Rheological Study of the Gelation Process of Agarose-Based Solutions

The gelation of agarose is investigated by rheological methods and electron microscopy, as well as the thickening properties of xanthan. The gelling and thickening agents have been investigated in pure water to compare the results with theoretical models. The gelation of agarose was shown to follow two steps upon cooling, which could be addressed to the formation of helices and their aggregation. In addition to the rheology, transmission electron micrographs of freeze-dried samples have been taken to underline the date by corresponding structures at different stages of the gelling process. The xanthan molecules, which have been approximated by rigid highly charged rodlike molecules, undergo a jamming transition at a critical concentration. This concentration shows a strong dependence on the length of the molecules, which supports the high thickening effect of xanthan. When both, agarose and xanthan are mixed, the gel structure becomes very different. The gelling process is now determined by one step only. It is proposed that the jamming xanthan molecules prevent the formation of the aggregates of the agarose gel. The gels themselves appear then less elastic, and should yield a better mouth feeling.     

Electric birefringence of dilute agarose solutions

The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting parallel to the electric field lines. The decay of the birefringence was rapid, consistent with the orientation of individual agarose helices. The amplitude of the birefringence, but not the birefringence decay times, increased as the agarose solution aged, suggesting that the helices formed slowly from the sol state. Increasing the amplitude or duration of the pulsed electric field caused additional negative, and then positive, birefringence signals to appear, characterized by much slower rise and decay times, consistent with the formation of aggregates. The slowest decay times ranged from 7.5-9.0 s, suggesting that the aggregates were several microns in size. When agarose was dissolved in dilute Tris buffer instead of deionized water, the fast positive birefringence signal was not observed, suggesting that individual helices were not present in solutions containing dilute buffer.     

Electric Birefringence of Dilute Agarose Solutions

Abstract

The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting parallel to the electric field lines. The decay of the birefringence was rapid, consistent with the orientation of individual agarose helices. The amplitude of the birefringence, but not the birefringence decay times, increased as the agarose solution aged, suggesting that the helices formed slowly from the sol state. Increasing the amplitude or duration of the pulsed electric field caused additional negative, and then positive, birefringence signals to appear, characterized by much slower rise and decay times, consistent with the formation of aggregates. The slowest decay times ranged from 7.5–9.0 s, suggesting that the aggregates were several microns in size. When agarose was dissolved in dilute Tris buffer instead of deionized water, the fast positive birefringence signal was not observed, suggesting that individual helices were not present in solutions containing dilute buffer.     

Studies on factor VIII-related protein. II. Estimation of molecular size differences between factor VIII oligomers.

Human factor VIII-related protein was isolated from cryoprecipitate by agarose (Sepharose CL-2B) gel filtration. Electrophoresis on SDS-2% polyacrylamide-0.5% agarose gels revealed size heterogeneity of factor VIII-related protein which was similar to that shown by SDS-1% agarose gel electrophoresis and electron microscopy. The apparent molecular weights were compared with those of crosslinked IgM oligomers and corresponded to values of up to 20 . 10(6) for factor VIII eluting close to the void volume of our gel filtration column. Measurement of mobility intervals on electrophoretic gels suggested a constant size difference between adjacent bands. Smaller aggregates were found in later eluates from Sepharose columns as well as following partial reduction of factor VIII with cysteine. In order to compare the size difference between small and large aggregates of factor VIII-related protein we calibrated the SDS-2% polyacrylamide-0.5% agarose gels with factor VIII which had been crosslinked with dimethyl suberimidate and subsequently disulfied-reduced with 2-metcaptoethanol. By combination of calibration ranges, constant intervals were measured for large and smaller factor VIII aggregates. The interval between any neighboring protein bands, which were immunologically identified as factor VIII-related protein, was equal to the dimer of the basic factor VIII subunit chain. We conclude that factor VIII aggregates correspond to multimers of a dimeric molecule, i.e. pairs of the basic subunit chain.     

Structure of amphotericin B aggregates based on calculations of optical spectra

The Degenerate ground state approximation was used to calculate the optical absorption and CD spectra for helical polymer models of amphotericin B aggregates in aqueous solution. Comparisons with experimental spectra indicate that a two-molecule/unit cell helical polymer model is a possible structure for aggregates of amphotericin B.     

Culture phases,cytotoxicity and protein expressions of agarose hydrogel induced Sp2/0, A549, MCF-7 cell line 3D cultures

Advancements in cell cultures are occurring at a rapid pace, an important direction is culturing cells in 3D conditions. We demonstrate the usefulness of agarose hydrogels in obtaining 3 dimensional aggregates of three cell lines, A549, MCF-7 and Sp2/0. The differences in culture phases, susceptibility to cisplatin-induced cytotoxicity are studied. Also, the 3D aggregates of the three cell lines were reverted into 2D cultures and the protein profile differences among the 2D, 3D and revert cultures were studied. The analysis of protein profile differences using UniProt data base further augment the usefulness of agarose hydrogels for obtaining 3D cell cultures.     

Analysis of cell viability and differential activity of mouse hepatocytes under 3D and 2D culture in agarose gel

Three-dimensional (3D) and two-dimensional (2D) cultures of hepatocytes in various concentrations (0.3–0.7%) of agarose gel revealed that the hepatocytes under 3D cultures in 0.3% agarose gel possess long-term (>3 weeks) viability, significant self-assembly to form tissue like aggregates, low lactate dehydrogenase release and high albumin synthesis. These were in contrast to 2D culture of hepatocytes. Our results suggest that the 3D culture of hepatocytes in agarose gel favors aggregate formation of functionally active cells and would be useful for liver transplantation as well as to analyze hepatocytes biology.     

Ultrastructural changes during reticulopod withdrawal in the foraminiferan protozoanAllogromia sp., strain NF

Summary Allogromia sp. is a benthic foraminiferan protozoan which extends and withdraws a dynamic network of branching and anastomosing pseudopodia,i.e., reticulopods. Each reticulopod contains an elongate cytoskeleton composed primarily of microtubules (MT). When withdrawal was induced with artificial seawater supplemented with MgCl₂, we found a time-dependent decrease in the number of reticulopodial MTs and a concomitant increase in 5-nm-diameter helical filaments. During the initial stages of withdrawal these helical filaments associated laterally to form loose aggregates. Later they formed dense paracrystalline aggregates, which appeared similar to those seen in the cell bodies of untreatedAllogromia juveniles prior to network extension. Similar results were obtained when withdrawal was induced by using seawater supplemented with other salts (NaCl, KCl). Treatment with an isotonic seawater substitute with an altered Na⁺:K⁺ ratio induced a momentary withdrawal, after which the organism recovered and reextended a network. During the withdrawal phase of this response, MTs became less abundant and aggregates of helical filaments more conspicuous. Together with earlier observations these findings suggest that helical filaments and paracrystalline material are an alternative or intermediate assembly form of MT proteins.     

Helical growth and macrofiber formation of Bacillus subtilis 168 autolytic enzyme deficient mutants

Two poorly lytic, chain-forming mutants of Bacillus subtilis 168, strains FJ3 and FJ6, each 90-95% deficient in the production of N-acetylmuramoyl-l-alanine amidase and endo-beta-N-acethyglucosaminidase, grew helically under a variety of cultural condtions. The structures formed ranged in complexity from double-standed helices to complex aggregates of entangled and interwoven single chains and multistransded helical fibres. Factors favoring this type of helical growth were investigated. Occasional tight single-standed corkscrew like forms were detected in the mutant cultrues. Two other poorly lytic mutant strains of Bacillus were also found to have helical growth capacity. These results have been interpreted as support for the recently proposed (1976) tension restricted helical growth model of Mendelson.     

Reproducible preparation of spheroids of pancreatic hormone positive cells from human iPS cells: An in vitro study

BackgroundTransplantation of islets of Langerhans is regarded as a promising therapy for type 1 diabetes. A large number of β-cells are required for the treatment of human type 1 diabetes. Pluripotent stem cells, such as embryonic stem cells and induced pluripotent stem cells, have been considered as new sources for cell replacement therapy.MethodsCell aggregates were prepared from human iPS cells using agarose microwell plates and differentiated into pancreatic endocrine cells by changing the culture media with different additives.ResultsAfter 20 days of culture, approximately 30% of cells in aggregates were positive for C-peptide. After another 14 days in culture, the cells gained an ability to alter C-peptide release in response to changes in the glucose concentration.ConclusionsUniform aggregates of human iPSCs were easily prepared on agarose microwell plates and efficiently differentiated into the pancreatic endocrine lineage. Thus, aggregate culture is a suitable method for preparing islet-like aggregates from human iPSCs.General significanceOur results indicate that the microwell plate is suitable for scaling up the preparation of pancreatic endocrine cells from human iPS cells in a robotic system.     

Nonpolar contributions to conformational specificity in assemblies of designed short helical peptides

A series of designed short helical peptides was used to study the effect of nonpolar interactions on conformational specificity. The consensus sequence was designed to obtain short helices (17 residues) and to minimize the presence of interhelical polar interactions. Furthermore, the sequence contained a heptad repeat (abcdefg), where positions a and d were occupied by hydrophobic residues Leu, Ile, or Val, and positions e and g were occupied by Ala. The peptides were named according to the identities of the residues in the adeg positions, respectively. The peptides llaa, liaa, ilaa, iiaa, ivaa, viaa, lvaa, vlaa, and vvaa were synthesized, and their characterization revealed marked differences in specificity. An experimental methodology was developed to study the nine peptides and their pairwise mixtures. These peptides and their mixtures formed a vast array of structural states, which may be classified as follows: helical tetramers and pentamers, soluble and insoluble helical aggregates, insoluble unstructured aggregates, and soluble unstructured monomers. The peptide liaa formed stable helical pentamers, and iiaa and vlaa formed stable helical tetramers. Disulfide cross-linking experiments indicated the presence of an antiparallel helix alignment in the helical pentamers and tetramers. Rates of amide proton exchange of the tetrameric form of vlaa were 10-fold slower than the calculated exchange rate for unfolded vlaa. In other work, the control of specificity has been attributed to polar interactions, especially buried polar interactions; this work demonstrated that subtle changes in the configuration of nonpolar interactions resulted in a large variation in the extent of conformational specificity of assemblies of designed short helical peptides. Thus, nonpolar interactions can have a significant effect on the conformational specificity of oligomeric short helices.     

Molecular modeling of agarose helices,leading to the prediction of crystalline allomorphs

The neutral polysaccharide agarose is a linear polymer whose idealized structure is made up of alternating residues of a 1 → 3 linked β-D -galactopyranose and 1 → 4 linked 3,6-anhydro-α-L -galactopyranose. Apparently conflicting reports have been published about the nature of the helical structure of agarose in the condense phase. Recent developments in the field of molecular modeling of polysaccharides offer some new opportunities to reexamine the structural basis underlying the formation and stabilization of ordered structures. The conformational spaces available for each disaccharide segments were investigated via molecular dynamics simulations. Then, making use of the available experimental information of the helical symmetry, axial advances, the optimal glycosidic torsion angles were assessed. The search for the lowest energy helix included both left- and right-handed, and both single- and double-helical, models. A further analysis considered all possible arrangements occurring between an agarose chain, in a given conformation, and another chain. Both parallel and antiparallel settings of the chains were evaluated. Unit-cell dimensions as well as lattice symmetry were derived from which intensities of x-ray reflections were calculated. The calculations lead to the prediction of three single-helical structure and one parallel double-helical model; they are all left-handed and the chains pack in an antiparallel way. The predicted crystalline structures compare favorably with available experimental data. Water can occupy 30–45% of the space in the crystal structures, which is in accordance with the gel-forming behavior. The models obtained may reflect the relative arrangements of agarose helices in some of the main allomorphs. They provide some insights into the common structural features and into the differences that accompany the conformational transitions between these allomorphs. © 1998 John Wiley & Sons, Inc. Biopoly 46: 11–29, 1998     

Hexafluoroisopropanol induces self‐assembly of β‐amyloid peptides into highly ordered nanostructures

Deposition of insoluble fibrillar aggregates of β‐amyloid (Aβ) peptides in the brain is a hallmark of Alzheimer's disease. Apart from forming fibrils, these peptides also exist as soluble aggregates. Fibrillar and a variety of nonfibrillar aggregates of Aβ have also been obtained in vitro. Hexafluoroisopropanol (HFIP) has been widely used to dissolve Aβ and other amyloidogenic peptides. In this study, we show that the dissolution of Aβ40, 42, and 43 in HFIP followed by drying results in highly ordered aggregates. Although α‐helical conformation is observed, it is not stable for prolonged periods. Drying after prolonged incubation of Aβ40, 42, and 43 peptides in HFIP leads to structural transition from α‐helical to β‐conformation. The peptides form short fibrous aggregates that further assemble giving rise to highly ordered ring‐like structures. Aβ16–22, a highly amyloidogenic peptide stretch from Aβ, also formed very similar rings when dissolved in HFIP and dried. HFIP could not induce α‐helical conformation in Aβ16–22, and rings were obtained from freshly dissolved peptide. The rings formed by Aβ40, 42, 43, and Aβ16–22 are composed of the peptides in β‐conformation and cause enhancement in thioflavin T fluorescence, suggesting that the molecular architecture of these structures is amyloid‐like. Our results clearly indicate that dissolution of Aβ40, 42 and 43 and the amyloidogenic fragment Aβ16–22 in HFIP results in the formation of annular amyloid‐like structures. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Polymer conformation: 1. Calculation and mapping of helical constraint surfaces for polymers with special application to polysaccharides

A method is presented for determining the backbone conformations of a polymer chain which conform to a given helical type. The method is illustrated by application to the polydisaccharide agarose, for which case, a convenient graphical representation has been devised.     

Early assembly pathways of type I collagen.

A method was developed for computing the free energy (delta Fi) of aggregates of type I collagen. The method was based on a treatment of Matheson and Flory describing phase equilibria of rigid rod polymers. It included a polymer-solvent interaction term that depended on near neighbor transfer energies. Extrahelical portions of the molecule were assigned local interaction energies differing from that assigned to the helix. Free energies of reaction for successive steps along assembly pathways (delta Fi-i+1) were computed. When allowance was made for specific pairing between extrahelical and helical domains, the so-called D-staggered (D = 670 A) alignment of molecules was preferred, as opposed to a nonstaggered, or nematic, alignment. Based on delta Fi-i+1 alone, it appeared that 1D-staggered oligomers arise first in assembly, followed later by addition of molecules in 4D alignment. Neither 4D dimers nor 4D-8D trimers were predicted to be major intermediates in assembly. This result is contrary to previous hypotheses. When energies of activation were included in the analysis, the prediction was less certain, and specific circumstances were identified in which 4D dimers and 4D-8D trimers were the earliest aggregated species in assembly.     

Microencapsulation of dopamine neurons derived from human induced pluripotent stem cells

Background

Dopamine neurons derived from induced pluripotent stem cells have been widely studied for the treatment of Parkinson's disease. However, various difficulties remain to be overcome, such as tumor formation, fragility of dopamine neurons, difficulty in handling large numbers of dopamine neurons, and immune reactions. In this study, human induced pluripotent stem cell-derived precursors of dopamine neurons were encapsulated in agarose microbeads. Dopamine neurons in microbeads could be handled without specific protocols, because the microbeads protected the fragile dopamine neurons from mechanical stress.

Methods

hiPS cells were seeded on a Matrigel-coated dish and cultured to induce differentiation into a dopamine neuronal linage. On day 18 of culture, cells were collected from the culture dishes and seeded into U-bottom 96-well plates to induce cell aggregate formation. After 5 days, cell aggregates were collected from the plates and microencapsulated in agarose microbeads. The microencapsulated aggregates were cultured for an additional 45 days to induce maturation of dopamine neurons.

Results

Approximately 60% of all cells differentiated into tyrosine hydroxylase-positive neurons in agarose microbeads. The cells released dopamine for more than 40 days. In addition, microbeads containing cells could be cryopreserved.

Conclusion

hiPS cells were successfully differentiated into dopamine neurons in agarose microbeads.

General significance

Agarose microencapsulation provides a good supporting environment for the preparation and storage of dopamine neurons.     

The structural relationship between the stacked disk and helical polymers of tobacco mosaic virus protein

An X-ray diffraction pattern from a well-oriented sol of the stacked disk rod aggregate of the protein of tobacco mosaic virus is presented. The helical parameters deduced from this are consistent with the stacked disk rod being a perturbed form of a stacked ring variant of the single helical polymer. Comparison of the intensity distributions in the X-ray diagrams of the two aggregates confirms their structural similarity.     

A modified method for the preparation of agarose.

A simple procedure for the preparation of agarose suitable for electrophoresis is developed in which anionic polysaccharides are removed by extracting the agar gel-granules with phosphate buffer (0.03 M, pH 6.8) containing urea (4 M), followed by electrophoresis in the same buffer system. Further, alkali treatment in the presence of sodium borohydride, eliminates electroendosmosis, giving essentially a neutral agarose, as judged by the electrophoretic behaviour of basic substances like crystal violet and cytochrome C. The purified agarose with yields 60-65%, has a sulphur content less than 0.1%, and forms rigid, transparent gels.     

Dependence of the electrophoretic mobility of DNA in gels on field intermittency

The electrophoretic mobility of double helical DNA in agarose and polyacrylamide gels increases as a function of time after the electric field is applied to the gel and decreases after the field is terminated. The changes are large for long (more than 10 kb) molecules. The effects of other variables are indicated.