs) transport across biological barriers is a significant challenge that could be addressed through understanding NPs diffusion in dense and confined media. Here, we report the ability of soft NPs to shrink in confined environments, therefore boosting their diffusion compared to hard, non-deformable particles. We demonstrate this behavior by embedding microgel NPs in agarose gels. The origin of the shrinking appears to be related to the overlap of the electrostatic double layers (EDL) surrounding the NPs and the agarose fibres. Indeed, it is shown that screening the EDL interactions, by increasing the ionic strength of the medium, prevents the soft particle shrinkage. The shrunken NPs diffuse up to 2 orders of magnitude faster in agarose gel than their hard NP counterparts. These findings provide valuable insights on the role of long range interactions on soft NPs dynamics in crowded environments, and help rationalize the design of more efficient NP-based transport systems.
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Affiliation(s)
- Pierre-Luc Latreille
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Vahid Adibnia
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Antone Nour
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
- Research Institute of the McGill University Health Centre, Injury Repair Recovery Program, Department of Surgery, Division of Orthopaedics, Montreal, QC, Canada
| | - Jean-Michel Rabanel
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
- INRS-Institut Armand-Frappier Research Centre, 531, boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Augustine Lalloz
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Jochen Arlt
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Wilson C K Poon
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Patrice Hildgen
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Vincent A Martinez
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Xavier Banquy
- Faculty of Pharmacy, Université de Montréal, PO Box 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada.
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7
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Guan J, Chen K, Jee AY, Granick S. DNA molecules deviate from shortest trajectory when driven through hydrogel. J Chem Phys 2018; 149:163331. [DOI: 10.1063/1.5033990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Juan Guan
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kejia Chen
- Google, Inc., Mountain View, California 94043, USA
| | - Ah-Young Jee
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - Steve Granick
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
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8
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Serwer P, Hunter B, Wright ET. Cell-gel interactions of in-gel propagating bacteria. BMC Res Notes 2018; 11:699. [PMID: 30286794 PMCID: PMC6172759 DOI: 10.1186/s13104-018-3811-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/30/2018] [Indexed: 11/17/2022] Open
Abstract
Objective Our immediate objective is to test the data-suggested possibility that in-agarose gel bacterial propagation causes gel fiber dislocation and alteration of cell distribution. We also test the further effect of lowering water activity. We perform these tests with both Gram-negative and Gram-positive bacteria. Data are obtained via electron microscopy of thin sections, which provides the first images of both bacteria and gel fibers in gel-supported bacterial lawns. The long-term objective is analysis of the effects of in-gel propagation on the DNA packaging of phages. Results We find that agarose gel-supported cells in lawns of Escherichia coli and Lysinibacillus (1) are primarily in clusters that increase in size with time and are surrounded by gel fibers, and (2) sometimes undergo gel-induced, post-duplication rotation and translation. Bacterial growth-induced dislocation of gel fibers is observed. One reason for clustering is that clustering promotes growth by increasing the growth-derived force applied to the gel fibers. Reactive force exerted by gel on cells explains cell movement. Finally, addition to growth medium of 0.94 M sucrose causes cluster-associated E. coli cells to become more densely packed and polymorphic. Shape is determined, in part, by neighboring cells, a novel observation to our knowledge.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Barbara Hunter
- Department of Pathology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
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9
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Palit S, Khajehpour Tadavani S, Yethiraj A. Realization of a stable, monodisperse water-in-oil droplet system with micro-scale and nano-scale confinement for tandem microscopy and diffusion NMR studies. SOFT MATTER 2018; 14:448-459. [PMID: 29261208 DOI: 10.1039/c7sm01508a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this work we generate stable and monodisperse water-in-oil emulsions using a co-flowing geometry that produced droplet sizes between 13 μm and 250 μm. The drops survived transfer to NMR tubes and were stable for at least 26 hours, enabling the performance of pulsed-field-gradient NMR experiments in addition to microscopy. The drops sizes achieved as a function of flow rate agree well with a simple model for droplet generation: this yields a precise measure of the interfacial tension. The design of a cell mimetic environment with nano-scale confinement has also been demonstrated with diffusion measurements on macromolecules (PEG and Ficoll70) within droplets that are further structured internally using agarose gel networks. Containing the agarose gel in droplets appears to provide very reproducible and homogeneous network environments, enabling quantitative agreement of Ficoll70 dynamics with a theoretical model, with no fit parameters, and, with PEG, yielding a systematic polymer-size dependent slowing down in the network. This is in contrast with bulk agarose, where identical macromolecular diffusion measurements indicate the presence of heterogeneities with water pockets.
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Affiliation(s)
- Swomitra Palit
- Physics and Physical Oceanography, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada.
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10
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Bikos DA, Mason TG. Influence of ionic constituents and electrical conductivity on the propagation of charged nanoscale objects in passivated gel electrophoresis. Electrophoresis 2017; 39:394-405. [PMID: 29114908 DOI: 10.1002/elps.201700310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 11/11/2022]
Abstract
When determining the electric field E acting on charged objects in gel electrophoresis, the electrical conductivity of the buffer solution is often overlooked; E is typically calculated by dividing the applied voltage by a separation distance between electrodes. However, as a consequence of electrolytic reactions, which occur at the electrodes, gradients in the ionic content of the buffer solution and its conductivity can potentially develop over time, thereby impacting E and affecting propagation velocities of charged objects, v, directly. Here, we explore how the types and concentrations of ionic constituents of the buffer solution, which largely control its conductivity, when used in passivated gel electrophoresis (P-gelEP), can influence E, thereby altering v of charged nanospheres propagating through large-pore gels. We measure the conductivity of the buffer solution in the center of the gel region near propagating bands of nanospheres, and we show that predictions of E based on conductivity closely correlate with v. We also explore P-gelEP involving two different types of passivation agents: nonionic polyethylene glycol (PEG) and anionic sodium dodecyl sulfate (SDS). Our observations indicate that using a conductivity model to determine E from the local current density and the conductivity where spheres are propagating can lead to a better estimate than the standard approach of a voltage divided by a separation. Moreover, this conductivity model also provides a starting point for interpreting the complex behavior created by amphiphilic ionic passivation agents, such as SDS, on propagating nanospheres used in some P-gelEP experiments.
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Affiliation(s)
- Dimitri A Bikos
- Department of Chemistry and Biochemistry, University of California- Los Angeles, Los Angeles, CA, USA
| | - Thomas G Mason
- Department of Chemistry and Biochemistry, University of California- Los Angeles, Los Angeles, CA, USA.,Department of Physics and Astronomy, University of California- Los Angeles, Los Angeles, CA, USA
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11
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Wang S, Herbst EB, Pye SD, Moran CM, Hossack JA. Pipe Phantoms With Applications in Molecular Imaging and System Characterization. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2017; 64:39-52. [PMID: 27845659 PMCID: PMC5490078 DOI: 10.1109/tuffc.2016.2626465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Pipe (vessel) phantoms mimicking human tissue and blood flow are widely used for cardiovascular related research in medical ultrasound. Pipe phantom studies require the development of materials and liquids that match the acoustic properties of soft tissue, blood vessel wall, and blood. Over recent years, pipe phantoms have been developed to mimic the molecular properties of the simulated blood vessels. In this paper, the design, construction, and functionalization of pipe phantoms are introduced and validated for applications in molecular imaging and ultrasound imaging system characterization. There are three major types of pipe phantoms introduced: 1) a gelatin-based pipe phantom; 2) a polydimethylsiloxane-based pipe phantom; and 3) the "Edinburgh pipe phantom." These phantoms may be used in the validation and assessment of the dynamics of microbubble-based contrast agents and, in the case of a small diameter tube phantom, for assessing imaging system spatial resolution/contrast performance. The materials and procedures required to address each of the phantoms are described.
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12
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Kojic M, Milosevic M, Kojic N, Koay EJ, Fleming JB, Ferrari M, Ziemys A. Mass release curves as the constitutive curves for modeling diffusive transport within biological tissue. Comput Biol Med 2016; 92:156-167. [PMID: 29182964 DOI: 10.1016/j.compbiomed.2016.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/15/2016] [Accepted: 06/24/2016] [Indexed: 11/17/2022]
Abstract
In diffusion governed by Fick's law, the diffusion coefficient represents the phenomenological material parameter and is, in general, a constant. In certain cases of diffusion through porous media, the diffusion coefficient can be variable (i.e. non-constant) due to the complex process of solute displacements within microstructure, since these displacements depend on porosity, internal microstructural geometry, size of the transported particles, chemical nature, and physical interactions between the diffusing substance and the microstructural surroundings. In order to provide a simple and general approach of determining the diffusion coefficient for diffusion through porous media, we have introduced mass release curves as the constitutive curves of diffusion. The mass release curve for a selected direction represents cumulative mass (per surface area) passed in that direction through a small reference volume, in terms of time. We have developed a methodology, based on numerical Finite Element (FE) and Molecular Dynamics (MD) methods, to determine simple mass release curves of solutes through complex media from which we calculate the diffusion coefficient. The diffusion models take into account interactions between solute particles and microstructural surfaces, as well as hydrophobicity (partitioning). We illustrate the effectiveness of our approach on several examples of complex composite media, including an imaging-based analysis of diffusion through pancreatic cancer tissue. The presented work offers an insight into the role of mass release curves in describing diffusion through porous media in general, and further in case of complex composite media such as biological tissue.
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Affiliation(s)
- M Kojic
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-117, Houston, TX 77030, United States; Bioengineering Research and Development Center BioIRC Kragujevac, Prvoslava Stojanovica 6, 3400 Kragujevac, Serbia; Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000 Belgrade, Serbia.
| | - M Milosevic
- Bioengineering Research and Development Center BioIRC Kragujevac, Prvoslava Stojanovica 6, 3400 Kragujevac, Serbia
| | - N Kojic
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - E J Koay
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX 77030, United States
| | - J B Fleming
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX 77030, United States
| | - M Ferrari
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-117, Houston, TX 77030, United States
| | - A Ziemys
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-117, Houston, TX 77030, United States
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Bikos D, Mason TG. Propagation and Separation of Charged Colloids by Cylindrical Passivated Gel Electrophoresis. J Phys Chem B 2016; 120:6160-5. [DOI: 10.1021/acs.jpcb.6b02165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitri Bikos
- Department
of Chemistry and Biochemistry, University of California—Los Angeles, Los Angeles, California 90095, United States
| | - Thomas G. Mason
- Department
of Chemistry and Biochemistry, University of California—Los Angeles, Los Angeles, California 90095, United States
- Department
of Physics and Astronomy, University of California—Los Angeles, Los Angeles, California 90095, United States
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14
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Separation of different shape biosynthesized gold nanoparticles via agarose gel electrophoresis. Sep Purif Technol 2015. [DOI: 10.1016/j.seppur.2015.07.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Wang S, Mauldin FW, Klibanov AL, Hossack JA. Ultrasound-based measurement of molecular marker concentration in large blood vessels: a feasibility study. ULTRASOUND IN MEDICINE & BIOLOGY 2015; 41:222-34. [PMID: 25308943 PMCID: PMC4258427 DOI: 10.1016/j.ultrasmedbio.2014.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/14/2014] [Accepted: 07/01/2014] [Indexed: 05/08/2023]
Abstract
Ultrasound molecular imaging has demonstrated efficacy in pre-clinical studies for cancer and cardiovascular inflammation. However, these techniques often require lengthy protocols because of waiting periods or additional control microbubble injections. Moreover, they are not capable of quantifying molecular marker concentration in human tissue environments that exhibit variable attenuation and propagation path lengths. Our group recently investigated a modulated acoustic radiation force-based imaging sequence, which was found to detect targeted adhesion independent of control measurements. In the present study, this sequence was tested against various experimental parameters to determine its feasibility for quantitative measurements of molecular marker concentration. Results indicated that measurements obtained from the sequence (residual-to-saturation ratio, Rresid) were independent of acoustic pressure and attenuation (p > 0.13, n = 10) when acoustic pressures were sufficiently low. The Rresid parameter exhibited a linear relationship with measured molecular marker concentration (R(2) > 0.94). Consequently, feasibility was illustrated in vitro, for quantification of molecular marker concentration in large vessels using a modulated acoustic radiation force-based sequence. Moreover, these measurements were independent of absolute acoustic reflection amplitude and used short imaging protocols (3 min) without control measurements.
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Affiliation(s)
- Shiying Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - F William Mauldin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - Alexander L Klibanov
- Division of Cardiovascular Medicine and Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
| | - John A Hossack
- Department of Biomedical Engineering and Electrical and Computer Engineering, University of Virginia, Charlottesville, Virginia, USA.
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16
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Zhu X, Mason TG. Passivated gel electrophoresis of charged nanospheres by light-scattering video tracking. J Colloid Interface Sci 2014; 428:199-207. [DOI: 10.1016/j.jcis.2014.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/12/2014] [Indexed: 01/20/2023]
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17
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Kojic M, Milosevic M, Kojic N, Kim K, Ferrari M, Ziemys A. A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING 2014; 269:123-138. [PMID: 24578582 PMCID: PMC3933172 DOI: 10.1016/j.cma.2013.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.
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Affiliation(s)
- M. Kojic
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-116, Houston, TX 77030, USA
- Belgrade Metropolitan University, Bioengineering Research and Development Center BioIRC Kragujevac, Prvoslava Stojanovica 6, 3400 Kragujevac, Serbia
| | - M. Milosevic
- Belgrade Metropolitan University, Bioengineering Research and Development Center BioIRC Kragujevac, Prvoslava Stojanovica 6, 3400 Kragujevac, Serbia
| | - N. Kojic
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - K. Kim
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-116, Houston, TX 77030, USA
| | - M. Ferrari
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-116, Houston, TX 77030, USA
| | - A. Ziemys
- Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-116, Houston, TX 77030, USA
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18
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Kunkel J, Asuri P. Function, structure, and stability of enzymes confined in agarose gels. PLoS One 2014; 9:e86785. [PMID: 24466239 PMCID: PMC3897775 DOI: 10.1371/journal.pone.0086785] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/13/2013] [Indexed: 01/21/2023] Open
Abstract
Research over the past few decades has attempted to answer how proteins behave in molecularly confined or crowded environments when compared to dilute buffer solutions. This information is vital to understanding in vivo protein behavior, as the average spacing between macromolecules in the cell cytosol is much smaller than the size of the macromolecules themselves. In our study, we attempt to address this question using three structurally and functionally different model enzymes encapsulated in agarose gels of different porosities. Our studies reveal that under standard buffer conditions, the initial reaction rates of the agarose-encapsulated enzymes are lower than that of the solution phase enzymes. However, the encapsulated enzymes retain a higher percentage of their activity in the presence of denaturants. Moreover, the concentration of agarose used for encapsulation had a significant effect on the enzyme functional stability; enzymes encapsulated in higher percentages of agarose were more stable than the enzymes encapsulated in lower percentages of agarose. Similar results were observed through structural measurements of enzyme denaturation using an 8-anilinonaphthalene-1-sulfonic acid fluorescence assay. Our work demonstrates the utility of hydrogels to study protein behavior in highly confined environments similar to those present in vivo; furthermore, the enhanced stability of gel-encapsulated enzymes may find use in the delivery of therapeutic proteins, as well as the design of novel strategies for biohybrid medical devices.
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Affiliation(s)
- Jeffrey Kunkel
- Department of Bioengineering, Santa Clara University, Santa Clara, California, United States of America
| | - Prashanth Asuri
- Department of Bioengineering, Santa Clara University, Santa Clara, California, United States of America
- * E-mail:
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19
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20
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Chang G, Morigaki K, Tatsu Y, Hikawa T, Goto T, Imaishi H. Vertically Integrated Human P450 and Oxygen Sensing Film for the Assays of P450 Metabolic Activities. Anal Chem 2011; 83:2956-63. [DOI: 10.1021/ac103059k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gang Chang
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, Faculty of Materials Sciences and Engineering, Hubei University, No. 11 Xueyuan Road, Wuchang, Wuhan 430062, China
| | - Kenichi Morigaki
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Yoshiro Tatsu
- National Institute of Advanced Industrial, Science and Technology (AIST), Midorigaoka, Ikeda 563-8577, Japan
| | - Takashi Hikawa
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Tatsushi Goto
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
| | - Hiromasa Imaishi
- Research Center for Environmental Genomics, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501 Japan
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21
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Boral S, Saxena A, Bohidar H. Syneresis in agar hydrogels. Int J Biol Macromol 2010; 46:232-6. [DOI: 10.1016/j.ijbiomac.2009.12.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/15/2009] [Accepted: 12/16/2009] [Indexed: 11/27/2022]
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22
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Basak S, Brogan D, Dietrich H, Ritter R, Dacey RG, Biswas P. Transport characteristics of nanoparticle-based ferrofluids in a gel model of the brain. Int J Nanomedicine 2009; 4:9-26. [PMID: 19421367 PMCID: PMC2720738 DOI: 10.2147/ijn.s4114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A current advance in nanotechnology is the selective targeting of therapeutics by external magnetic field-guided delivery. This is an important area of research in medicine. The use of magnetic forces results in the formation of agglomerated structures in the field region. The transport characteristics of these agglomerated structures are explored. A nonintrusive method based on in situ light-scattering techniques is used to characterize the velocity of such particles in a magnetic field gradient. A transport model for the chain-like agglomerates is developed based on these experimental observations. The transport characteristics of magnetic nanoparticle drug carriers are then explored in gel-based simulated models of the brain. Results of such measurements demonstrate decreased diffusion of magnetic nanoparticles when placed in a high magnetic field gradient.
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Affiliation(s)
- Soubir Basak
- Aerosol and Air Quality Research Laboratory, Department of Energy, Environmental and Chemical, Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Fatin-Rouge N, Wilkinson KJ, Buffle J. Combining small angle neutron scattering (SANS) and fluorescence correlation spectroscopy (FCS) measurements to relate diffusion in agarose gels to structure. J Phys Chem B 2007; 110:20133-42. [PMID: 17034188 DOI: 10.1021/jp060362e] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small angle neutron scattering (SANS) and fluorescence correlation spectroscopy (FCS) measurements were carried out on agarose hydrogels to link their microscopic structure to the diffusivity of solutes at different scales. SANS allowed for the determination of the distribution of void volumes within the gels. They were shown to be compatible with a random network of cylindrical fibers as described by the Ogston model. FCS measured solute diffusivity in spaces similar in size to the void volumes, and thus, the results reflected the gel heterogeneity. Solute diffusivity was predicted by modeling the gel as microscopic geometrical cells. Variations in the diffusivity of solutes of different sizes could be predicted from the structural parameters of the gel using theory, taking into account obstruction by cylindrical cells and solute hydrodynamics. Prediction of the FCS autocorrelation functions for solutes from a cell model demonstrated a lack of sensitivity of this technique for multicomponent analysis.
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Affiliation(s)
- Nicolas Fatin-Rouge
- Analytical and Biophysical Environmental Chemistry, Sciences II, University of Geneva, 30 Quai E. Ansermet, CH-1211 Geneva 4, Switzerland.
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Xiong JY, Liu XY, Li JL, Vallon MW. Architecture of Macromolecular Network of Soft Functional Materials: from Structure to Function. J Phys Chem B 2007; 111:5558-63. [PMID: 17472367 DOI: 10.1021/jp070600l] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An enhanced macromolecular nanofiber network and its implications have been developed by employing the understanding of its formation with an emphasis on its topological aspect. Using agarose aqueous solution as a typical example, the macromolecular nanofiber network of soft functional materials has been clearly visualized for the first time using the developed technique of field emission scanning electronic microscopy coupled with flash-freeze-drying. Both the systematic kinetic study and the image evidence indicates that the nanofiber network in soft functional materials such as agarose turns out to form through a self-expitaxial nucleation-controlled process. This new understanding enables us to engineer ultra functions of soft materials via nanofiber network architecture, which in turn opens up a new direction in nano fabrication.
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Affiliation(s)
- Jun-Ying Xiong
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542, Singapore
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25
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Cole KD, Åkerman B. The Influence Of Agarose Concentration In Gels On The Electrophoretic Trapping Of Circular Dna. SEP SCI TECHNOL 2003. [DOI: 10.1081/ss-120021616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Labropoulos K, Niesz D, Danforth S, Kevrekidis P. Dynamic rheology of agar gels: theory and experiments. Part I. Development of a rheological model. Carbohydr Polym 2002. [DOI: 10.1016/s0144-8617(02)00084-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Gauthier MG, Slater GW. Exactly solvable Ogston model of gel electrophoresis. IX. Generalizing the lattice model to treat high field intensities. J Chem Phys 2002. [DOI: 10.1063/1.1505857] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Valentine MT, Kaplan PD, Thota D, Crocker JC, Gisler T, Prud'homme RK, Beck M, Weitz DA. Investigating the microenvironments of inhomogeneous soft materials with multiple particle tracking. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2001; 64:061506. [PMID: 11736190 DOI: 10.1103/physreve.64.061506] [Citation(s) in RCA: 188] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2001] [Revised: 09/07/2001] [Indexed: 05/23/2023]
Abstract
We develop a multiple particle tracking technique for making precise, localized measurements of the mechanical microenvironments of inhomogeneous materials. Using video microscopy, we simultaneously measure the Brownian dynamics of roughly one hundred fluorescent tracer particles embedded in a complex medium and interpret their motions in terms of local viscoelastic response. To help overcome the inherent statistical limitations due to the finite imaging volume and limited imaging times, we develop statistical techniques and analyze the distribution of particle displacements in order to make meaningful comparisons of individual particles and thus characterize the diversity and properties of the microenvironments. The ability to perform many local measurements simultaneously allows more precise measurements even in systems that evolve in time. We show several examples of inhomogeneous materials to demonstrate the flexibility of the technique and learn new details of the mechanics of the microenvironments that small particles explore. This technique extends other microrheological methods to allow simultaneous measurements of large numbers of probe particles, enabling heterogeneous samples to be studied more effectively.
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Affiliation(s)
- M T Valentine
- Department of Physics and DEAS, Harvard University, Cambridge, Massachusetts 02138, USA
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29
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Abstract
Fractionation via a gel electrophoretic ratchet has previously succeeded for comparatively large (radius R > or = 95 nm) spheres (Serwer, P, Griess, G.A., Anal. Chim. Acta 1998, 372, 299-306). The electrical oscillations are the following electrical field pulses: high field --> low field --> high field, etc. The field is inverted after each pulse; the time-integral of the field can be zero. Response to the ratchet is caused by steric trapping in the high field-direction, but not in the low field-direction. Trapping and, therefore, response to the ratchet decrease as R decreases. The smaller spheres do not respond to the ratchet. In the present study, spheres with R values smaller than 95 nm are made, for the first time, to respond to a similar gel electrophoretic ratchet. To achieve this objective, the heterogeneity of pore size is increased for the gel used. The heterogeneity of pore size is increased by (i) forming the gel with degraded hydroxyethyl agarose, and (ii) gelling at comparatively high temperature. If a particle still does not respond to the ratchet (because the particle is too small), this particle has a net migration in the high field-direction, when the above-described pulsed field is biased in the high field-direction. If a particle does respond to the improved ratchet, the particle has a net migration in the low field-direction. Here, the R of ratchet-responding spheres is reduced to 30-50 nm. These ratchet-responding spheres include both intact bacteriophage particles (R = 30 nm) and latex spheres. The smaller ratchet-responding spheres have an electrophoretic mobility that decreases in magnitude as the electrical field increases in magnitude. A ratchet-based procedure is developed here to achieve continuous preparative gel electrophoresis.
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Affiliation(s)
- G A Griess
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio 78284-7760, USA
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30
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Ramzi M, Rochas C, Guenet JM. On the occurrence of ternary complexes in agarose gels as studied by the contrast variation method. Int J Biol Macromol 2000; 27:163-70. [PMID: 10771067 DOI: 10.1016/s0141-8130(00)00114-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The contrast variation method by isotopic labelling as used in small-angle neutron scattering experiments is applied to the case of agarose systems (sol and gels) in order to cast some light on the occurrence of complexes (crystallosolvates). This approach proves to be helpful for giving further support to the existence of ternary complexes in agarose/water/DMSO gels and in agarose/DMSO sols. The results are discussed in the light of temperature-composition phase diagrams established previously.
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Affiliation(s)
- M Ramzi
- Laboratoire de Dynamique des Fluides Complexes, Université Louis Pasteur-CNRS UMR 7506, 4 rue Blaise Pascal, F-67070, Strasbourg, France
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31
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Pluen A, Netti PA, Jain RK, Berk DA. Diffusion of macromolecules in agarose gels: comparison of linear and globular configurations. Biophys J 1999; 77:542-52. [PMID: 10388779 PMCID: PMC1300351 DOI: 10.1016/s0006-3495(99)76911-0] [Citation(s) in RCA: 386] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The diffusion coefficients (D) of different types of macromolecules (proteins, dextrans, polymer beads, and DNA) were measured by fluorescence recovery after photobleaching (FRAP) both in solution and in 2% agarose gels to compare transport properties of these macromolecules. Diffusion measurements were conducted with concentrations low enough to avoid macromolecular interactions. For gel measurements, diffusion data were fitted according to different theories: polymer chains and spherical macromolecules were analyzed separately. As chain length increases, diffusion coefficients of DNA show a clear shift from a Rouse-like behavior (DG congruent with N0-0.5) to a reptational behavior (DG congruent with N0-2.0). The pore size, a, of a 2% agarose gel cast in a 0.1 M PBS solution was estimated. Diffusion coefficients of the proteins and the polymer beads were analyzed with the Ogston model and the effective medium model permitting the estimation of an agarose gel fiber radius and hydraulic permeability of the gels. Not only did flexible macromolecules exhibit greater mobility in the gel than did comparable-size rigid spherical particles, they also proved to be a more useful probe of available space between fibers.
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Affiliation(s)
- A Pluen
- Edwin L. Steele Laboratory, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
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32
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Serwer P, Griess GA. Advances in the separation of bacteriophages and related particles. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 722:179-90. [PMID: 10068140 DOI: 10.1016/s0378-4347(98)00404-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nondenaturing gel electrophoresis is used to both characterize multimolecular particles and determine the assembly pathways of these particles. Characterization of bacteriophage-related particles has yielded strategies for characterizing multimolecular particles in general. Previous studies have revealed means for using nondenaturing gel electrophoresis to determine both the effective radius and the average electrical surface charge density of any particle. The response of electrophoretic mobility to increasing the magnitude of the electrical field is used to detect rod-shaped particles. To increase the capacity of nondenaturing gel electrophoresis to characterize comparatively large particles, some current research is directed towards either determining the structure of gels used for electrophoresis or inducing steric trapping of particles in dead-end regions within the fibrous network that forms a gel. A trapping-dependent technique of pulsed-field gel electrophoresis is presented with which a DNA-protein complex can be made to electrophoretically migrate in a direction opposite to the direction of migration of protein-free DNA.
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Affiliation(s)
- P Serwer
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio 78284-7760, USA.
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33
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Griess GA, Guiseley KB, Miller MM, Harris RA, Serwer P. The formation of small-pore gels by an electrically charged agarose derivative. J Struct Biol 1998; 123:134-42. [PMID: 9843667 DOI: 10.1006/jsbi.1998.4021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous studies have shown that, during the formation of an underivatized agarose gel, agarose molecules laterally aggregate to form thicker fibers called suprafibers; the suprafibers branch to form a gelled network. In the present study, electron microscopy of thin sections is used to investigate both the thickness and the spacing of the fibers of gels formed by agarose chemically derivatized with carboxymethyl (negatively charged) groups. For carboxymethyl agarose, electron microscopy reveals that gels cast in water consist of both fibers narrower and pores smaller than those observed for water-cast underivatized agarose gels at the same concentration. This result is confirmed by using the electrophoretic sieving of spheres to determine the radius (PE) of the effective pore of the gel. At a given concentration of gel less than 1%, the PE for a water-cast carboxymethyl agarose gel is 0.25-0.30x the PE for a water-cast underivatized agarose gel. The value of PE predicts the extent of the electrophoretic sieving that is observed when double-stranded DNA is subjected to electrophoresis through a water-cast carboxymethyl agarose gel; DNA bands formed in a water-cast carboxymethyl agarose gel are comparable in quality to DNA bands formed in a water-cast underivatized agarose gel of equal PE. The following observation supports the hypothesis that electrical charge-charge repulsion among carboxymethyl agarose molecules inhibits the formation of suprafibers in water-cast carboxymethyl agarose gels: Increased content of suprafibers in carboxymethyl agarose gels is observed when the ionic strength is raised by the presence of NaCl, MgCl2, or any of several buffers during gelation of carboxymethyl agarose.
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Affiliation(s)
- G A Griess
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78284-7760, USA
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34
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Serwer P, Griess GA. Adaptation of pulsed-field gel electrophoresis for the improved fractionation of spheres. Anal Chim Acta 1998. [DOI: 10.1016/s0003-2670(98)00341-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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35
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Ramzi M, Rochas C, Guenet JM. Structure−Properties Relation for Agarose Thermoreversible Gels in Binary Solvents. Macromolecules 1998. [DOI: 10.1021/ma9801220] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohamed Ramzi
- Laboratoire de Dynamique des Fluides Complexes,§ Université Louis Pasteur, CNRS UMR 7506, 4, rue Blaise Pascal, 67070 Strasbourg Cedex, France, and Laboratoire de Spectromètrie Physique, Université J. Fourier, CNRS UMR 5588, BP87, 38402 Saint Martin D'heres Cedex, France
| | - Cyrille Rochas
- Laboratoire de Dynamique des Fluides Complexes,§ Université Louis Pasteur, CNRS UMR 7506, 4, rue Blaise Pascal, 67070 Strasbourg Cedex, France, and Laboratoire de Spectromètrie Physique, Université J. Fourier, CNRS UMR 5588, BP87, 38402 Saint Martin D'heres Cedex, France
| | - Jean-Michel Guenet
- Laboratoire de Dynamique des Fluides Complexes,§ Université Louis Pasteur, CNRS UMR 7506, 4, rue Blaise Pascal, 67070 Strasbourg Cedex, France, and Laboratoire de Spectromètrie Physique, Université J. Fourier, CNRS UMR 5588, BP87, 38402 Saint Martin D'heres Cedex, France
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36
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Borkenhagen M, Clémence JF, Sigrist H, Aebischer P. Three-dimensional extracellular matrix engineering in the nervous system. JOURNAL OF BIOMEDICAL MATERIALS RESEARCH 1998; 40:392-400. [PMID: 9570070 DOI: 10.1002/(sici)1097-4636(19980603)40:3<392::aid-jbm8>3.0.co;2-c] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Growing neurites are guided through their environment during development and regeneration via different cellular and extracellular matrix (ECM) molecular cues. To mimic cell-matrix interactions, a three-dimensional (3D) hydrogel-based ECM equivalent containing a covalently immobilized laminin oligopeptide sequence was designed to facilitate nerve regeneration. This study illustrates that the oligopeptide domain CDPGYIGSR covalently linked to an agarose gel as a bioartificial 3D substrate successfully supports neurite outgrowth from dorsal root ganglia (DRG) in vitro. The specificity of the neurite promoting activity was illustrated through the inhibition of neurite outgrowth from DRG in a CDPGYIGSR-derivatized gel in the presence of solubilized CDPGYIGSR peptide. Gels derivatized with CDPGYIGSK and CDPGRGSYI peptides stimulated a smaller increase of neurite outgrowth. In vivo experiments revealed the capability of a CDPGYIGSR-derivatized gel to enhance nerve regeneration in a transected rat dorsal root model compared to an underivatized gel, a CDPGRGSYI gel, and saline-filled nerve guidance channels. These data suggest the feasibility of a 3D hydrogel-based ECM equivalent capable of enhancing neurite outgrowth in vitro and in vivo.
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Affiliation(s)
- M Borkenhagen
- Division of Surgical Research, Centre Hospitalier Universitaire Vaudois, Lausanne University Medical School, Switzerland
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37
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Tercier ML, Buffle J. Antifouling Membrane-Covered Voltammetric Microsensor for in Situ Measurements in Natural Waters. Anal Chem 1996. [DOI: 10.1021/ac960265p] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M.-L. Tercier
- Department of Inorganic, Analytical and Applied Chemistry, Sciences II, University of Geneva, 30 Quai E.-Ansermet, 1211 Geneva 4, Switzerland
| | - J. Buffle
- Department of Inorganic, Analytical and Applied Chemistry, Sciences II, University of Geneva, 30 Quai E.-Ansermet, 1211 Geneva 4, Switzerland
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38
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Small-angle scattering from complex, hierarchically structured polymer and biopolymer networks. J Mol Struct 1996. [DOI: 10.1016/s0022-2860(96)09293-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Serwer P, Harris RA, Miller MM, Griess GA. Use of excluded volume to increase the heterogeneity of pore size in agarose gels. Electrophoresis 1996; 17:971-6. [PMID: 8832161 DOI: 10.1002/elps.1150170603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
When testing theoretical models that quantitatively describe the sieving of macromolecules during gel electrophoresis, investigators have been limited by absence of control of the heterogeneity of the size of pores in the gel. In a recent study performed by electron microscopy of thin sections (G. A. Griess et al., J. Struct. Biol. 1993, III, 39-47), pore size heterogeneity has been increased for agarose gels by a combination of both derivatization and molecular weight reduction of the polysaccharide chains of agarose. In the present study, pore size heterogeneity is increased by a mechanism that appears to have an origin different from the origin of this previously observed increase in heterogeneity: Pore size heterogeneity is increased by addition of a polyethylene glycol (PEG) of high molecular weight (18,500) to molten agarose before gelation. In contrast, the use of a lower molecular weight PEG (either 4,000 or 7,500) causes the formation of micron-sized precipitates within a gelled network of agarose fibers. Thus far, the PEG-induced heterogeneity of pore size occurs primarily in 100-1,000 microns scale zones separated from each other by interzone regions of decreased agarose fiber density. More uniform gels are needed for the study of sieving.
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Affiliation(s)
- P Serwer
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA.
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40
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41
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Serwer P, Estrada A, Harris RA. Video light microscopy of 670-kb DNA in a hanging drop: shape of the envelope of DNA. Biophys J 1995; 69:2649-60. [PMID: 8599671 PMCID: PMC1236502 DOI: 10.1016/s0006-3495(95)80135-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Although its conformation has not been observed directly, double-stranded DNA in solution is usually assumed to be randomly coiled at the level of the DNA double helix. By video light microscopy of ethidium-stained DNA at equilibrium in a nonturbulent hanging drop, in the present study, the 670 kb linear bacteriophage G DNA is found to form a flexible filament that has on average 17 double helical segments across its width. This flexible filament 1) has both asymmetry and dimensions expected of a random coil and 2) has ends that move according to the statistics expected of a random walk. After unraveling the flexible filament-associated DNA double helix near the surface of a hanging drop, recompaction occurs without perceptible rotation of the DNA. Both conformational change and intermolecular tangling of the DNA are observed when G DNA undergoes nondiffusive motion in a hanging drop. The characteristics of the G DNA flexible filament are explained by the assumption that the flexible filament is a random coil of double helical segments that are unperturbed by motion of the suspending medium.
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Affiliation(s)
- P Serwer
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA.
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42
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Bellamkonda R, Ranieri JP, Bouche N, Aebischer P. Hydrogel-based three-dimensional matrix for neural cells. JOURNAL OF BIOMEDICAL MATERIALS RESEARCH 1995; 29:663-71. [PMID: 7622552 DOI: 10.1002/jbm.820290514] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The ability to organize cells in three dimensions (3D) is an important component of tissue engineering. This study sought to develop an extracellular matrix (ECM) equivalent with a physicochemical structure capable of supporting neurite extension from primary neural cells in 3D. Rat embryonic day 14 striatal cells and chick embryonic day 9 dorsal root ganglia extended neurites in 3D in agarose hydrogels in a gel concentration-dependent manner. Primary neural cells did not extend neurites above a threshold agarose gel concentration of 1.25% wt/vol. Gel characterization by hydraulic permeability studies revealed that the average pore radius of a 1.25% agarose gel was 150 mm. Hydraulic permeability studies for calculating average gel pore radius and gel morphology studies by environmental and scanning electron micrography showed that the average agarose gel por size decreased exponentially as the gel concentration increased. It is hypothesized that the average gel porosity plays an important role in determining the ability of agarose gels to support neurite extension. Lamination of alternating nonpermissive, permissive, and nonpermissive gel layers facilitated the creation of 3D neural tracts in vitro. This ability of agarose hydrogels to organize, support, and direct neurite extension from neural cells may be useful for applications such as 3D neural cell culture and nerve regeneration. Agarose hydrogel substrates also offer the possibility of manipulating cells in 3D, and may be used as 3D templates for tissue engineering efforts in vitro and in vivo.
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Affiliation(s)
- R Bellamkonda
- Division of Surgical Research, Centre Hospitalier Universitaire Vaudois, Lausanne University Medical School, Switzerland
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Serwer P, Khan SA, Griess GA. Non-denaturing gel electrophoresis of biological nanoparticles: viruses. J Chromatogr A 1995; 698:251-61. [PMID: 7773365 DOI: 10.1016/0021-9673(94)01259-h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although gel electrophoresis is usually used for the fractionation of monomolecular particles, it is also applicable to the fractionation of the multimolecular complexes produced during both cellular metabolism and assembly of viruses in virus-infected cells. Gel electrophoretic procedures have been developed for determining both the size of a spherical particle and some aspects of the shape of a non-spherical particle. Capsids bound to DNA outside of the capsid can also be both fractionated and characterized. The procedures developed will be used for screening viral mutants; they also can potentially be used for diagnostic virology. Sensitivity of detection, the major current limitation, is being improved by use of both improved stains and scanning fluorimetry. The gels used for fractionation sometimes approximate random straight fiber gels, but become increasingly biphasic as the gel concentration is decreased.
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Affiliation(s)
- P Serwer
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760, USA
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Krueger S, Andrews AP, Nossal R. Small angle neutron scattering studies of structural characteristics of agarose gels. Biophys Chem 1994; 53:85-94. [PMID: 7841333 DOI: 10.1016/0301-4622(94)00079-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The 30 m small angle neutron scattering facility at the National Institutes of Standards and Technology has been used to examine neutron scattering from agarose gels formed in D2O. Differential scattering cross sections have been acquired over a continuous range of Q between 0.005 and 0.3 A-1. Subtle changes in gel structure are observed when pre-gelation agarose concentration is varied. Similarly, except when the gelling solution is rapidly cooled to a low temperature, the rate at which the gels are formed does not seem to have much effect. Clearer evidence of structural rearrangement is observed when the solvent quality is changed by the addition of dimethyl sulfoxide, or when the temperature of the gel is elevated above 70 degrees C. These data are consistent with a description of a randomly structured polymer network containing discrete self-similar, hydrogen-bonded, junctions normally of minimal thickness approximately 35-40 A.
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Affiliation(s)
- S Krueger
- Reactor Radiation Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
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