Segregative phase separation in agarose/whey protein systems induced by sequence-dependent trapping and change in pH

The structural properties and morphology of mixed gels made of aqueous preparations of agarose and whey protein were modified by changing thermal treatment and pH. The conformationally dissimilar polymers phase separated and this process was followed by small-deformation dynamic oscillation in shear, differential scanning calorimetry and environmental scanning electron microscopy. Experimental protocol encourages formation of a range of two-phase systems from continuous agarose matrices perforated by liquid-like whey protein inclusions to phase inverted preparations where a soft protein matrix suspends hard agarose-filler particles. These distinct morphologies have widely different mechanical moduli, which were followed by adapting a theoretical analysis (isostress-isostrain and Lewis-Nielsen blending laws) from the literature in synthetic block polymers and polyblends. Based on this framework of thought, reasonable predictions of the elastic moduli in the composite gels were made that led to patterns of solvent partition between the two polymeric networks. It was shown that proteins, in mixture with polysaccharide, exhibit favorable relative affinity (P-factor) for water molecules at a pH above their isoelectric point. This is an unexpected outcome that adds to the central finding of a single P value for the distribution of solvent between the continuous matrix and discontinuous inclusions of binary gels. It was thus proposed that phase continuity and solvent distribution in agarose/whey protein systems are under kinetic control that can be heavily governed by pH changes in the aqueous environment.     

Gelation and Its Related Changes in Amylose Solution

The phase change for an amylose solution in the binary solvent system of dimethylsulfoxide (DMSO) with water was investigated under various conditions from sol to gel. The phase change was determined with measurements of the fluorescent depolarization and other methods by varying the solvent constitution at 25°C, and then varying the temperature at 10% of DMSO concentration.

The phase diagrams obtained with both variables were substantially similar and were also similar to those for an aqueous agarose solution. This similarity in phase diagram suggests a similar gel formation mechanism of amylose to agarose.

It was found that the phase separation point for the amylose solution agreed with the gel formation point and also with the starting point of retrogradation.     

Bridging the divide between the high- and low-solid analyses in the gelatin/kappa-carrageenan mixture

Over the past few years, a considerable amount of work has been done in several laboratories on the measurement of structural properties of low-solid biopolymer mixtures or high-solid materials of a single biopolymer in the presence of co-solute. The main objective of this work has been to establish a correlation between the two types of systems and extend it to a binary mixture in a high-solid environment. In doing so, it employed well-characterized kappa-carrageenan and gelatin samples in an aqueous preparation or in the presence of glucose syrup and sucrose. The phase behavior of the composite gel was ascertained using small-deformation dynamic oscillation, differential scanning calorimetry, and light microscopy. Experimental observations were built into polymer blending laws that argued for an explicit phase topology and distribution of solvent between the two networks. A working hypothesis was formulated and applied to high-solid mixtures thus identifying phase or state transitions in the time/temperature function. This led to the development of a mechanical glass transition temperature as the threshold of two distinct molecular processes governing the "rubber-to-glass" transformation. A stage was reached at which the predictions of the hypothesis were found to be in good agreement with the experimental development of viscoelasticity in the high-solid kappa-carrageenan/gelatin mixture ranging from the rubbery plateau and the transition region to the glassy state.     

Challenges in Detecting Magnesium Stearate Distribution in Tablets

Magnesium stearate (MS) is the most commonly used lubricant in pharmaceutical industry. During blending, MS particles form a thin layer on the surfaces of the excipient and drug particles prohibiting the bonding from forming between the particles. This hydrophobic layer decreases the tensile strength of tablets and prevents water from penetrating into the tablet restraining the disintegration and dissolution of the tablets. Although overlubrication of the powder mass during MS blending is a well-known problem, the lubricant distribution in tablets has traditionally been challenging to measure. There is currently no adequate analytical method to investigate this phenomenon. In this study, the distribution of MS in microcrystalline cellulose (MCC) tablets was investigated using three different blending scales. The crushing strength of the tablets was used as a secondary response, as its decrease is known to result from the overlubrication. In addition, coating of the MCC particles by MS in intact tablets was detected using Raman microscopic mapping. MS blending was more efficient in larger scales. Raman imaging was successfully applied to characterize MS distribution in MCC tablets despite low concentration of MS. The Raman method can provide highly valuable visual information about the proceeding of the MS blending process. However, the measuring set-up has to be carefully planned to establish reliable and reproducible results.     

A Versatile Composite Gel Column for the Electrophoretic Separation of Ribonucleic Acid Molecules

A composite gel column system containing 2.4% acry I amide, 0.14% N,n¹-methylene bisacrylamide, 0.6% agarose and 15% glycerol as a component has been developed for the electrophoretlc separation of all kinds of ribonucleic acid molecules extracted from eucaryotlc cells. The separations achieved In this composite gel are due to the sieving of RNA molecules of various sizes with similar charge. As a result of the addition of glycerol the polymerization time of the composite gel is extended and the gel has increased mechanical stability. These stable gels can be sliced at room temperature for such procedures as measuring radioactivity or extraction. Their suitability for staining and absorbance scanning is not altered.     

Enzymatic liquefaction of agarose above the sol–gel transition temperature using a thermostable endo-type β-agarase,Aga16B

The main carbohydrate of red macroalgae is agarose, a heterogeneous polysaccharide composed of d-galactose and 3,6-anhydro-l-galactose. When saccharifying agarose by enzymes, the unique physical properties of agarose, namely the sol–gel transition and the near-insolubility of agarose in water, limit the accessibility of agarose to the enzymes. Due to the lower accessibility of agarose to enzymes in the gel state than to the sol state, it is important to prevent the sol–gel transition by performing the enzymatic liquefaction of agarose at a temperature higher than the sol–gel transition temperature of agarose. In this study, a thermostable endo-type β-agarase, Aga16B, originating from Saccharophagus degradans 2-40^T, was characterized and introduced in the liquefaction process. Aga16B was thermostable up to 50 °C and depolymerized agarose mainly into neoagarooligosaccharides with degrees of polymerization 4 and 6. Aga16B was applied to enzymatic liquefaction of agarose at 45 °C, which was above the sol–gel transition temperature of 1 % (w/v) agarose (∼35 °C) when cooling agarose. This is the first systematic demonstration of enzymatic liquefaction of agarose, enabled by determining the sol–gel temperature of agarose under specific conditions and by characterizing the thermostability of an endo-type β-agarase.

     

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb¹. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits². During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel''s molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight³. The leading model for DNA movement through an agarose gel is "biased reptation", whereby the leading edge moves forward and pulls the rest of the molecule along⁴. The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation⁵; 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: 1. Understand the mechanism by which DNA fragments are separated within a gel matrix 2. Understand how conformation of the DNA molecule will determine its mobility through a gel matrix 3. Identify an agarose solution of appropriate concentration for their needs 4. Prepare an agarose gel for electrophoresis of DNA samples 5. Set up the gel electrophoresis apparatus and power supply 6. Select an appropriate voltage for the separation of DNA fragments 7. Understand the mechanism by which ethidium bromide allows for the visualization of DNA bands 8. Determine the sizes of separated DNA fragments       

Improved Isolation of SlaA and SlaB S-layer proteins in Sulfolobus acidocaldarius

The Sulfolobus acidocaldarius S-layer is composed of two main proteins: SlaA, which forms the ordered structure of the S-layer matrix, and SlaB, which supports and anchors the S-layer into the tetraether lipid membrane. While SlaA has previously been purified by exploiting its thermotolerance and high resistance to detergents, SlaB has resisted isolation, particularly from the cell membrane. Removal of proteins other than those of the S-layer is especially difficult if large batch-scale culture volumes are unavailable. Here, we describe a benchtop-scale protocol for the purification of SlaA from S. acidocaldarius, enabling isolation of SlaB using size exclusion chromatography (gel filtration). Using this protocol, we were able to identify for the first time tetraether lipids strongly attached to SlaB via heat- and detergent-resistant interactions.

     

Combination of static-field gel electrophoresis and densitometric scanning for the determination of radiation-induced DNA double-strand breaks in CHO cells

An experimental setup using static-field gel electrophoresis (SFGE) was developed to determine radiation-induced DNA double-strand breaks (DSBs) in CHO-K1 cells after exposure to X-rays or heavy charged particles. The fraction of DNA eluted into the gel matrix depends on the quantity of DSBs introduced. In agreement with a recent report, SFGE and pulsed-field electrophoresis were found to be equally sensitive in DSB detection. With radiolabeled DNA from cell cultures, the absolute amount of DNA migrating out of agarose plugs into the gel was quantified by determining the radioactivity in the gel lane. Alternatively, relative measurements of the amount of DNA released into the gel were achieved with a standardized protocol for both SFGE and a subsequent densitometric scanning of photographic negatives from gels stained with ethidium bromide. After calibration with the radioactive method, the fractions of DNA retained could be calculated directly from the data obtained with the densitometric assay to set up classical dose-effect curves. This procedure was validated for its application with heavy ions using an 500 MeV/u lead beam.     

Effect of pericellular matrix formation by chondrocytes cultured in agarose gel on the viscoelastic properties of agarose gel matrix

The viscoelasticity of chondrocyte-seeded agarose gel (AGC0) and that of chondrocyte-seeded agarose gel after 21 days of cultivation (AGC3) were investigated. In AGC3, pericellular matrix (PCM)-like material around each chondrocyte was found to be constructed, which was confirmed by an optical micrograph in conjunction with toluidine blue staining. The relaxation modulus of each of the chondrocyte-agarose gel composite systems was measured by a non-constrained indentation method. Stress-strain curves for all of the specimens examined had a toe region followed by a linear region terminated by specimen fracture. The slope of the linear region of AGC0 was smaller than that of AG, while the SS curve of AGC0 was indistinguishable from that of AGC3. All of the relaxation curves studied were typical of gels, having a fast relaxation process up to 10³ s followed by a plateau. The relaxation modulus of AGC0 was smaller than that of agarose gel (AG), the decrement in relaxation modulus from AG to AGC0 being attributed to the seeding of chondrocytes that have a smaller modulus than that of agarose gels. However, the relaxation modulus of AGC3 was increased at the early viscoelastic region in particular, as compared with that of AGC0. The increments in the relaxation modulus in AGC3 were attributed to the PCM-like material produced by chondrocytes, where the produced material may provide crosslink points and reinforce the agarose gel.     

Separation and visualization of apolipoprotein B species by sodium dodecyl sulfate-agarose gel electrophoresis and immunoblotting

A method for separation and visualization of the different apolipoprotein B species using 0.2% sodium dodecyl sulfate-1.5% agarose gel electrophoresis and immunoblotting is described. The method is capable of demonstrating the different forms of apolipoprotein B (apo B) in plasma volumes of 10-50 microliters without prior ultracentrifugation. After ultracentrifugation of samples, estimation of the ratio between apo B 48 and apo B 100 is possible by scanning of Coomassie-stained gels or immunoblots.     

Interpenetrating network formation in agarose–sodium gellan gel composites

Aqueous cold-set gels from mixtures of agarose and sodium gellan have been characterised structurally and mechanically using optical and electron microscopy, turbidity measurements, differential scanning calorimetry, mechanical spectroscopy and compression testing. Consistent with expectations for charged–uncharged polymer combinations at low ionic strength there is no liquid–liquid demixing in sols prior to gelation, and although transmission electron microscopy reveals heterogeneities in gel microstructures at the higher polymer concentrations, these are small in extent, and are unlikely to arise from normal segregative demixing. Overall, ‘molecularly’ interpenetrating networks (IPNs) are indicated, in which the gellan and agarose architectures pass through one another on a distance scale comparable to their pore sizes. At concentrations greater than 2% w/w gellan, where gellan is the first gelling species, and when the agarose concentration is greater than 0.5% w/w, the composite modulus falls below that expected for the agarose alone. At 0.5% w/w agarose, on the other hand, modulus contributions from the components are much closer to additive. These findings are reflected in the results of large deformation compression testing where breaking stresses show similar trends.     

Isoelectric focusing in polyacrylamide-agarose

A procedure using a 2.5% acrylamide-0.5% agarose gel for slab or tube isoelectric focusing is described. This composite gel is durable and enables a rapid focusing of high-molecular-weight compounds.     

Sodium dodecyl sulfate-agarose gel electrophoresis for the detection and isolation of amyloid curli fibers

Curli are amyloid-like fibers on the surface of some strains of Escherichia coli and Salmonella enteritidis. We tested the use of horizontal sodium dodecyl sulfate (SDS)–agarose gel electrophoresis to detect, isolate, and quantitate curli. Cell extracts fractionated in SDS–agarose gels and stained with Coomassie blue exhibited a soluble fraction that entered the gel and an insoluble fraction that remained in the well. Much more insoluble material was observed with curli-proficient strains than with strains that do not make curli. Both highly purified curli and the insoluble material isolated from an SDS–agarose gel could be dissociated into monomers when treated with formic acid. For quantitation, we immobilized samples in SDS–agarose prior to electrophoresis. This avoids losses during the staining of the gel. Our methods provide a rapid and simple fractionation of curli using equipment that is readily available.     

Nanocellulose 3, 5‐Dimethylphenylcarbamate Derivative Coated Chiral Stationary Phase: Preparation and Enantioseparation Performance

Nanocrystalline cellulose (NCC) with high surface area and high ordered crystalline structure was prepared from microcrystalline cellulose (MCC) under the hydrolysis of sodium hypochlorite. NCC was further reacted with 3,5‐dimethylphenyl isocyanate to obtain the nanocellulose derivative, and then coated successfully on the surface of silica gel to a prepared NCC‐coated chiral stationary phase (CSP) as a new kind of chiral separation material. Similarly, MCC derivative‐coated CSP was also prepared as contrast. The chiral separation performance of NCC‐based CSP was evaluated and compared with MCC‐based CSP by high‐performance liquid chromatography. Moreover, the effects of the alcohol modifiers, mobile phase additives, and flow rates on chiral separations were investigated in detail. The results showed that 10 chiral compounds were separated on NCC‐based CSP with better peak shape and higher column efficiency than MCC‐based CSP, which confirmed that NCC‐based CSP was a promising packing material for the resolution of chiral compounds.Chirality 28:376–381, 2016. © 2016 Wiley Periodicals, Inc.     

A method for the purification of Shiga-like toxin 1 subunit B using a commercially available galabiose–agarose resin

We describe a procedure for the affinity purification of Shiga toxin 1 subunit B (SLTB) using a commercial galabiose–agarose resin. Recombinant SLTB was purified to 99% homogeneity in a single-step protocol, from the periplasmic extracts of Vibrio cholerae 0395 N1/pSBC54. SDS–PAGE of the affinity purified SLTB showed one band of 8 kDa MW. SLTB purified by this procedure retained its chemical and biological activity as demonstrated by re-binding to the galabiose–agarose resin, and receptor-mediated binding and uptake in Vero cells. The galabiose–agarose resin could isolate roughly 1 mg of SLTB/mL of gel. The resin was stable over 3 years and 500 cycles/year of usage. Hence, this method is a straightforward approach to the large-scale preparation of SLTB at a reasonable cost.     

Phase equilibria and gelation in gelatin/maltodextrin systems — Part IV: composition-dependence of mixed-gel moduli

The storage moduli (G′) of phase-separated co-gels formed by quench-cooling mixed solutions of gelatin and potato maltodextrin (Paselli SA-2 and SA-6) have been related quantitatively to the experimentally-determined concentration-dependence of G′ for the constituent polymers. Distribution of water between the phases was examined explicitly by using polymer blending laws to derive calculated moduli for gelatin-continuous and maltodextrin-continuous networks over the entire range of solvent partition. Allowance was made for the direct contribution of polymer chains, and for density differences between the phases, in calculating relative phase-volumes. The effect of gel formation prior to phase-separation was calculated using classical theory for network de-swelling. Good agreement with observed moduli for more than 30 gelatin/maltodextrin combinations was achieved using a single adjustable parameter, p (the ratio of solvent to polymer in the gelatin phase divided by the same ratio for the maltodextrin phase), with an optimum value of p ≈ 1·8 for both SA-6 and SA-2.     

Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: RNA interactions

Interactions between proteins and nucleic acids are frequently analyzed using electrophoretic mobility shift assays (EMSAs). This technique separates bound protein:nucleic acid complexes from free nucleic acids by electrophoresis, most commonly using polyacrylamide gels. The current study utilizes recent advances in agarose gel electrophoresis technology to develop a new EMSA protocol that is simpler and faster than traditional polyacrylamide methods. Agarose gels are normally run at low voltages (∼10 V/cm) to minimize heating and gel artifacts. In this study we demonstrate that EMSAs performed using agarose gels can be run at high voltages (≥20 V/cm) with 0.5 × TB (Tris-borate) buffer, allowing for short run times while simultaneously yielding high band resolution. Several parameters affecting band and image quality were optimized for the procedure, including gel thickness, agarose percentage, and applied voltage. Association of the siRNA-binding protein p19 with its target RNA was investigated using the new system. The agarose gel and conventional polyacrylamide gel methods generated similar apparent binding constants in side-by-side experiments. A particular advantage of the new approach described here is that the short run times (5–10 min) reduce opportunities for dissociation of bound complexes, an important concern in non-equilibrium nucleic acid binding experiments.     

A rapid method for determining the relationship between cDNA clones

We describe a technique for rapidly screening the inserts of plasmids for homology to each other by using DNA fragments isolated in agarose gels to probe Southern blots of DNA prepared by the "miniprep" alkaline lysis method. The procedure includes a technique for labeling DNA fragments in agarose gel slices without further purification. The protocol results in a significant savings in time and expense and a considerable increase in fragment yield over methods involving fragment purification from polyacrylamide or agarose gels.     

Importance of Small Pores in Microcrystalline Cellulose for Controlling Water Distribution during Extrusion–Spheronization

The purpose of this research was to investigate the effects of particle size on the wet massing behavior of microcrystalline cellulose (MCC). In this study, a series of six fractionated MCC grades were customized and specially classified to yield different particle size varieties of the standard grade, Comprecel M101. All seven MCC grades were extensively characterized for the physical properties and wet massing behavior using mixer torque rheometry. Effects of MCC physical properties on the maximum torque (Torque_max) were determined using partial least squares (PLS) analysis. Most physical properties varied systematically with particle size and morphological changes. Marked differences were observed in the small pore volumes (V _highP) and BET surface areas of the MCC grades. Variables that exerted dominant influences on Torque_max were identified. In particular, the significance of V _highP in governing wet mass consistency was established. The role of V _highP has not been reported in any study because this small but significant variation is likely to be obliterated or compensated by variation in other physical properties from MCC grades from different suppliers. The findings demonstrated the role of small pores in governing the wet mass consistency of MCC and provide a better understanding of MCC’s superior performance as a spheronization aid by the ability to fulfill the function as a molecular sponge to facilitate pellet formation during wet granulation processes.