Sample records for agarose gels polyacrylamide

  1. Electrophoresis of DNA in agarose gels, polyacrylamide gels and in free solution

    PubMed Central

    Stellwagen, Nancy C.

    2009-01-01

    This review describes the electrophoresis of curved and normal DNA molecules in agarose gels, polyacrylamide gels and in free solution. These studies were undertaken to clarify why curved DNA molecules migrate anomalously slowly in polyacrylamide gels but not in agarose gels. Two milestone papers are cited, in which Ferguson plots were used to estimate the effective pore size of agarose and polyacrylamide gels. Subsequent studies on the effect of the electric field on agarose and polyacrylamide gel matrices, DNA interactions with the two gel matrices, and the effect of curvature on the free solution mobility of DNA are also described. The combined results suggest that the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due primarily to preferential interactions of curved DNAs with the polyacrylamide gel matrix; the restrictive pore size of the matrix is of lesser importance. In free solution, DNA mobilities increase with increasing molecular mass until leveling off at a plateau value of (3.17 ± 0.01) × 10-4 cm2/Vs in 40 mM Tris-acetate-EDTA buffer at 20°C. Curved DNA molecules migrate anomalously slowly in free solution as well as in polyacrylamide gels, explaining why the Ferguson plots of curved and normal DNAs containing the same number of base pairs extrapolate to different mobilities at zero gel concentration. PMID:19517510

  2. Comparison of polyacrylamide and agarose gel thin-layer isoelectric focusing for the characterization of beta-lactamases.

    PubMed

    Vecoli, C; Prevost, F E; Ververis, J J; Medeiros, A A; O'Leary, G P

    1983-08-01

    Plasmid-mediated beta-lactamases from strains of Escherichia coli and Pseudomonas aeruginosa were separated by isoelectric focusing on a 0.8-mm thin-layer agarose gel with a pH gradient of 3.5 to 9.5. Their banding patterns and isoelectric points were compared with those obtained with a 2.0-mm polyacrylamide gel as the support medium. The agarose method produced banding patterns and isoelectric points which corresponded to the polyacrylamide gel data for most samples. Differences were observed for HMS-1 and PSE-1 beta-lactamases. The HMS-1 sample produced two highly resolvable enzyme bands in agarose gels rather than the single faint enzyme band observed on polyacrylamide gels. The PSE-1 sample showed an isoelectric point shift of 0.2 pH unit between polyacrylamide and agarose gel (pI 5.7 and 5.5, respectively). The short focusing time, lack of toxic hazard, and ease of formulation make agarose a practical medium for the characterization of beta-lactamases.

  3. Comparison of polyacrylamide and agarose gel thin-layer isoelectric focusing for the characterization of beta-lactamases.

    PubMed Central

    Vecoli, C; Prevost, F E; Ververis, J J; Medeiros, A A; O'Leary, G P

    1983-01-01

    Plasmid-mediated beta-lactamases from strains of Escherichia coli and Pseudomonas aeruginosa were separated by isoelectric focusing on a 0.8-mm thin-layer agarose gel with a pH gradient of 3.5 to 9.5. Their banding patterns and isoelectric points were compared with those obtained with a 2.0-mm polyacrylamide gel as the support medium. The agarose method produced banding patterns and isoelectric points which corresponded to the polyacrylamide gel data for most samples. Differences were observed for HMS-1 and PSE-1 beta-lactamases. The HMS-1 sample produced two highly resolvable enzyme bands in agarose gels rather than the single faint enzyme band observed on polyacrylamide gels. The PSE-1 sample showed an isoelectric point shift of 0.2 pH unit between polyacrylamide and agarose gel (pI 5.7 and 5.5, respectively). The short focusing time, lack of toxic hazard, and ease of formulation make agarose a practical medium for the characterization of beta-lactamases. Images PMID:6605714

  4. Agarose and Polyacrylamide Gel Electrophoresis Methods for Molecular Mass Analysis of 5–500 kDa Hyaluronan

    PubMed Central

    Bhilocha, Shardul; Amin, Ripal; Pandya, Monika; Yuan, Han; Tank, Mihir; LoBello, Jaclyn; Shytuhina, Anastasia; Wang, Wenlan; Wisniewski, Hans-Georg; de la Motte, Carol; Cowman, Mary K.

    2011-01-01

    Agarose and polyacrylamide gel electrophoresis systems for the molecular mass-dependent separation of hyaluronan (HA) in the size range of approximately 5–500 kDa have been investigated. For agarose-based systems, the suitability of different agarose types, agarose concentrations, and buffers systems were determined. Using chemoenzymatically synthesized HA standards of low polydispersity, the molecular mass range was determined for each gel composition, over which the relationship between HA mobility and logarithm of the molecular mass was linear. Excellent linear calibration was obtained for HA molecular mass as low as approximately 9 kDa in agarose gels. For higher resolution separation, and for extension to molecular masses as low as approximately 5 kDa, gradient polyacrylamide gels were superior. Densitometric scanning of stained gels allowed analysis of the range of molecular masses present in a sample, and calculation of weight-average and number-average values. The methods were validated for polydisperse HA samples with viscosity-average molecular masses of 112, 59, 37, and 22 kDa, at sample loads of 0.5 µg (for polyacrylamide) to 2.5 µg (for agarose). Use of the methods for electrophoretic mobility shift assays was demonstrated for binding of the HA-binding region of aggrecan (recombinant human aggrecan G1-IGD-G2 domains) to a 150 kDa HA standard. PMID:21684248

  5. Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.

    PubMed

    Day, I N; Humphries, S E

    1994-11-01

    Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

  6. Agarose gel electrophoresis for the separation of DNA fragments.

    PubMed

    Lee, Pei Yun; Costumbrado, John; Hsu, Chih-Yuan; Kim, Yong Hoon

    2012-04-20

    Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb(1). Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits(2). 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 weight(3). 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 along(4). 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 conformation(5); 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: Understand the mechanism by which DNA fragments are separated within a gel matrix Understand how conformation of the DNA molecule will determine its mobility through a gel matrix Identify an agarose solution of appropriate

  7. Electroblotting from Polyacrylamide Gels.

    PubMed

    Goldman, Aaron; Ursitti, Jeanine A; Mozdzanowski, Jacek; Speicher, David W

    2015-11-02

    Transferring proteins from polyacrylamide gels onto retentive membranes is now primarily used for immunoblotting. A second application that was quite common up to about a decade ago was electroblotting of proteins for N-terminal and internal sequencing using Edman chemistry. This unit contains procedures for electroblotting proteins from polyacrylamide gels onto a variety of membranes, including polyvinylidene difluoride (PVDF) and nitrocellulose. In addition to the commonly used tank or wet transfer system, protocols are provided for electroblotting using semidry and dry systems. This unit also describes procedures for eluting proteins from membranes using detergents or acidic extraction with organic solvents for specialized applications. Copyright © 2015 John Wiley & Sons, Inc.

  8. Posing for a picture: vesicle immobilization in agarose gel

    NASA Astrophysics Data System (ADS)

    Lira, Rafael B.; Steinkühler, Jan; Knorr, Roland L.; Dimova, Rumiana; Riske, Karin A.

    2016-05-01

    Taking a photo typically requires the object of interest to stand still. In science, imaging is potentiated by optical and electron microscopy. However, living and soft matter are not still. Thus, biological preparations for microscopy usually include a fixation step. Similarly, immobilization strategies are required for or substantially facilitate imaging of cells or lipid vesicles, and even more so for acquiring high-quality data via fluorescence-based techniques. Here, we describe a simple yet efficient method to immobilize objects such as lipid vesicles with sizes between 0.1 and 100 μm using agarose gel. We show that while large and giant unilamellar vesicles (LUVs and GUVs) can be caged in the pockets of the gel meshwork, small molecules, proteins and micelles remain free to diffuse through the gel and interact with membranes as in agarose-free solutions, and complex biochemical reactions involving several proteins can proceed in the gel. At the same time, immobilization in agarose has no adverse effect on the GUV size and stability. By applying techniques such as FRAP and FCS, we show that the lateral diffusion of lipids is not affected by the gel. Finally, our immobilization strategy allows capturing high-resolution 3D images of GUVs.

  9. UNIT 10.7 Electroblotting from Polyacrylamide Gels

    PubMed Central

    Goldman, Aaron; Speicher, David W.

    2015-01-01

    Transferring proteins from polyacrylamide gels onto retentive membranes is now primarily used for immunoblotting. A second application that was quite common up to about a decade ago was electroblotting of proteins for N-terminal and internal sequencing using Edman chemistry. This unit contains procedures for electroblotting proteins from polyacrylamide gels onto a variety of membranes, including polyvinylidene difluoride (PVDF) and nitrocellulose. In addition to the commonly used tank or wet transfer system, protocols are provided for electroblotting using semidry and dry systems. This unit also describes procedures for eluting proteins from membranes using detergents or acidic extraction with organic solvents for specialized applications. PMID:26521711

  10. Topology evolution and gelation mechanism of agarose gel.

    PubMed

    Xiong, Jun-Ying; Narayanan, Janaky; Liu, Xiang-Yang; Chong, Tan Kok; Chen, Shing Bor; Chung, Tai-Shung

    2005-03-31

    Kinetics as well as the evolution of the agarose gel topology is discussed, and the agarose gelation mechanism is identified. Aqueous high melting (HM) agarose solution (0.5% w/v) is used as the model system. It is found that the gelation process can be clearly divided into three stages: induction stage, gelation stage, and pseudoequilibrium stage. The induction stage of the gelation mechanism is identified using an advanced rheological expansion system (ARES, Rheometric Scientific). When a quench rate as large as 30 deg C/min is applied, gelation seems to occur through a nucleation and growth mechanism with a well-defined induction time (time required for the formation of the critical nuclei which enable further growth). The relationship between the induction time and the driving force which is determined by the final setting temperature follows the 3D nucleation model. A schematic representation of the three stages of the gelation mechanism is given based on turbidity and rheological measurements. Aggregation of agarose chains is promoted in the polymer-rich phase and this effect is evident from the increasing mass/length ratio of the fiber bundles upon gelation. Continuously increasing pore size during gelation may be attributed to the coagulation of the local polymer-rich phase in order to achieve the global minimum of the free energy of the gelling system. The gel pore size determined using turbidity measurements has been verified by electrophoretic mobility measurements.

  11. Molecular-sieve chromatography and electrophoresis in polyacrylamide gels

    PubMed Central

    Morris, C. J. O. R.; Morris, Peggy

    1971-01-01

    1. The absolute electrophoretic mobilities of eight proteins have been measured at pH8.76, I 0.05, in polyacrylamide gels of 20 different compositions at 10°C. 2. The partition coefficients of these proteins have been determined chromatographically under the same conditions by using columns of granulated polyacrylamide gel prepared simultaneously. 3. The electrophoretic mobilities are an exponential function of the gel concentrations when the latter are corrected for water uptake. The constants of this function have been determined by curvefitting methods. They have been shown to be related to the free solution mobility and to the mean molecular radius respectively. 4. The reduced mobilities have been shown to be a linear function of the partition coefficients by statistical analyses. 5. The physical significance of the relation between electrophoretic mobility and chromatographic phase distribution in gel media is discussed in the context of these results. PMID:5135238

  12. Function, structure, and stability of enzymes confined in agarose gels.

    PubMed

    Kunkel, Jeffrey; Asuri, Prashanth

    2014-01-01

    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.

  13. Impact of saccharides on the drying kinetics of agarose gels measured by in-situ interferometry

    NASA Astrophysics Data System (ADS)

    Mao, Bosi; Divoux, Thibaut; Snabre, Patrick

    2017-01-01

    Agarose gels are viscoelastic soft solids that display a porous microstructure filled with water at 90% w/w or more. Despite an extensive use in food industry and microbiology, little is known about the drying kinetics of such squishy solids, which suffers from a lack of time-resolved local measurements. Moreover, only scattered empirical observations are available on the role of the gel composition on the drying kinetics. Here we study by in-situ interferometry the drying of agarose gels of various compositions cast in Petri dishes. The gel thinning is associated with the displacement of interference fringes that are analyzed using an efficient spatiotemporal filtering method, which allows us to assess local thinning rates as low as 10 nm/s with high accuracy. The gel thinning rate measured at the center of the dish appears as a robust observable to quantify the role of additives on the gel drying kinetics and compare the drying speed of agarose gels loaded with various non-gelling saccharides of increasing molecular weights. Our work shows that saccharides systematically decrease the agarose gel thinning rate up to a factor two, and exemplifies interferometry as a powerful tool to quantify the impact of additives on the drying kinetics of polymer gels.

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

    PubMed

    Kim, Jung Hyun; Yun, Eun Ju; Seo, Nari; Yu, Sora; Kim, Dong Hyun; Cho, Kyung Mun; An, Hyun Joo; Kim, Jae-Han; Choi, In-Geol; Kim, Kyoung Heon

    2017-02-01

    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.

  15. Photopatterned free-standing polyacrylamide gels for microfluidic protein electrophoresis.

    PubMed

    Duncombe, Todd A; Herr, Amy E

    2013-06-07

    Designed for compatibility with slab-gel polyacrylamide gel electrophoresis (PAGE) reagents and instruments, we detail development of free-standing polyacrylamide gel (fsPAG) microstructures supporting electrophoretic performance rivalling that of microfluidic platforms. For the protein electrophoresis study described here, fsPAGE lanes are comprised of a sample reservoir and contiguous separation gel. No enclosed microfluidic channels are employed. The fsPAG devices (120 μm tall) are directly photopatterned atop of and covalently attached to planar polymer or glass surfaces. Leveraging the fast <1 h design-prototype-test cycle - significantly faster than mold based fabrication techniques - we optimize the fsPAG architecture to minimize injection dispersion for rapid (<1 min) and short (1 mm) protein separations. The facile fabrication and prototyping of the fsPAGE provides researchers a powerful tool for developing custom analytical assays. We highlight the utility of assay customization by fabricating a polyacrylamide gel with a spatial pore-size distribution and demonstrate the resulting enhancement in separation performance over a uniform gel. Further, we up-scale from a unit separation to an array of 96 concurrent fsPAGE assays in 10 min run time driven by one electrode pair. The fsPAG array layout matches that of a 96-well plate to facilitate integration of the planar free standing gel array with multi-channel pipettes while remaining compatible with conventional slab-gel PAGE reagents, such as staining for label-free protein detection. Notably, the entire fsPAGE workflow from fabrication, to operation, and readout uses readily available materials and instruments - making this technique highly accessible.

  16. Mucin Agarose Gel Electrophoresis: Western Blotting for High-molecular-weight Glycoproteins.

    PubMed

    Ramsey, Kathryn A; Rushton, Zachary L; Ehre, Camille

    2016-06-14

    Mucins, the heavily-glycosylated proteins lining mucosal surfaces, have evolved as a key component of innate defense by protecting the epithelium against invading pathogens. The main role of these macromolecules is to facilitate particle trapping and clearance while promoting lubrication of the mucosa. During protein synthesis, mucins undergo intense O-glycosylation and multimerization, which dramatically increase the mass and size of these molecules. These post-translational modifications are critical for the viscoelastic properties of mucus. As a result of the complex biochemical and biophysical nature of these molecules, working with mucins provides many challenges that cannot be overcome by conventional protein analysis methods. For instance, their high-molecular-weight prevents electrophoretic migration via regular polyacrylamide gels and their sticky nature causes adhesion to experimental tubing. However, investigating the role of mucins in health (e.g., maintaining mucosal integrity) and disease (e.g., hyperconcentration, mucostasis, cancer) has recently gained interest and mucins are being investigated as a therapeutic target. A better understanding of the production and function of mucin macromolecules may lead to novel pharmaceutical approaches, e.g., inhibitors of mucin granule exocytosis and/or mucolytic agents. Therefore, consistent and reliable protocols to investigate mucin biology are critical for scientific advancement. Here, we describe conventional methods to separate mucin macromolecules by electrophoresis using an agarose gel, transfer protein into nitrocellulose membrane, and detect signal with mucin-specific antibodies as well as infrared fluorescent gel reader. These techniques are widely applicable to determine mucin quantitation, multimerization and to test the effects of pharmacological compounds on mucins.

  17. Polyacrylamide gel ingestion leading to fatal intestinal obstruction in two birds in a zoological collection.

    PubMed

    Miller, Christine L; Bischoff, Karyn L; Hoff, Brent

    2009-12-01

    Two birds from a zoological collection suffered fatal intestinal obstruction after each ingested single particles of polyacrylamide gel. Polyacrylamide gel, used in soils for gardening and agriculture, exists as small granules in the dehydrated state but expands markedly upon exposure to water. Polyacrylamide gel might, therefore, be an unrecognized hazard for captive and wild birds and other small animals if consumed.

  18. In situ observation of sol-gel transition of agarose aqueous solution by fluorescence measurement.

    PubMed

    Wang, Zheng; Yang, Kun; Li, Haining; Yuan, Chaosheng; Zhu, Xiang; Huang, Haijun; Wang, Yongqiang; Su, Lei; Fang, Yapeng

    2018-06-01

    Sol-gel transition behavior of agarose aqueous solution was investigated by using rheology and fluorescence measurement. On heating, the storage modulus G' decreased gradually, then deviated abruptly at the temperature of about 65°C, and finally decreased slowly again. For fluorescence measurement, the phase transition point kept almost at the temperature of 65°C, which was consistent with that in rheology measurement. Upon compression, it was indicated that the fluorescence lifetime for the probe in the agarose aqueous solution showed a dramatic change in the vicinity of the phase transition point. T vs. P phase diagram of agarose aqueous solution was constructed, which showed that the melting point was an increasing function of pressure. Based on the phase diagram, the agarose gels were prepared by cooling under atmospheric pressure and the pressure of 300MPa, respectively. From the result of the recovered samples studied by optical rheometry, it was found that agarose gel prepared under high pressure had a higher elasticity and lower viscosity index, compared with that under atmospheric pressure. It could be speculated that such kinds of properties might be attributed to the smaller pore size during gelation under high pressure. Copyright © 2018. Published by Elsevier B.V.

  19. [Analysis of antibiotic diffusion from agarose gel by spectrophotometry and laser interferometry methods].

    PubMed

    Arabski, Michał; Wasik, Sławomir; Piskulak, Patrycja; Góźdź, Natalia; Slezak, Andrzej; Kaca, Wiesław

    2011-01-01

    The aim of this study was to analysis of antibiotics (ampicilin, streptomycin, ciprofloxacin or colistin) release from agarose gel by spectrophotmetry and laser interferometry methods. The interferometric system consisted of a Mach-Zehnder interferometer with a He-Ne laser, TV-CCD camera, computerised data acquisition system and a gel system. The gel system under study consists of two cuvettes. We filled the lower cuvette with an aqueous 1% agarose solution with the antibiotics at initial concentration of antibiotics in the range of 0.12-2 mg/ml for spectrophotmetry analysis or 0.05-0.5 mg/ml for laser interferometry methods, while in the upper cuvette there was pure water. The diffusion was analysed from 120 to 2400 s with a time interval of deltat = 120 s by both methods. We observed that 0.25-1 mg/ml and 0,05 mg/ml are minimal initial concentrations detected by spectrophotometric and laser interferometry methods, respectively. Additionally, we observed differences in kinetic of antibiotic diffusion from gel measured by both methods. In conclusion, the laser interferometric method is a useful tool for studies of antibiotic release from agarose gel, especially for substances are not fully soluble in water, for example: colistin.

  20. Blood grouping based on PCR methods and agarose gel electrophoresis.

    PubMed

    Sell, Ana Maria; Visentainer, Jeane Eliete Laguila

    2015-01-01

    The study of erythrocyte antigens continues to be an intense field of research, particularly after the development of molecular testing methods. More than 300 specificities have been described by the International Society for Blood Transfusion as belonging to 33 blood group systems. The polymerase chain reaction (PCR) is a central tool for red blood cells (RBC) genotyping. PCR and agarose gel electrophoresis are low cost, easy, and versatile in vitro methods for amplifying defined target DNA (RBC polymorphic region). Multiplex-PCR, AS-PCR (Specific Allele Polymerase Chain Reaction), and RFLP-PCR (Restriction Fragment Length Polymorphism-Polymerase Chain Reaction) techniques are usually to identify RBC polymorphisms. Furthermore, it is an easy methodology to implement. This chapter describes the PCR methodology and agarose gel electrophoresis to identify the polymorphisms of the Kell, Duffy, Kidd, and MNS blood group systems.

  1. Anomalous diffusion of poly(ethylene oxide) in agarose gels.

    PubMed

    Brenner, Tom; Matsukawa, Shingo

    2016-11-01

    We report on the effect of probe size and diffusion time of poly(ethylene) oxide in agarose gels. Time-dependence of the diffusion coefficient, reflecting anomalous diffusion, was observed for poly(ethylene) oxide chains with hydrodynamic radii exceeding about 20nm at an agarose concentration of 2%. The main conclusion is that the pore distribution includes pores that are only several nm across, in agreement with scattering reports in the literature. Interpretation of the diffusion coefficient dependence on the probe size based on a model of entangled rigid rods yielded a rod length of 72nm. Copyright © 2016. Published by Elsevier B.V.

  2. Maintenance of biological activity of pertussis toxin radioiodinated while bound to fetuin-agarose

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Armstrong, G.D.; Peppler, M.S.

    1987-05-01

    We developed a method to produce radioiodinated pertussis toxin (PT) which was active in the goose erythrocyte agglutination and CHO cell assay systems. The procedure used fetuin coupled to agarose to prevent inactivation of the toxin during the iodination reaction. Analysis of the labeled PT by affinity chromatography on fetuin-agarose and wheat germ agglutinin-agarose and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that there were minimal amounts of labeled fetuin or other contaminants in the labeled PT preparations. All five of the subunits of the toxin appeared to be labeled by the procedure. The labeling method will facilitate further investigationsmore » into the nature of the interaction and activity of PT in host tissues.« less

  3. Rheological properties of reactive extrusion modified waxy starch and waxy starch-polyacrylamide copolymer gels

    USDA-ARS?s Scientific Manuscript database

    The rheological properties of modified waxy starch and waxy starch-polyacrylamide graft copolymers prepared by reactive extrusion were investigated. Both materials can absorb huge amount of water and form gels. The modified waxy starch and waxy starch-polyacrylamide graft copolymer gels all exhibite...

  4. Bleach Gel: A Simple Agarose Gel for Analyzing RNA Quality

    PubMed Central

    Aranda, Patrick S.; LaJoie, Dollie M.; Jorcyk, Cheryl L.

    2013-01-01

    RNA-based applications requiring high quality, non-degraded RNA are a foundational element of many research studies. As such, it is paramount that the integrity of experimental RNA is validated prior to cDNA synthesis or other downstream applications. In the absence of expensive equipment such as microfluidic electrophoretic devices, and as an alternative to the costly and time-consuming standard formaldehyde gel, RNA quality can be quickly analyzed by adding small amounts of commercial bleach to TAE buffer-based agarose gels prior to electrophoresis. In the presence of low concentrations of bleach, the secondary structure of RNA is denatured and potential contaminating RNases are destroyed. Because of this, the ‘bleach gel’ is a functional approach that addresses the need for an inexpensive and safe way to evaluate RNA integrity and will improve the ability of researchers to rapidly analyze RNA quality. PMID:22222980

  5. Serum protein concentrations from clinically healthy horses determined by agarose gel electrophoresis.

    PubMed

    Riond, Barbara; Wenger-Riggenbach, Bettina; Hofmann-Lehmann, Regina; Lutz, Hans

    2009-03-01

    Serum protein electrophoresis is a useful screening test in equine laboratory medicine. The method can provide valuable information about changes in the concentrations of albumin and alpha-, beta-, and gamma-globulins and thereby help characterize dysproteinemias in equine patients. Reference values for horses using agarose gel as a support medium have not been reported. The purpose of this study was to establish reference intervals for serum protein concentrations in adult horses using agarose gel electrophoresis and to assess differences between warm-blooded and heavy draught horses. In addition, the precision of electrophoresis for determining fraction percentages and the detection limit were determined. Blood samples were obtained from 126 clinically healthy horses, including 105 Thoroughbreds and 21 heavy draught horses of both sexes and ranging from 2 to 20 years of age. The total protein concentration was determined by an automated biuret method. Serum protein electrophoresis was performed using a semi-automated agarose gel electrophoresis system. Coefficients of variation (CVs) were calculated for within-run and within-assay precision. Data from warm-blooded and draught horses were compared using the Mann-Whitney U test. Within-run and within-assay CVs were <5% for all protein fractions. No significant difference was found between warm-blooded and heavy draught horses and so combined reference intervals (2.5-97.5%) were calculated for total protein (51.0-72.0 g/L), albumin (29.6-38.5 g/L), alpha(1)-globulin (1.9-3.1 g/L), alpha(2)-globulin (5.3-8.7 g/L), beta(1)-globulin (2.8-7.3g/L), beta(2)-globulin (2.2-6.0 g/L), and gamma-globulin (5.8-12.7 g/L) concentrations, and albumin/globulin ratio (0.93-1.65). Using agarose gel as the supporting matrix for serum protein electrophoresis in horses resulted in excellent resolution and accurate results that facilitated standardization into 6 protein fractions.

  6. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, C.S.; Tollaksen, S.L.

    1987-09-04

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a dc power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. 8 figs.

  7. Penis invalidating cicatricial outcomes in an enlargement phalloplasty case with polyacrylamide gel (Formacryl).

    PubMed

    Parodi, P C; Dominici, M; Moro, U

    2006-01-01

    The present article reports the case of a patient subjected to polyacrylamide polymers-composed gel cutaneous infiltration in the penis for cosmetic purposes, resulting in severe invalidating outcomes. A significant tissue reaction to the subcutaneous injection of polyacrylamide gel for the penis enlargement purpose resulted in permanent and invalidating scars both on the esthetic and functional levels. Such a result must be simply taken into account both singly and in the light of the international literature to exclude this method as standard uro-andrologic activity.

  8. Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.

    PubMed

    Hegedüs, Eva; Kókai, Endre; Kotlyar, Alexander; Dombrádi, Viktor; Szabó, Gábor

    2009-09-01

    Double-stranded (ds), as well as denatured, single-stranded (ss) DNA samples can be analyzed on urea-agarose gels. Here we report that after denaturation by heat in the presence of 8 M urea, the two strands of the same ds DNA fragment of approximately 1-20-kb size migrate differently in 1 M urea containing agarose gels. The two strands are readily distinguished on Southern blots by ss-specific probes. The different migration of the two strands could be attributed to their different, base composition-dependent conformation impinging on the electrophoretic mobility of the ss molecules. This phenomenon can be exploited for the efficient preparation of strand-specific probes and for the separation of the complementary DNA strands for subsequent analysis, offering a new tool for various cell biological research areas.

  9. Detection of sequence variation in parasite ribosomal DNA by electrophoresis in agarose gels supplemented with a DNA-intercalating agent.

    PubMed

    Zhu, X Q; Chilton, N B; Gasser, R B

    1998-05-01

    This study evaluated the use of a commercially available DNA intercalating agent (Resolver Gold) in agarose gels for the direct detection of sequence variation in ribosomal DNA (rDNA). This agent binds preferentially to AT sequence motifs in DNA. Regions of nuclear rDNA, known to provide genetic markers for the identification of species of parasitic ascarid nematodes (order Ascaridida), were amplified by polymerase chain reaction (PCR) and subjected to electrophoresis in standard agarose gels versus gels supplemented with Resolver Gold. Individual taxa examined could not be distinguished reliably based on the size of their amplicons in standard agarose gels, whereas they could be readily delineated based on mobility using Resolver Gold-supplemented gels. The latter was achieved because of differences (approximately 0.1-8.2%) in the AT content of the fragments among different taxa, which were associated with significant interspecific differences (approximately 11-39%) in the rDNA sequences employed. There was a tendency for fragments with higher AT content to migrate slower in supplemented agarose gels compared with those of lower AT content. The results indicate the usefulness of this electrophoretic approach to rapidly screen for sequence variability within or among PCR-amplified rDNA fragments of similar sizes but differing AT contents. Although evaluated on rDNA of parasites, the approach has potential to be applied to a range of genes of different groups of infectious organisms.

  10. An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels.

    PubMed

    Gonçalves, A M; Nehme, N S; Morel, C M

    1990-01-01

    A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980)]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels are applied to gradient gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

  11. Migration of fresh and cryopreserved human spermatozoa in polyacrylamide gel.

    PubMed

    Goldstein, M C; Wix, L S; Foote, R H; Feldschuh, R; Feldschuh, J

    1982-05-01

    The ability of freshly collected and frozen human spermatozoa to migrate in round capillary tubes containing specially formulated polyacrylamide gel was investigated, using 33 ejaculates from 27 donors. Each semen sample was divided; one portion was left undiluted, and the other portion was diluted to 50 x 10(6) sperm/ml. Glycerol was used as the cryoprotectant. The percentage of motile sperm cells was determined before and after freezing. Fresh semen contained a higher percentage of motile cells, which migrated farther than those of cryopreserved-thawed semen. Various correlations between the percentage of motile sperm and migration distance ranged from 0.57 to 0.62. There was a low positive correlation of migration distance with sperm cell concentration per milliliter, r = 0.25 to 0.34; and thus adjusting semen samples to a standard sperm concentration improved the accuracy of the test only slightly. The regression coefficient of migration distance on the percentage of motile sperm in fresh semen was 0.65, indicating that for each 10% increase in sperm motility, migration distance is predicted to increase 6.5 mm. Five batches of polyacrylamide gel gave uniform results, and the application of this stable gel to fertility investigations is discussed.

  12. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, Carol S.; Tollaksen, Sandra L.

    1989-01-01

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.

  13. Glycosaminoglycan blotting on nitrocellulose membranes treated with cetylpyridinium chloride after agarose-gel electrophoretic separation.

    PubMed

    Maccari, Francesca; Volpi, Nicola

    2002-09-01

    We describe a method for blotting and immobilizing several nonsulfated and sulfated complex polysaccharides on membranes made hydrophilic and positively charged by a cationic detergent after their separation by conventional agarose gel electrophoresis. Nitrocellulose membranes were derivatized with the cationic detergent cetylpyridinium chloride (CPC) and mixtures of glycosaminoglycans (GAGs) were capillary-blotted after their separation in agarose gel electrophoresis in barium acetate/1,2-diaminopropane. Single purified species of variously sulfated polysaccharides were transferred onto the derivatized membranes after electrophoresis with an efficiency of 100% and stained with alcian blue (irreversible staining) and toluidine blue (reversible staining) permitting about 0.1 nug threshold of detection. Nonsulfated polyanions, hyaluronic acid, a fructose-containing polysaccharide with a chondroitin backbone purified from Escherichia coli U1-41, and its defructosylated product, were also electrophoretically separated and transferred onto membranes. The limit of detection for desulfated GAGs was about 0.1-0.5 nug after irreversible or reversible staining. GAG extracts from bovine, lung and aorta, and human aorta and urine were separated by agarose gel electrophoresis and blotted on CPC-treated nitrocellulose membranes. The polysaccharide composition of these extracts was determined. The membrane stained with toluidine blue (reversible staining) was destained and the same lanes used for immunological detection or other applications. Reversible staining was also applied to recover single species of polysaccharides after electrophoretic separation of mixtures of GAGs and their transfer onto membranes. Single bands were released from the membrane with an efficiency of 70-100% for further biochemical characterization.

  14. In-gel staining of proteins in native polyacrylamide gel electrophoresis using meso-tetrakis(4-sulfonatophenyl) porphyrin.

    PubMed

    Divakar, K; Devi, G Nandhini; Gautam, Pennathur

    2012-01-01

    Protein identification in polyacrylamide gel electrophoresis (PAGE) requires post-electrophoretic steps like fixing, staining, and destaining of the gel, which are time-consuming and cumbersome. A new method for direct visualization of protein bands in PAGE has been developed using meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) as a dye without the need for any post-electrophoretic steps; thus, separation and recovery of enzymes become much easier for further analysis. Activity staining was carried out to show that the biochemical activity of the enzymes was preserved after electrophoresis.

  15. A direct method to visualise the aryl acylamidase activity on cholinesterases in polyacrylamide gels

    PubMed Central

    Jaganathan, Lakshmanan; Boopathy, Rathanam

    2000-01-01

    Background In vertebrates, two types of cholinesterases exist, acetylcholinesterase and butyrylcholinesterase. The function of acetylcholinesterase is to hydrolyse acetylcholine, thereby terminating the neurotransmission at cholinergic synapse, while the precise physiological function of butyrylcholinesterase has not been identified. The presence of cholinesterases in tissues that are not cholinergically innervated indicate that cholinesterases may have functions unrelated to neurotransmission. Furthermore, cholinesterases display a genuine aryl acylamidase activity apart from their predominant acylcholine hydrolase activity. The physiological significance of this aryl acylamidase activity is also not known. The study on the aryl acylamidase has been, in part hampered by the lack of a specific method to visualise this activity. We have developed a method to visualise the aryl acylamidase activity on cholinesterase in polyacrylamide gels. Results The o-nitroaniline liberated from o-nitroacetanilide by the action of aryl acylamidase activity on cholinesterases, in the presence of nitrous acid formed a diazonium compound. This compound gave an azo dye complex with N-(1-napthyl)-ethylenediamine, which appeared as purple bands in polyacrylamide gels. Treating the stained gels with trichloroacetic acid followed by Tris-HCl buffer helped in fixation of the stain in the gels. By using specific inhibitors for acetylcholinesterase and butyrylcholinesterase, respectively, differential staining for the aryl acylamidase activities on butyrylcholinesterase and acetylcholinesterase in a sample containing both these enzymes has been demonstrated. A linear relationship between the intensity of colour developed and activity of the enzyme was obtained. Conclusions A novel method to visualise the aryl acylamidase activity on cholinesterases in polyacrylamide gels has been developed. PMID:11231883

  16. A direct method to visualise the aryl acylamidase activity on cholinesterases in polyacrylamide gels.

    PubMed

    Jaganathan, L; Boopathy, R

    2000-01-01

    In vertebrates, two types of cholinesterases exist, acetylcholinesterase and butyrylcholinesterase. The function of acetylcholinesterase is to hydrolyse acetylcholine, thereby terminating the neurotransmission at cholinergic synapse, while the precise physiological function of butyrylcholinesterase has not been identified. The presence of cholinesterases in tissues that are not cholinergically innervated indicate that cholinesterases may have functions unrelated to neurotransmission. Furthermore, cholinesterases display a genuine aryl acylamidase activity apart from their predominant acylcholine hydrolase activity. The physiological significance of this aryl acylamidase activity is also not known. The study on the aryl acylamidase has been, in part hampered by the lack of a specific method to visualise this activity. We have developed a method to visualise the aryl acylamidase activity on cholinesterase in polyacrylamide gels. The o-nitroaniline liberated from o-nitroacetanilide by the action of aryl acylamidase activity on cholinesterases, in the presence of nitrous acid formed a diazonium compound. This compound gave an azo dye complex with N-(1-napthyl)-ethylenediamine, which appeared as purple bands in polyacrylamide gels. Treating the stained gels with trichloroacetic acid followed by Tris-HCl buffer helped in fixation of the stain in the gels. By using specific inhibitors for acetylcholinesterase and butyrylcholinesterase, respectively, differential staining for the aryl acylamidase activities on butyrylcholinesterase and acetylcholinesterase in a sample containing both these enzymes has been demonstrated. A linear relationship between the intensity of colour developed and activity of the enzyme was obtained. A novel method to visualise the aryl acylamidase activity on cholinesterases in polyacrylamide gels has been developed.

  17. Western Blot of Stained Proteins from Dried Polyacrylamide Gels

    NASA Technical Reports Server (NTRS)

    Gruber, Claudia; Stan-Lotter, Helga

    1996-01-01

    Western blotting of proteins is customarily performed following their separation on polyacrylamide gels, either prior to staining (1) or, as recently reported, following staining (2). We describe here Western blotting with stained gels, which had been dried and some of which had been stored for years. This procedure permits immunological analysis of proteins, to which antisera may have become available only later, or where the application of newly developed sensitive detection methods is desired. Once rehydration of the gels is achieved, proteins can be-transferred to blotting membranes by any appropriate protocol. Proteins stained with Coomassie Blue have to be detected with a non-chromogenic method, such as the film-based enhanced chemiluminescence (ECL)2) procedure (3). Silver stained proteins, which transfer in the colorless form, may be visualized by any detection method, although, because of the usually very low amounts of proteins, detection by ECL is preferable. Blotting of stained proteins from rehydrated gels is as rapid and as quantitative as from freshly prepared gels, in contrast to blotting from wet stained gels, which requires extensive washing and results in low transfer efficiency (2). Together with a photographic record of the gel pattern, unambiguous identification of immunoreactive proteins from complex mixtures is possible. Some further applications of this work are discussed.

  18. Pellet pestle homogenization of agarose gel slices at 45 degrees C for deoxyribonucleic acid extraction.

    PubMed

    Kurien, B T; Kaufman, K M; Harley, J B; Scofield, R H

    2001-09-15

    A simple method for extracting DNA from agarose gel slices is described. The extraction is rapid and does not involve harsh chemicals or sophisticated equipment. The method involves homogenization of the excised gel slice (in Tris-EDTA buffer), containing the DNA fragment of interest, at 45 degrees C in a microcentrifuge tube with a Kontes pellet pestle for 1 min. The "homogenate" is then centrifuged for 30 s and the supernatant is saved. The "homogenized" agarose is extracted one more time and the supernatant obtained is combined with the previous supernatant. The DNA extracted using this method lent itself to restriction enzyme analysis, ligation, transformation, and expression of functional protein in bacteria. This method was found to be applicable with 0.8, 1.0, and 2.0% agarose gels. DNA fragments varying from 23 to 0.4 kb were extracted using this procedure and a yield ranging from 40 to 90% was obtained. The yield was higher for fragments 2.0 kb and higher (70-90%). This range of efficiency was maintained when the starting material was kept between 10 and 300 ng. The heat step was found to be critical since homogenization at room temperature failed to yield any DNA. Extracting DNA with our method elicited an increased yield (up to twofold) compared with that extracted with a commercial kit. Also, the number of transformants obtained using the DNA extracted with our method was at least twice that obtained using the DNA extracted with the commercial kit. Copyright 2001 Academic Press.

  19. Non-Gradient Blue Native Polyacrylamide Gel Electrophoresis.

    PubMed

    Luo, Xiaoting; Wu, Jinzi; Jin, Zhen; Yan, Liang-Jun

    2017-02-02

    Gradient blue native polyacrylamide gel electrophoresis (BN-PAGE) is a well established and widely used technique for activity analysis of high-molecular-weight proteins, protein complexes, and protein-protein interactions. Since its inception in the early 1990s, a variety of minor modifications have been made to this gradient gel analytical method. Here we provide a major modification of the method, which we call non-gradient BN-PAGE. The procedure, similar to that of non-gradient SDS-PAGE, is simple because there is no expensive gradient maker involved. The non-gradient BN-PAGE protocols presented herein provide guidelines on the analysis of mitochondrial protein complexes, in particular, dihydrolipoamide dehydrogenase (DLDH) and those in the electron transport chain. Protocols for the analysis of blood esterases or mitochondrial esterases are also presented. The non-gradient BN-PAGE method may be tailored for analysis of specific proteins according to their molecular weight regardless of whether the target proteins are hydrophobic or hydrophilic. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  20. Capillary pressure as related to water holding in polyacrylamide and chicken protein gels.

    PubMed

    Stevenson, Clinton D; Dykstra, Michael J; Lanier, Tyre C

    2013-02-01

    The ability of food gels to hold water affects product yield and organoleptic quality. Most researchers believe that water is held by capillarity such that gels having smaller mean pore diameter and a more hydrophilic surface hold water more tightly. To date, however, only qualitative evidence relating pore size to water holding (WH) properties has been provided. The present study sought to provide quantitative confirmation of this hypothesis. Scanning electron microscopy coupled with image analysis was used to measure pore size, and water contact angle with the gel surface was measured by the captive bubble method, in both model polyacrylamide gels and heat-induced protein (minced chicken breast) gels. These were related to water lost during cooking of meat pastes to form gels (cooking loss (CL)), as well as water lost upon centrifugation (expressible water (EW)) or by capillary suction (CSL) of all prepared gels, as inverse measures of WH. As predicted by the Young-Laplace equation for calculating capillary pressure, the presumed mechanism of WH, gels with lower water losses exhibited a more hydrophilic surface (smaller contact angle). Yet, both lower CL and CSL correlated with larger mean pore diameter of gels, not smaller as had been expected. Polyacrylamide gels varied more in WH than did prepared meat gels, yet only the capillary suction method was sensitive enough to detect these differences.  The ability of gels to hold water is important for economics of processing, food quality, and food safety. This study investigated the prevailing theory for how gels hold water, capillarity. Both the pore sizes of gel microstructures and the degree of hydrophilicity of the polymers comprising each gel were quantitatively assessed and related to water holding (WH) properties, and this was the first report using such methodologies. It appeared that the degree of hydrophilicity was much more important explaining WH properties than pore size, and that future research of

  1. Agarose-gel electrophoresis for the quality assurance and purity of heparin formulations.

    PubMed

    Volpi, Nicola; Buzzega, Dania

    2012-01-01

    The adulteration of raw heparin (Hep) with a synthetic oversulfated chondroitin sulfate (OSCS) not found in nature produced in 2007-2008 a global crisis giving rise to the development of additional, new and specific methods for its quality assurance and purity. In this study, a simple and sensitive agarose-gel electrophoresis method has been developed for the visualization of OSCS in Hep samples along with other natural glycosaminoglycans possibly present as "process-related impurities", in particular dermatan sulfate (DS) and chondroitin sulfate (CS). Agarose-gel electrophoresis under non-conventional conditions is able to separate OSCS from Hep with its two components, the slow-moving and fast-moving species, DS and CS by performing separation for 15 h (overnight) and under high voltage (100 mA, ∼200 V). Densitometric scanning enabled us to calculate a limit of detection of ∼0.5 μg OSCS with a linear behaviour from 0.1 to 5 μg, comparable to CS/DS. Contaminated samples from Hep manufacturers were analyzed and quantitative data were found comparable to previous studies. Due to its capacity to process many samples in a single run and to the equipment commonly available in laboratories, this analytical method would be suitable for the identification and quantification of contamination by other polysaccharides, in particular OSCS and DS, within Hep preparations and formulations. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Method for long-term preservation of thin-layer polyacrylamide gels by producing a gelatine coating.

    PubMed

    Hofmann, K

    1991-02-01

    Thin-layer polyacrylamide gels can be preserved and stored for unlimited periods by covering them with a gelatine coating. The method is inexpensive and simple. After air-drying, the gel is immersed in an aqueous 10% solution of highly viscous gelatine between 55 and 60 degrees C. The coated gel is dried by hanging it in air. The method was checked successfully with gels of different thicknesses (0.15-0.50 mm) and after using different staining methods, e.g., with silver, Coomassie Brilliant Blue and pseudoperoxidase.

  3. Procedures and computer program for deriving the Ferguson plot from electrophoresis in a single pore gradient gel: application to agarose gel and a polystyrene particle.

    PubMed

    Tietz, D; Gombocz, E; Chrambach, A

    1991-10-01

    This study presents a computerized evaluation of pore gradient gel electrophoretograms to arrive at estimates for both the particle-free mobility and retardation coefficient, which is related to particle size. Agarose pore gradient gels ranging from 0.2 to 1.1% agarose were formed. Gel gradients were stabilized during their formation by a density gradient of 0-20% 5-(N-2,3-dihydroxypropylacetamido)- 2,4,6-triiodo-N,N'bis-(2,3-dihydroxypropyl)-isophthalamide (Nycodenz). Densitometry of gelled-in Bromophenol Blue showed that these pore gradients exhibited a linear central segment and were reproducible. Migration distances of polystyrene sulfate microspheres (36.5 nm radius) in agarose pore gradient gel electrophoresis were determined by time-lapse photography at several durations of electrophoresis. These migration distances were evaluated as a function of migration time as previously reported (D. Tietz, Adv. Electrophoresis 1988, 2, 109-169). Although this is not necessarily required, the mathematical approach used in this study assumed linearity of both the pore gradient and the Ferguson plot for reasons of simplicity. The data evaluation on the basis of the extended Ogston model is incorporated in a user-friendly program, GRADFIT, which is designed for personal computers (Macintosh). The results obtained are compared with (1) conventional electrophoresis using several gels of single concentration with and without Nycodenz, and (ii) a different mathematical approach for the analysis of gradient gels (Rodbard et al., Anal. Biochem. 1971, 40, 135-157). Moreover, a simple procedure for evaluating linear pore gradient gels using linear regression analysis is presented. It is concluded that the values of particle-free mobility and retardation coefficient derived from pore gradient gel electrophoresis using the different mathematical methods are statistically indistinguishable from each other. However, these values are different, albeit close, to those obtained from

  4. Agarose template for the fabrication of macroporous metal oxide structures.

    PubMed

    Zhou, Jingfang; Zhou, Meifang; Caruso, Rachel A

    2006-03-28

    Agarose gels have been applied as templates for the formation of macroporous metal oxide structures. The preparation of the agarose template is extremely simple, and with variation of the agarose content, control over morphology is demonstrated: The average pore size decreases from 180 to 55 nm and the surface area increases from 238 to 271 m2 g(-1) with increasing agarose content in the gel. The gelling temperature was also found to influence the final template morphology. Conducting sol-gel chemistry within the template structure followed by removal of the template by heating to 450 degrees C gives porous inorganic oxides. The technique has been demonstrated for the oxides of titanium, zirconium, niobium, and tin. The final morphology of the metal oxide is homogeneous and results from a coating of the agarose structure. The pore diameter decreased and the specific surface area of the titanium dioxide materials increased from 28 to 66 m2 g(-1) as the agarose content in the template is increased from 0.5 to 5.0 wt%. The overall pore size and surface area are lower than the original gel due to shrinkage occurring with the sol-gel process, as well as crystallization and a loss of microporosity in the final material.

  5. An agarose gel electrophoretic method for analysis of hyaluronan molecular weight distribution.

    PubMed

    Lee, H G; Cowman, M K

    1994-06-01

    An electrophoretic method is described for determining the molecular weight distribution of hyaluronan (HA). The method involves separation of HA by electrophoresis on a 0.5% agarose gel, followed by detection of HA using the cationic dye Stains-All (3,3'-dimethyl-9-methyl-4,5,4'5'-dibenzothiacarbocyanine). The recommended sample load is 7 micrograms. Calibration of the method with HA standards of known molecular weight has established a linear relationship between electrophoretic mobility and the logarithm of the weight-average molecular weight over the range of approximately 0.2-6 x 10(6). The separated HA pattern may also be visualized after electrotransfer of HA from the agarose gel to a nylon membrane. The membrane may be stained with the dye alcian blue. Alternatively, specific detection of HA from impure samples can be achieved by probing the nylon membrane with biotin-labeled HA-binding protein and subsequent interaction with a streptavidin-linked gold reagent and silver staining for amplification. The electrophoretic method was used to analyze HA in two different liquid connective tissues. Normal human knee joint synovial fluid showed a narrow HA molecular weight distribution, with a peak at 6-7 x 10(6). Owl monkey vitreous HA also showed a narrow molecular weight distribution, with a peak at 5-6 x 10(6). These results agree well with available published data and indicate the applicability of the method to the analysis of impure HA samples which may be available in limited amounts.

  6. Improved Characterization of Groundwater Flow in Heterogeneous Aquifers Using Granular Polyacrylamide (PAM) Gel as Temporary Grout

    NASA Astrophysics Data System (ADS)

    Klepikova, Maria V.; Roques, Clement; Loew, Simon; Selker, John

    2018-02-01

    The range of options for investigation of hydraulic behavior of aquifers from boreholes has been limited to rigid, cumbersome packers, and inflatable sleeves. Here we show how a new temporary borehole sealing technique using soft grains of polyacrylamide (PAM) gel as a sealing material can be used to investigate natural groundwater flow dynamics and discuss other possible applications of the technology. If no compressive stress is applied, the gel packing, with a permeability similar to open gravel, suppresses free convection, allowing for local temperature measurements and chemical sampling through free-flowing gel packing. Active heating laboratory and field experiments combined with temperature measurements along fiber optic cables were conducted in water-filled boreholes and boreholes filled with soft grains of polyacrylamide gel. The gel packing is shown to minimize the effect of free convection within the well column and enable detection of thin zones of relatively high or low velocity in a highly transmissive alluvial aquifer, thus providing a significant improvement compared to temperature measurements in open boreholes. Laboratory experiments demonstrate that under modest compressive stress to the gel media the permeability transitions from highly permeable to nearly impermeable grouting. Under this configuration the gel packing could potentially allow for monitoring local response pressure from the formation with all other locations in the borehole hydraulically isolated.

  7. Direct detection of rutin-degrading isozymes with polyacrylamide gel electrophoresis.

    PubMed

    Li, Yuping; Deng, Dandan; Zhang, Xuebin; Zhang, Haina; Wang, Cong; Chen, Peng

    2013-12-15

    Rutin-degrading enzymes (RDEs) specifically hydrolyze the glycosidic linkages of rutin, producing quercetin and rutinose. Here we report a reliable and sensitive polyacrylamide gel electrophoresis and staining method for the detection of RDE isozymes, which is based on the aqueous solubility difference between rutin and quercetin, as well as the ultraviolet absorbance of quercetin. With this novel method, we achieved a detection limit of 12 ng with 107 U of RDE activity, enabling us to detect at least five RDE isozymes in tartary buckwheat seeds. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Enhanced mixing in polyacrylamide gels containing embedded silica nanoparticles as internal electroosmotic pumps.

    PubMed

    Matos, Marvi A; White, Lee R; Tilton, Robert D

    2008-02-15

    Many biosensors, including those based on sensing agents immobilized inside hydrogels, suffer from slow response dynamics due to mass transfer limitations. Here we present an internal pumping strategy to promote convective mixing inside crosslinked polymer gels. This is envisioned as a potential tool to enhance biosensor response dynamics. The method is based on electroosmotic flows driven by non-uniform, oscillating electric fields applied across a polyacrylamide gel that has been doped with charged colloidal silica inclusions. Evidence for enhanced mixing was obtained from florescence recovery after photobleaching (FRAP) measurements with fluorescein tracer dyes dissolved in the gel. Mixing rates in silica-laden gels under the action of the applied electric fields were more than an order of magnitude faster than either diffusion or electrophoretically driven mixing in gels that did not contain silica. The mixing enhancement was due in comparable parts to the electroosmotic pumping and to the increase in gel swelling caused by the presence of the silica inclusions. The latter had the effect of increasing tracer mobility in the silica-laden gels.

  9. Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.

    PubMed

    Nguyen, Phi-Vu; Ghezal, Ali; Hsueh, Ya-Chih; Boudier, Thomas; Gan, Samuel Ken-En; Lee, Hwee Kuan

    2016-08-01

    In biomedical research, gel band size estimation in electrophoresis analysis is a routine process. To facilitate and automate this process, numerous software have been released, notably the GelApp mobile app. However, the band detection accuracy is limited due to a band detection algorithm that cannot adapt to the variations in input images. To address this, we used the Monte Carlo Tree Search with Upper Confidence Bound (MCTS-UCB) method to efficiently search for optimal image processing pipelines for the band detection task, thereby improving the segmentation algorithm. Incorporating this into GelApp, we report a significant enhancement of gel band detection accuracy by 55.9 ± 2.0% for protein polyacrylamide gels, and 35.9 ± 2.5% for DNA SYBR green agarose gels. This implementation is a proof-of-concept in demonstrating MCTS-UCB as a strategy to optimize general image segmentation. The improved version of GelApp-GelApp 2.0-is freely available on both Google Play Store (for Android platform), and Apple App Store (for iOS platform). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Platelet-rich plasma combined with agarose as a bioactive scaffold to enhance cartilage repair: an in vitro study.

    PubMed

    Yin, Zhaowei; Yang, Xiaofei; Jiang, Yiqiu; Xing, Linzi; Xu, Yang; Lu, Yiming; Ding, Peng; Ma, Junxin; Xu, Yan; Gui, Jianchao

    2014-03-01

    The purpose of this study was to determine whether the platelet-rich plasma-agarose gel scaffold could be a bioactive scaffold capable of growth factors release for cartilage repair. Porcine chondrocytes were seeded in agarose gel and platelet-rich plasma-agarose gel. During the 28-days culture, microstructure of hydrogels and morphologies of chondrocytes seeded in the hydrogels were observed using scanning electron microscope; viability of chondrocytes in gels was examined by live/dead assay; qualitative and quantitative analysis of glycosaminoglycan, collagen and DNA were assessed by histological, immunohistochemical staining and biochemical assay; gene expression was measured by real-time polymerase chain reaction. In vitro cartilage ring models were used to evaluate the integration of the scaffolds, and the integration strength was analyzed by mechanical push-out tests. Scanning electron microscope revealed both scaffolds had highly uniform porous structure. Live/dead scaffolds showed 100% cells alive in both groups. After 28-days culture, glycosaminoglycan, collagen, DNA content and chondrocyte-related genes expression in platelet-rich plasma-agarose gel were significantly higher than pure agarose gel. Integration strength in platelet-rich plasma-agarose gel was also higher compared to pure agarose gel. Platelet-rich plasma showed a positive effect on chondrocytes proliferation, differentiation and integration between native cartilage and engineered tissue when combined with agarose gel. Our findings suggest that platelet-rich plasma-agarose gel scaffold is a promising bioactive scaffold for future cartilage tissue engineering and future clinical works.

  11. Analysis of Endonuclease R·EcoRI Fragments of DNA from Lambdoid Bacteriophages and Other Viruses by Agarose-Gel Electrophoresis

    PubMed Central

    Helling, Robert B.; Goodman, Howard M.; Boyer, Herbert W.

    1974-01-01

    By means of agarose-gel electrophoresis, endonuclease R·EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, φ80, and hybrid phages were constructed. Images PMID:4372397

  12. Wheat gliadin: digital imaging and database construction using a 4-band reference system of agarose isoelectric focusing patterns.

    PubMed

    Black, J A; Waggamon, K A

    1992-01-01

    An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.

  13. Performing Isoelectric Focusing and Simultaneous Fractionation of Proteins on A Rotary Valve Followed by Sodium Dodecyl – Polyacrylamide Gel Electrophoresis

    PubMed Central

    Wang, Wei; Lu, Joann J.; Gu, Congying; Zhou, Lei; Liu, Shaorong

    2013-01-01

    In this technical note, we design and fabricate a novel rotary valve and demonstrate its feasibility for performing isoelectric focusing and simultaneous fractionation of proteins, followed by sodium dodecyl – polyacrylamide gel electrophoresis. The valve has two positions. In one position, the valve routes a series of capillary loops together into a single capillary tube where capillary isoelectric focusing (CIEF) is performed. By switching the valve to another position, the CIEF-resolved proteins in all capillary loops are isolated simultaneously, and samples in the loops are removed and collected in vials. After the collected samples are briefly processed, they are separated via sodium dodecyl – polyacrylamide gel electrophoresis (SDS-PAGE, the 2nd-D separation) on either a capillary gel electrophoresis instrument or a slab-gel system. The detailed valve configuration is illustrated, and the experimental conditions and operation protocols are discussed. PMID:23819755

  14. DNA electrophoresis in agarose gels: effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length.

    PubMed

    Rill, Randolph L; Beheshti, Afshin; Van Winkle, David H

    2002-08-01

    Electrophoretic mobilities of DNA molecules ranging in length from 200 to 48 502 base pairs (bp) were measured in agarose gels with concentrations T = 0.5% to 1.3% at electric fields from E = 0.71 to 5.0 V/cm. This broad data set determines a range of conditions over which the new interpolation equation nu(L) = (beta+alpha(1+exp(-L/gamma))(-1) can be used to relate mobility to length with high accuracy. Mobility data were fit with chi(2) > 0.999 for all gel concentrations and fields ranging from 2.5 to 5 V/cm, and for lower fields at low gel concentrations. Analyses using so-called reptation plots (Rousseau, J., Drouin, G., Slater, G. W., Phys. Rev. Lett. 1997, 79, 1945-1948) indicate that this simple exponential relation is obeyed well when there is a smooth transition from the Ogston sieving regime to the reptation regime with increasing DNA length. Deviations from this equation occur when DNA migration is hindered, apparently by entropic-trapping, which is favored at low fields and high gel concentrations in the ranges examined.

  15. Application of polyacrylamide gel as a new membrane in electromembrane extraction for the quantification of basic drugs in breast milk and wastewater samples.

    PubMed

    Asadi, Sakine; Tabani, Hadi; Nojavan, Saeed

    2018-03-20

    Introducing new membranes with green chemistry approach seems to be a great challenge for the development of a practical method in separation science. In this regard, for the first time, polyacrylamide gel as a new membrane in electromembrane extraction (EME) was used for the extraction of three model basic drugs (pseudoephedrine (PSE), lidocaine (LID), and propranolol (PRO)), followed by HPLC-UV. In comparison with conventional EME, in this method neither organic solvent nor carrier agents were used for extraction of mentioned drugs. Different variables for fabrication of polyacrylamide gel and extraction process were evaluated. Polyacrylamide gel (containing 12% (w/v) acrylamide, and 3.0% (w/w) bisacrylamide) with 2 mm thickness at pH = 1.5 was fabricated as membrane. The drugs were extracted from aqueous samples, through a polyacrylamide gel membrane, to an aqueous acceptor phase on membrane. Under the optimized extraction conditions (Voltage: 85 V, extraction time: 28 min, acceptor phase's pH: 4.0, and donor phase's pH: 7.0) limits of quantification and detection were in the ranges of 1.0-20.0 ng mL -1 and 0.3-6.0 ng mL -1 , respectively. Applying the proposed method to determine and quantify intended drugs in breast milk, and wastewater samples have revealed acceptable results. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Fiber based optical tweezers for simultaneous in situ force exertion and measurements in a 3D polyacrylamide gel compartment.

    PubMed

    Ti, Chaoyang; Thomas, Gawain M; Ren, Yundong; Zhang, Rui; Wen, Qi; Liu, Yuxiang

    2015-07-01

    Optical tweezers play an important role in biological applications. However, it is difficult for traditional optical tweezers based on objective lenses to work in a three-dimensional (3D) solid far away from the substrate. In this work, we develop a fiber based optical trapping system, namely inclined dual fiber optical tweezers, that can simultaneously apply and measure forces both in water and in a 3D polyacrylamide gel matrix. In addition, we demonstrate in situ, non-invasive characterization of local mechanical properties of polyacrylamide gel by measurements on an embedded bead. The fiber optical tweezers measurements agree well with those of atomic force microscopy (AFM). The inclined dual fiber optical tweezers provide a promising and versatile tool for cell mechanics study in 3D environments.

  17. A Novel Technique for Micro-patterning Proteins and Cells on Polyacrylamide Gels

    PubMed Central

    Tang, Xin; Ali, M. Yakut; Saif, M. Taher A.

    2012-01-01

    Spatial patterning of proteins (extracellular matrix, ECM) for living cells on polyacrylamide (PA) hydrogels has been technically challenging due to the compliant nature of the hydrogels and their aqueous environment. Traditional micro-fabrication process is not applicable. Here we report a simple, novel and general method to pattern a variety of commonly used cell adhesion molecules, i.e. Fibronectin (FN), Laminin (LN) and Collagen I (CN), etc. on PA gels. The pattern is first printed on a hydrophilic glass using polydimethylsiloxane (PDMS) stamp and micro-contact printing (μCP). Pre-polymerization solution is applied on the patterned glass and is then sandwiched by a functionalized glass slide, which covalently binds to the gel. The hydrophilic glass slide is then peeled off from the gel when the protein patterns detach from the glass, but remain intact with the gel. The pattern is thus transferred to the gel. The mechanism of pattern transfer is studied in light of interfacial mechanics. It is found that hydrophilic glass offers strong enough adhesion with ECM proteins such that a pattern can be printed, but weak enough adhesion such that they can be completely peeled off by the polymerized gel. This balance is essential for successful pattern transfer. As a demonstration, lines of FN, LN and CN with widths varying from 5–400 μm are patterned on PA gels. Normal fibroblasts (MKF) are cultured on the gel surfaces. The cell attachment and proliferation are confined within these patterns. The method avoids the use of any toxic chemistry often used to pattern different proteins on gel surfaces. PMID:23002394

  18. Molecular mass determination and assay of venom hyaluronidases by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

    PubMed

    Cevallos, M A; Navarro-Duque, C; Varela-Julia, M; Alagon, A C

    1992-08-01

    We describe a procedure for molecular mass determination of hyaluronidases present in animal venoms from different families. Hyaluronidases can be revealed, following their electrophoretic separation in sodium dodecyl sulfate-polyacrylamide gel containing hyaluronic acid, by incubating the gel in Triton X-100 to remove sodium dodecyl sulfate and restore in situ enzyme activity. This method allows the detection of as little as 0.025 turbidity-reducing units after 2 hr incubation. All the hyaluronidases from the analyzed invertebrate venoms had a mass below 50,000 and showed only one component, while those from vertebrate venoms were more than 60,000 and in many instances contained more than one form.

  19. Scalable lithography from Natural DNA Patterns via polyacrylamide gel

    NASA Astrophysics Data System (ADS)

    Qu, Jiehao; Hou, Xianliang; Fan, Wanchao; Xi, Guanghui; Diao, Hongyan; Liu, Xiangdon

    2015-12-01

    A facile strategy for fabricating scalable stamps has been developed using cross-linked polyacrylamide gel (PAMG) that controllably and precisely shrinks and swells with water content. Aligned patterns of natural DNA molecules were prepared by evaporative self-assembly on a PMMA substrate, and were transferred to unsaturated polyester resin (UPR) to form a negative replica. The negative was used to pattern the linear structures onto the surface of water-swollen PAMG, and the pattern sizes on the PAMG stamp were customized by adjusting the water content of the PAMG. As a result, consistent reproduction of DNA patterns could be achieved with feature sizes that can be controlled over the range of 40%-200% of the original pattern dimensions. This methodology is novel and may pave a new avenue for manufacturing stamp-based functional nanostructures in a simple and cost-effective manner on a large scale.

  20. Accommodating brightness and exposure levels in densitometry of stained polyacrylamide electrophoresis gels

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tan, Han Yen; Ng, Tuck Wah; Liew, Oi Wah

    2010-03-20

    Flatbed scanner densitometers can be operated under various illumination and recording exposure levels. In this work, we show that optical density measurement accuracy, sensitivity, and stability of stained polyacrylamide electrophoresis gel densitometry are crucially dependent on these two factors (brightness and exposure level), notwithstanding that the source is monochromatic, spatially uniform, and the measurements are made using an accurately calibrated step wedge in tandem. We further outline a method to accommodate the intensity deviations over a range of illumination and exposure levels in order to maintain sensitivity and repeatability in the computed optical densities. Comparisons were also made with resultsmore » from a commercial densitometer.« less

  1. Measurement of the ferric diffusion coefficient in agarose and gelatine gels by utilization of the evolution of a radiation induced edge as reflected in relaxation rate images.

    PubMed

    Pedersen, T V; Olsen, D R; Skretting, A

    1997-08-01

    A method has been developed to determine the diffusion coefficients of ferric ions in ferrous sulphate doped gels. A radiation induced edge was created in the gel, and two spin-echo sequences were used to acquire a pair of images of the gel at different points of time. For each of these image pairs, a longitudinal relaxation rate image was derived. From profiles through these images, the standard deviations of the Gaussian functions that characterize diffusion were determined. These data provided the basis for the determination of the ferric diffusion coefficients by two different methods. Simulations indicate that the use of single spin-echo images in this procedure may in some cases lead to a significant underestimation of the diffusion coefficient. The technique was applied to different agarose and gelatine gels that were prepared, irradiated and imaged simultaneously. The results indicate that the diffusion coefficient is lower in a gelatine gel than in an agarose gel. Addition of xylenol orange to a gelatine gel lowers the diffusion coefficient from 1.45 to 0.81 mm2 h-1, at the cost of significantly lower Rl sensitivity. The addition of benzoic acid to the latter gel did not increase the Rl sensitivity.

  2. Interactions of trace metals with hydrogels and filter membranes used in DET and DGT techniques.

    PubMed

    Garmo, Oyvind A; Davison, William; Zhang, Hao

    2008-08-01

    Equilibrium partitioning of trace metals between bulk solution and hydrogels/filter was studied. Under some conditions, trace metal concentrations were higher in the hydrogels or filter membranes compared to bulk solution (enrichment). In synthetic soft water, enrichment of cationic trace metals in polyacrylamide hydrogels decreased with increasing trace metal concentration. Enrichment was little affected by Ca and Mg in the concentration range typically encountered in natural freshwaters, indicating high affinity but low capacity binding of trace metals to solid structure in polyacrylamide gels. The apparent binding strength decreased in the sequence: Cu > Pb > Ni approximately to Cd approximately to Co and a low concentration of cationic Cu eliminated enrichment of weakly binding trace metal cations. The polyacrylamide gels also had an affinity for fulvic acid and/or its trace metal complexes. Enrichment of cationic Cd in agarose gel and hydrophilic polyethersulfone filter was independent of concentration (10 nM to 5 microM) but decreased with increasing Ca/ Mg concentration and ionic strength, suggesting that it is mainly due to electrostatic interactions. However, Cu and Pb were enriched even after equilibration in seawater, indicating that these metals additionally bind to sites within the agarose gel and filter. Compared to the polyacrylamide gels, agarose gel had a lower affinity for metal-fulvic complexes. Potential biases in measurements made with the diffusive equilibration in thin-films (DET) technique, identified by this work, are discussed.

  3. Electro-driven extraction of polar compounds using agarose gel as a new membrane: Determination of amino acids in fruit juice and human plasma samples.

    PubMed

    Sedehi, Samira; Tabani, Hadi; Nojavan, Saeed

    2018-03-01

    In this work, polypropylene hollow fiber was replaced by agarose gel in conventional electro membrane extraction (EME) to develop a novel approach. The proposed EME method was then employed to extract two amino acids (tyrosine and phenylalanine) as model polar analytes, followed by HPLC-UV. The method showed acceptable results under optimized conditions. This green methodology outperformed conventional EME, and required neither organic solvents nor carriers. The effective parameters such as the pH values of the acceptor and the donor solutions, the thickness and pH of the gel, the extraction voltage, the stirring rate, and the extraction time were optimized. Under the optimized conditions (acceptor solution pH: 1.5; donor solution pH: 2.5; agarose gel thickness: 7mm; agarose gel pH: 1.5; stirring rate of the sample solution: 1000rpm; extraction potential: 40V; and extraction time: 15min), the limits of detection and quantification were 7.5ngmL -1 and 25ngmL -1 , respectively. The extraction recoveries were between 56.6% and 85.0%, and the calibration curves were linear with correlation coefficients above 0.996 over a concentration range of 25.0-1000.0ngmL -1 for both amino acids. The intra- and inter-day precisions were in the range of 5.5-12.5%, and relative errors were smaller than 12.0%. Finally, the optimized method was successfully applied to preconcentrate, clean up, and quantify amino acids in watermelon and grapefruit juices as well as a plasma sample, and acceptable relative recoveries in the range of 53.9-84.0% were obtained. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Macroporous polyacrylamide monolithic gels with immobilized metal affinity ligands: the effect of porous structure and ligand coupling chemistry on protein binding.

    PubMed

    Plieva, Fatima; Bober, Beata; Dainiak, Maria; Galaev, Igor Yu; Mattiasson, Bo

    2006-01-01

    Macroporous polyacrylamide gels (MPAAG) with iminodiacetic acid (IDA) functionality were prepared by (i) chemical modification of polyacrylamide gel, (ii) co-polymerization of acrylamide with allyl glycidyl ether (AGE) and N,N'metylene-bis(acrylamide) (MBAAm) followed by coupling IDA ligand or (iii) by copolymerization of acrylamide and MBAAm with functional monomer carrying IDA-functionality (1-(N,N-bis(carboxymethyl)amino-3-allylglycerol). Screening for optimized conditions for the production of the MPAAG with required porous properties was performed in a 96-well chromatographic format that allowed parallel production and analysis of the MPAAG prepared from reaction mixtures with different compositions. Scanning electron microscopy of the fabricated MPAAG revealed two different types of the porous structures: monomodal macroporous structure with large interconnected pores separated by dense non-porous pore walls in case of plain gels or gels produced via copolymerization with AGE. The other type of the MPAAG (gel produced via co-polymerization with functional monomer carrying IDA-functionality) had bimodal pore structure with large interconnected pores separated by the pore walls pierced through with micropores. The effect of different modifications of MPAAG monoliths and of porous structure of the MPAAG (monomodal and bimodal porous structure) on protein binding has been evaluated. Copyright 2006 John Wiley & Sons, Ltd.

  5. Agarose gel electrophoresis of joint fluid using Hyrys-Hydrasys SEBIA system as a new prognostic tool for periprosthetic osteolysisin revision arthroplasty

    PubMed Central

    Chiva, A

    2013-01-01

    Rationale. Prevention of wear-mediated osteolysis, the most common complication in total joint arthroplasty, is a great challenge for orthopedic surgery. Despite the diversity of current biomarkers of periprosthetic osteolysis (products of wear, bone turnover and inflammatory biomarkers), the major interferences and the great amount of sample necessary for analysis limit their use in clinical practice. Objective. The aim of this paper is to present three new electrophoretic methods using Hyrys-Hydrasys SEBIA system that have been used for the first time in Electrophoresis Laboratory of our hospital in the analysis of joint fluid for the prevention of periprosthetic osteolysis in revision arthroplasty. Methods and results. Analytical aspects of agarose gel electrophoresis of joint fluid proteins and lipoproteins as well as SDS-agarose gel electrophoresis of joint fluid proteins, their performances and clinical value are presented. The decreased level of albumin and increased level of alpha1 and alpha2 globulins were frequent changes detected on SEBIA electropherograms and good indicator for the presence of an inflammatory reaction generated by particle debris. In addition, a slightly increase of LDL mobility could provide good information about a high oxidative stress. Moreover, the Ig G assessed by using SDS-agarose gel electrophoresis could be a potential biomarker for an immunological reaction towards orthopedic implants. Discussion. Electrophoresis of joint fluid using Hyrys-Hydrasys SEBIA France system is a new analytical technique able to remove the most of current biomarkers disadvantages due to the determination of particular proteins (acute phase proteins, albumin, lipoproteins, and immunoglobulins) by using minimal amounts of joint fluid with minor interferences, minimal cost and rapid results. Abbreviations CTX, crosslinked C-telopeptide; IL- interleukins; Ig G, immunoglobulin G; LDL, low density lipoprotein; NTX, crosslinked N-telopeptide; PICP

  6. Thermal lens and all optical switching of new organometallic compound doped polyacrylamide gel

    NASA Astrophysics Data System (ADS)

    Badran, Hussain Ali

    In this work thermal lens spectrometry (TLS) is applied to investigate the thermo-optical properties of new organometallic compound containing azomethine group, Dichloro bis [2-(2-hydroxybenzylideneamino)-5-methylphenyl] telluride platinum(II), doped polyacrylamide gel using transistor-transistor logic (TTL) modulated cw 532 nm laser beam as an excitation beam modulated at 10 Hz frequency and probe beam wavelength 635 nm at 14 mW. The technique is applied to determine the thermal diffusivities, ds/dT and the linear thermal expansion coefficient of the sample. All-optical switching effects with low background and high stability are demonstrated.

  7. Room temperature synthesis of agarose/sol-gel glass pieces with tailored interconnected porosity.

    PubMed

    Cabañas, M V; Peña, J; Román, J; Vallet-Regí, M

    2006-09-01

    An original shaping technique has been applied to prepare porous bodies at room temperature. Agarose, a biodegradable polysaccharide, was added as binder of a sol-gel glass in powder form, yielding an easy to mold paste. Interconnected tailored porous bodies can be straightforwardly prepared by pouring the slurry into a polymeric scaffold, previously designed by stereolitography, which is subsequently eliminated by alkaline dissolution at room temperature. The so obtained pieces behave like a hydrogel with an enhanced consistency that makes them machinable and easy to manipulate. These materials generate an apatite-like layer when immersed in a simulated body fluid, indicating a potential in vivo bioactivity. The proposed method can be applied to different powdered materials to produce pieces, at room temperature, with various shapes and sizes and with tailored interconnected porosity.

  8. Fabrication of Self-Healable and Patternable Polypyrrole/Agarose Hybrid Hydrogels for Smart Bioelectrodes.

    PubMed

    Park, Nokyoung; Chae, Seung Chul; Kim, Il Tae; Hur, Jaehyun

    2016-02-01

    We present a new class of electrically conductive, mechanically moldable, and thermally self-healable hybrid hydrogels. The hybrid gels consist of polypyrrole and agarose as the conductive component and self-healable matrix, respectively. By using the appropriate oxidizing agent under conditions of mild temperature, the polymerization of pyrrole occurred along the three-dimensional network of the agarose hydrogel matrix. In contrast to most commercially available hydrogels, the physical crosslinking of agarose gel allows for reversible gelation in the case of our hybrid gel, which could be manipulated by temperature variation, which controls the electrical on/off behavior of the hybrid gel electrode. Exploiting this property, we fabricated a hybrid conductive hydrogel electrode which also self-heals thermally. The novel composite material we report here will be useful for many technological and biological applications, especially in reactive biomimetic functions and devices, artificial muscles, smart membranes, smart full organic batteries, and artificial chemical synapses.

  9. A rapid method to visualize von willebrand factor multimers by using agarose gel electrophoresis, immunolocalization and luminographic detection.

    PubMed

    Krizek, D R; Rick, M E

    2000-03-15

    A highly sensitive and rapid clinical method for the visualization of the multimeric structure of von Willebrand Factor in plasma and platelets is described. The method utilizes submerged horizontal agarose gel electrophoresis, followed by transfer of the von Willebrand Factor onto a polyvinylidine fluoride membrane, and immunolocalization and luminographic visualization of the von Willebrand Factor multimeric pattern. This method distinguishes type 1 from types 2A and 2B von Willebrand disease, allowing timely evaluation and classification of von Willebrand Factor in patient plasma. It also allows visualization of the unusually high molecular weight multimers present in platelets. There are several major advantages to this method including rapid processing, simplicity of gel preparation, high sensitivity to low concentrations of von Willebrand Factor, and elimination of radioactivity.

  10. Intrinsic protein fluorescence interferes with detection of tear glycoproteins in SDS-polyacrylamide gels using extrinsic fluorescent dyes.

    PubMed

    Zhao, Zhenjun; Aliwarga, Yulina; Willcox, Mark D P

    2007-12-01

    Intrinsic protein fluorescence may interfere with the visualization of proteins after SDS-polyacrylamide electrophoresis. In an attempt to analyze tear glycoproteins in gels, we ran tear samples and stained the proteins with a glycoprotein-specific fluorescent dye. The fluorescence detected was not limited to glycoproteins. There was strong intrinsic fluorescence of proteins normally found in tears after soaking the gels in 40% methanol plus 1-10% acetic acid and, to a lesser extent, in methanol or acetic acid alone. Nanograms of proteins gave visible native fluorescence and interfere with extrinsic fluorescent dye detection. Poly-L-lysine, which does not contain intrinsically fluorescent amino acids, did not fluoresce.

  11. Intrinsic Protein Fluorescence Interferes with Detection of Tear Glycoproteins in SDS-Polyacrylamide Gels Using Extrinsic Fluorescent Dyes

    PubMed Central

    Zhao, Zhenjun; Aliwarga, Yulina; Willcox, Mark DP

    2007-01-01

    Intrinsic protein fluorescence may interfere with the visualization of proteins after SDS-polyacrylamide electrophoresis. In an attempt to analyze tear glycoproteins in gels, we ran tear samples and stained the proteins with a glycoprotein-specific fluorescent dye. The fluorescence detected was not limited to glycoproteins. There was strong intrinsic fluorescence of proteins normally found in tears after soaking the gels in 40% methanol plus 1–10% acetic acid and, to a lesser extent, in methanol or acetic acid alone. Nanograms of proteins gave visible native fluorescence and interfere with extrinsic fluorescent dye detection. Poly-L-lysine, which does not contain intrinsically fluorescent amino acids, did not fluoresce. PMID:18166676

  12. Evaluation of agarose gel electrophoresis for characterization of silver nanoparticles in industrial products.

    PubMed

    Jimenez, Maria S; Luque-Alled, Jose M; Gomez, Teresa; Castillo, Juan R

    2016-05-01

    Agarose gel electrophoresis (AGE) has been used extensively for characterization of pure nanomaterials or mixtures of pure nanomaterials. We have evaluated the use of AGE for characterization of Ag nanoparticles (NPs) in an industrial product (described as strong antiseptic). Influence of different stabilizing agents (PEG, SDS, and sodium dodecylbenzenesulfonate), buffers (TBE and Tris Glycine), and functionalizing agents (mercaptosuccinic acid (TMA) and proteins) has been investigated for the characterization of AgNPs in the industrial product using different sizes-AgNPs standards. The use of 1% SDS, 0.1% TMA, and Tris Glycine in gel, electrophoresis buffer and loading buffer led to the different sizes-AgNPs standards moved according to their size/charge ratio (obtaining a linear relationship between apparent mobility and mean diameter). After using SDS and TMA, the behavior of the AgNPs in the industrial product (containing a casein matrix) was completely different, being not possible their size characterization. However we demonstrated that AGE with LA-ICP-MS detection is an alternative method to confirm the protein corona formation between the industrial product and two proteins (BSA and transferrin) maintaining NPs-protein binding (what is not possible using SDS-PAGE). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Analysis of polypeptide composition and antigenic components of Rickettsia tsutsugamushi by polyacrylamide gel electrophoresis and immunoblotting.

    PubMed Central

    Tamura, A; Ohashi, N; Urakami, H; Takahashi, K; Oyanagi, M

    1985-01-01

    Polyacrylamide gel electrophoresis of lysates of purified Rickettsia tsutsugamushi revealed as many as 30 polypeptide bands, including major bands corresponding to molecular sizes of 70, 60, 54 to 56, and 46 to 47 kilodaltons. Compared with the polypeptide composition of the rickettsiae of Gilliam, Karp, and Kato strains and a newly isolated Shimokoshi strain, the major polypeptide in the Kato strain (54-56K) and in the Karp strain (46-47K) migrated a little faster and slower, respectively, than the corresponding polypeptides in the other strains. The largest major polypeptide (54-56K) was digestible by the treatment of intact rickettsiae with trypsin and variable in content in separate preparations, suggesting that the polypeptide exists on the rickettsial surface and is easily degraded during the handling of these microorganisms. Several surface polypeptides of rickettsiae, including the 54-56K and 46-47K polypeptides, were detected by radioiodination of intact rickettsiae followed by polyacrylamide gel electrophoresis of the lysate; however, the 70K and 60K polypeptides were not labeled. Immunoblotting experiments with hyperimmune sera prepared in guinea pigs against each strain demonstrated that the 70K, 54-56K, and 46-47K polypeptides showed antigenic activities. The 54-56K polypeptide appeared to be strain specific, whereas the 70K and 46-47K polypeptides cross-reacted with the heterologous antisera. Images PMID:3922893

  14. Study of kinetic desorption rate constant in fish muscle and agarose gel model using solid phase microextraction coupled with liquid chromatography with tandem mass spectrometry.

    PubMed

    Togunde, Oluranti Paul; Oakes, Ken; Servos, Mark; Pawliszyn, Janusz

    2012-09-12

    This study aims to use solid phase microextraction (SPME), a simple tool to investigate diffusion rate (time) constant of selected pharmaceuticals in gel and fish muscle by comparing desorption rate of diffusion of the drugs in both agarose gel prepared with phosphate-buffered saline (PBS; pH 7.4) and fish muscle. The gel concentration (agarose gel model) that could be used to simulate tissue matrix (fish muscle) for free diffusion of drugs under in vitro and in vivo conditions was determined to model mass transfer phenomena between fibre polymer coating and environmental matrix such that partition coefficients and desorption time constant (diffusion coefficient) can be determined. SPME procedure involves preloading the extraction phase (fibre) with the standards from spiked PBS for 1h via direct extraction. Subsequently, the preloaded fibre is introduced to the sample such fish or agarose gel for specified time ranging from 0.5 to 60 h. Then, fibre is removed at specified time and desorbed in 100 μL of desorption solution (acetonitrile: water 1:1) for 90 min under agitation speed of 1000 rpm. The samples extract were immediately injected to the instrument and analysed using liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS). The limit of detection of the method in gel and fish muscle was 0.01-0.07 ng mL(-1) and 0.07-0.34 ng g(-1), respectively, while the limit quantification was 0.10-0.20 ng mL(-1) in gel samples and 0.40-0.97 ng g(-1) in fish sample. The reproducibility of the method was good (5-15% RSD). The results suggest that kinetics of desorption of the compounds in fish tissue and different viscosity of gel can be determined using desorption time constant. In this study, desorption time constant which is directly related to desorption rate (diffusion kinetics) of selected drugs from the fibre to the gel matrix is faster as the viscosity of the gel matrix reduces from 2% (w/v) to 0.8% (w/v). As the concentration of gel reduces

  15. Agarose droplet microfluidics for highly parallel and efficient single molecule emulsion PCR.

    PubMed

    Leng, Xuefei; Zhang, Wenhua; Wang, Chunming; Cui, Liang; Yang, Chaoyong James

    2010-11-07

    An agarose droplet method was developed for highly parallel and efficient single molecule emulsion PCR. The method capitalizes on the unique thermoresponsive sol-gel switching property of agarose for highly efficient DNA amplification and amplicon trapping. Uniform agarose solution droplets generated via a microfluidic chip serve as robust and inert nanolitre PCR reactors for single copy DNA molecule amplification. After PCR, agarose droplets are gelated to form agarose beads, trapping all amplicons in each reactor to maintain the monoclonality of each droplet. This method does not require cocapsulation of primer labeled microbeads, allows high throughput generation of uniform droplets and enables high PCR efficiency, making it a promising platform for many single copy genetic studies.

  16. Agarose coated spherical micro resonator for humidity measurements.

    PubMed

    Mallik, Arun Kumar; Liu, Dejun; Kavungal, Vishnu; Wu, Qiang; Farrell, Gerald; Semenova, Yuliya

    2016-09-19

    A new type of fiber optic relative humidity (RH) sensor based on an agarose coated silica microsphere resonator is proposed and experimentally demonstrated. Whispering gallery modes (WGMs) in the micro resonator are excited by evanescent coupling using a tapered fiber with ~3.3 µm waist diameter. A change in the relative humidity of the surrounding the resonator air induces changes in the refractive index (RI) and thickness of the Agarose coating layer. These changes in turn lead to a spectral shift of the WGM resonances, which can be related to the RH value after a suitable calibration. Studies of the repeatability, long-term stability, measurement accuracy and temperature dependence of the proposed sensor are carried out. The RH sensitivity of the proposed sensor depends on the concentration of the agarose gel which determines the initial thickness of the deposited coating layer. Studies of the micro- resonators with coating layers fabricated from gels with three different Agarose concentrations of 0.5%, 1.125% and 2.25 wt./vol.% showed that an increase in the initial thickness of the coating material results in an increase in sensitivity but also leads to a decrease of quality factor (Q) of the micro resonator. The highest sensitivity achieved in our experiments was 518 pm/%RH in the RH range from 30% to 70%. The proposed sensor offers the advantages of a very compact form factor, low hysteresis, good repeatability, and low cross sensitivity to temperature.

  17. Disaggregation of adenylate cyclase during polyacrylamide-gel electrophoresis in mixtures of ionic and non-ionic detergents.

    PubMed

    Newby, A C; Chrambach, A

    1979-02-01

    1. Adenylate cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] solubilized from the rat liver plasma membrane with 1% Lubrol PX and partially purified by gel filtration in buffer containing 0.01% Lubrol PX was physically characterized by polyacrylamide-gel electrophoresis. 2. The molecular radius determined for the partially purified enzyme was 4.9nm, compared with the value of 3.9nm obtained for the enzyme before gel filtration. 3. This difference, representing an approximate doubling of the molecular volume of the enzyme, implied that aggregation with itself or other proteins had occurred during partial purification. 4. Aggregation was not reversed by electrophoresis in the presence of high Lubrol concentrations. 5. Substitution of deoxycholate or N-dodecylsarcosinate for Lubrol PX either for solubilization or during electrophoresis led to poorer resolution of membrane proteins at concentrations giving greater than 70% loss of enzyme activity. 6. Partially purified adenylate cyclase was electrophoresed in the presence of mixed micelles of Lubrol PX and deoxycholate or Lubrol PX and N-dodecylsarcosinate. Different mixtures were examined simultaneously in a suitable apparatus. 7. Electrophoresis in the presence of 0.1% Lubrol plus 0.03% deoxycholate decreased the molecular radius of the cyclase to 4.0nm, with greater than 90% recovery of enzymic activity. The net charge of the enzyme was also increased, indicating ionic detergent binding. 8. With 0.1% Lubrol plus 0.03% N-dodecylsarcosinate the molecular radius was 4.3nm, recovery approx. 50% and net charge similar to that seen in Lubrol plus deoxycholate. 9. The resolution of cyclase from bulk protein, on an analytical scale, was improved in the presence of detergent mixtures, as compared with resolution in Lubrol alone. 10. The results demonstrate the usefulness of polyacrylamide-gel electrophoresis to detect and overcome aggregation problems with membrane proteins and suggest that detergent mixtures in

  18. Disaggregation of adenylate cyclase during polyacrylamide-gel electrophoresis in mixtures of ionic and non-ionic detergents

    PubMed Central

    Newby, Andrew C.; Chrambach, Andreas

    1979-01-01

    1. Adenylate cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] solubilized from the rat liver plasma membrane with 1% Lubrol PX and partially purified by gel filtration in buffer containing 0.01% Lubrol PX was physically characterized by polyacrylamide-gel electrophoresis. 2. The molecular radius determined for the partially purified enzyme was 4.9nm, compared with the value of 3.9nm obtained for the enzyme before gel filtration. 3. This difference, representing an approximate doubling of the molecular volume of the enzyme, implied that aggregation with itself or other proteins had occurred during partial purification. 4. Aggregation was not reversed by electrophoresis in the presence of high Lubrol concentrations. 5. Substitution of deoxycholate or N-dodecylsarcosinate for Lubrol PX either for solubilization or during electrophoresis led to poorer resolution of membrane proteins at concentrations giving greater than 70% loss of enzyme activity. 6. Partially purified adenylate cyclase was electrophoresed in the presence of mixed micelles of Lubrol PX and deoxycholate or Lubrol PX and N-dodecylsarcosinate. Different mixtures were examined simultaneously in a suitable apparatus. 7. Electrophoresis in the presence of 0.1% Lubrol plus 0.03% deoxycholate decreased the molecular radius of the cyclase to 4.0nm, with greater than 90% recovery of enzymic activity. The net charge of the enzyme was also increased, indicating ionic detergent binding. 8. With 0.1% Lubrol plus 0.03% N-dodecylsarcosinate the molecular radius was 4.3nm, recovery approx. 50% and net charge similar to that seen in Lubrol plus deoxycholate. 9. The resolution of cyclase from bulk protein, on an analytical scale, was improved in the presence of detergent mixtures, as compared with resolution in Lubrol alone. 10. The results demonstrate the usefulness of polyacrylamide-gel electrophoresis to detect and overcome aggregation problems with membrane proteins and suggest that detergent mixtures in

  19. SU-E-T-105: Development of 3D Dose Verification System for Volumetric Modulated Arc Therapy Using Improved Polyacrylamide-Based Gel Dosimeter

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ono, K; Fujimoto, S; Akagi, Y

    2014-06-01

    Purpose: The aim of this dosimetric study was to develop 3D dose verification system for volumetric modulated arc therapy (VMAT) using polyacrylamide-based gel (PAGAT) dosimeter improved the sensitivity by magnesium chloride (MgCl{sub 2}). Methods: PAGAT gel containing MgCl{sub 2} as a sensitizer was prepared in this study. Methacrylic-acid-based gel (MAGAT) was also prepared to compare the dosimetric characteristics with PAGAT gel. The cylindrical glass vials (4 cm diameter, 12 cm length) filled with each polymer gel were irradiated with 6 MV photon beam using Novalis Tx linear accelerator (Varian/BrainLAB). The irradiated polymer gel dosimeters were scanned with Signa 1.5 Tmore » MRI system (GE), and dose calibration curves were obtained using T{sub 2} relaxation rate (R{sub 2} = 1/T{sub 2}). Dose rate (100-600 MU min{sup −1}) and fractionation (1-8 fractions) were varied. In addition, a cubic acrylic phantom (10 × 10 × 10 cm{sup 3}) filled with improved PAGAT gel inserted into the IMRT phantom (IBA) was irradiated with VMAT (RapidArc). C-shape structure was used for the VMAT planning by the Varian Eclipse treatment planning system (TPS). The dose comparison of TPS and measurements with the polymer gel dosimeter was accomplished by the gamma index analysis, overlaying the dose profiles for a set of data on selected planes using in-house developed software. Results: Dose rate and fractionation dependence of improved PAGAT gel were smaller than MAGAT gel. A high similarity was found by overlaying the dose profiles measured with improved PAGAT gel dosimeter and the TPS dose, and the mean pass rate of the gamma index analysis using 3%/3 mm criteria was achieved 90% on orthogonal planes for VMAT using improved PAGAT gel dosimeter. Conclusion: In-house developed 3D dose verification system using improved polyacrylamide-based gel dosimeter had a potential as an effective tool for VMAT QA.« less

  20. Structure of gels layers with cells

    NASA Astrophysics Data System (ADS)

    Pokusaev, B. G.; Karlov, S. P.; Vyazmin, A. V.; Nekrasov, D. A.; Zakharov, N. S.; Khramtsov, D. P.; Skladnev, D. A.; Tyupa, D. V.

    2017-11-01

    The structure of two-layer agarose gels containing yeast cells is investigated experimentally by spectrometry, to shed a light on the theoretical foundations for the development of bioreactors by the method of 3D bioprinting. Due to division, cells overcome the layer of the dispersion phase separating successively applied layers of the agarose gel. However a gel layer of 100 μm thick with a high concentration of silver nanoparticles completely excludes the infiltration of yeast cells through it. A special sort of agarose is suggested where the concentration of silver nanoparticles formed by cells from salt of silver can serve as an indicator of the state of the yeast cells in the volume of the gel.

  1. Laminin active peptide/agarose matrices as multifunctional biomaterials for tissue engineering.

    PubMed

    Yamada, Yuji; Hozumi, Kentaro; Aso, Akihiro; Hotta, Atsushi; Toma, Kazunori; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

    2012-06-01

    Cell adhesive peptides derived from extracellular matrix components are potential candidates to afford bio-adhesiveness to cell culture scaffolds for tissue engineering. Previously, we covalently conjugated bioactive laminin peptides to polysaccharides, such as chitosan and alginate, and demonstrated their advantages as biomaterials. Here, we prepared functional polysaccharide matrices by mixing laminin active peptides and agarose gel. Several laminin peptide/agarose matrices showed cell attachment activity. In particular, peptide AG73 (RKRLQVQLSIRT)/agarose matrices promoted strong cell attachment and the cell behavior depended on the stiffness of agarose matrices. Fibroblasts formed spheroid structures on the soft AG73/agarose matrices while the cells formed a monolayer with elongated morphologies on the stiff matrices. On the stiff AG73/agarose matrices, neuronal cells extended neuritic processes and endothelial cells formed capillary-like networks. In addition, salivary gland cells formed acini-like structures on the soft matrices. These results suggest that the peptide/agarose matrices are useful for both two- and three-dimensional cell culture systems as a multifunctional biomaterial for tissue engineering. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Protein-tRNA Agarose Gel Retardation Assays for the Analysis of the N 6-threonylcarbamoyladenosine TcdA Function.

    PubMed

    Fernández, Francisco J; Gómez, Sara; Navas-Yuste, Sergio; López-Estepa, Miguel; Vega, M Cristina

    2017-06-21

    We demonstrate methods for the expression and purification of tRNA(UUU) in Escherichia coli and the analysis by gel retardation assays of the binding of tRNA(UUU) to TcdA, an N 6 -threonylcarbamoyladenosine (t 6 A) dehydratase, which cyclizes the threonylcarbamoyl side chain attached to A37 in the anticodon stem loop (ASL) of tRNAs to cyclic t 6 A (ct 6 A). Transcription of the synthetic gene encoding tRNA(UUU) is induced in E. coli with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and the cells containing tRNA are harvested 24 h post-induction. The RNA fraction is purified using the acid phenol extraction method. Pure tRNA is obtained by a gel filtration chromatography that efficiently separates the small-sized tRNA molecules from larger intact or fragmented nucleic acids. To analyze TcdA binding to tRNA(UUU), TcdA is mixed with tRNA(UUU) and separated on a native agarose gel at 4 °C. The free tRNA(UUU) migrates faster, while the TcdA-tRNA(UUU) complexes undergo a mobility retardation that can be observed upon staining of the gel. We demonstrate that TcdA is a tRNA(UUU)-binding enzyme. This gel retardation assay can be used to study TcdA mutants and the effects of additives and other proteins on binding.

  3. A single-step simultaneous protein staining procedure for polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis.

    PubMed

    Pal, Jayanta K; Berwal, Sunil K; Soni, Rupali N

    2012-01-01

    A simple method for staining of proteins simultaneously on sodium dodecyl sulfate (SDS) polyacrylamide gels and nitrocellulose membranes by Alta during western blot analysis is described. A 5% solution of Alta, a commercially available cosmetic preparation, is added in the upper tank buffer during electrophoresis. On completion of electrophoresis, the gel is washed in distilled water and viewed on a white light plate and a transilluminator to photograph the protein profiles. The gel is processed for western blot transfer of proteins onto a nitrocellulose membrane, and upon completion, the protein profiles on the membrane are viewed and photographed as stated above. The membrane can then be processed for immunostaining as per the standard procedure. Thus, the staining procedure using Alta is simple, rapid (without any need of destaining), and cost-effective.

  4. Kinetic resolution of racemic mixtures in gel media

    NASA Astrophysics Data System (ADS)

    Petrova, Rositza Iordanova

    The goal of this research was to investigate the effect of chiral gels on the chiral crystal nucleation and growth and assess the gels' potential as media for kinetic separation of racemic mixtures. The morphologies of asparagine monohydrate and sodium bromate crystals grown in different gel media were examined in order to discern the effect of gel structure and density on the relative growth rates of those materials. Different crystal habits were observed when the gel chemical composition, density and solute concentration were varied. These studies showed that the physical properties of the gel, such as gel density and pore size, as well as its chemical composition affect the crystal habit. The method of kinetic resolution in gel media was first applied to sodium chlorate, which is achiral in solution but crystallizes in a chiral space group. Crystallization in agarose gels yielded an enantiomorphic bias, the direction and magnitude of which could be affected by changing the temperature or by the addition of an achiral cosolvent. Aqueous gels at 6°C produced crystalline mixtures enriched with the d-enantiomorph, while crystallization under MeOH diffusion favored l-crystals. Optimized conditions yielded e.e. of 53% of l-enantiomorph. The method was next applied to the organic molecular crystals of asparagine monohydrate and threonine. Asparagine monohydrate growth in aqueous agarose and iota-carrageenan gels produced crystal mixtures enriched with D-enantiomer. The degree of resolution was higher when the total amount of asparagine crystallized was low. The success of the resolution depends strongly on the concentrations of solute and the geling substance. Growth from agarose gels yielded e.e. of 44% under optimized conditions. The same method was applied to the resolution of Thr, albeit with modest success. In an effort to improve the resolution of asparagine monohydrate, agarose was synthetically modified by esterifying its side chains with homochiral asparagyl

  5. Coupling Sodium Dodecyl Sulfate–Capillary Polyacrylamide Gel Electrophoresis with MALDI-TOF-MS via a PTFE Membrane

    PubMed Central

    Lu, Joann J.; Zhu, Zaifang; Wang, Wei; Liu, Shaorong

    2011-01-01

    Sodium dodecyl sulfate (SDS)–polyacrylamide gel electrophoresis (PAGE) is a fundamental analytical technique for proteomic research, and SDS–capillary gel electrophoresis (CGE) is its miniaturized version. Compared to conventional slab-gel electrophoresis, SDS-CGE has many advantages such as increased separation efficiency, reduced separation time and automated operation. SDS-CGE is not widely accepted in proteomic research primarily due to the difficulties in identifying the well-resolved proteins. MALDI–TOF–MS is an outstanding platform for protein identifications. Coupling the two would solve the problem but is extremely challenging because the MS detector has no access to the SDS-CGE resolved proteins and the SDS interferes with MS detection. In this work we introduce an approach to address these issues. We discover that poly(tetrafluoroethylene) (PTFE) membranes are excellent materials for collecting SDS-CGE separated proteins. We demonstrate that we can wash off the SDS bound to the collected proteins and identify these proteins on-membrane with MALDI-TOF-MS. We also show that we can immunoblot and Coomassie-stain the proteins collected on these membranes. PMID:21309548

  6. Dosimetry Evolution in Teletherapy: Polimer Gel

    NASA Astrophysics Data System (ADS)

    Hamann, J. H.; Peixoto, J. G. P.

    2018-03-01

    Polymer gels evolution and chemical composition used in dosimetry. Type Composition First gels Folin’s Phenol or Gallic Acid Polymer Gel Agarose and N,N’-methylene-bis-acrylamide BANANA Bis, acrylamide, nitrous oxide and agarose BANG-1TM Bis, acrylamide, nitrogen and gelatin BANG-2TM Bis, acrylic acid, sodium hydroxide, nitrogen and gelatin BANG-3TM Bis, methacrylate acid, sodium hydroxide, nitrogen and gelatin MAGIC Methacrylate acid, ascorbic acid, gelatin and copper sulphate

  7. Problem-Solving Test: Southwestern Blotting

    ERIC Educational Resources Information Center

    Szeberényi, József

    2014-01-01

    Terms to be familiar with before you start to solve the test: Southern blotting, Western blotting, restriction endonucleases, agarose gel electrophoresis, nitrocellulose filter, molecular hybridization, polyacrylamide gel electrophoresis, proto-oncogene, c-abl, Src-homology domains, tyrosine protein kinase, nuclear localization signal, cDNA,…

  8. Comparative two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of human milk to identify dysregulated proteins in breast cancer.

    PubMed

    Aslebagh, Roshanak; Channaveerappa, Devika; Arcaro, Kathleen F; Darie, Costel C

    2018-05-13

    Breast cancer (BC) remains a major cause of mortality, and early detection is considered important for reducing BC-associated deaths. Early detection of BC is challenging in young women, due to the limitations of mammography on the dense breast tissue of young women. We recently reported results of a pilot proteomics study, using one-dimensional polyacrylamide gel electrophoresis (1D-PAGE) and mass spectrometry (MS) to investigate differences in milk proteins from women with and without BC. Here, we applied two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and MS to compare the protein pattern in milk from the breasts of a single woman who was diagnosed with BC in one breast 24 months after donating her milk. Statistically different gel spots were picked for protein digestion followed by nanoliquid chromatography tandem MS (nanoLC-MS/MS) analysis. The upregulated proteins in BC versus control are alpha-amylase, gelsolin isoform a precursor, alpha-2-glycoprotein 1 zinc isoform CRA_b partial, apoptosis-inducing factor 2 and vitronectin. Several proteins were downregulated in the milk of the breast later diagnosed with cancer as compared to the milk from the healthy breast, including different isoforms of albumin, cholesterol esterase, different isoforms of lactoferrin, different proteins from the casein family and different isoforms of lysozyme. Results warrant further studies to determine the usefulness of these milk proteins for assessing risk and detecting occult disease. MS data is available via ProteomeXchange with identifier PXD009860. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Borehole testing methods using a new temporary polyacrylamide packers technology

    NASA Astrophysics Data System (ADS)

    Klepikova, Maria V.; Roques, Clement; Selker, John

    2017-04-01

    Range of options for investigation of hydraulic behavior of aquifers from boreholes has been limited to rigid, cumbersome packers, and inflatable sleeves. Here we propose a new temporary polyacrylamide packers (TAMP) technology that uses soft grains of polyacrylamide gel as a borehole sealing material and discuss its possible applications. Polyacrylamide gel, also called hydrogel or water-absorbing polymer, consists of long chains of molecules that can absorb over a hundred times their weight in liquids. Soft gel grains are mainly made of water, but the water inside these particles does not contribute to the flow of the suspension. The gel packing (permeability similar to open gravel) placed to a well suppresses free convection, allowing for local temperature and chemical sampling through free-flowing gel. Minimizing the effect of free convection within the well column would be beneficial for active thermal tests where free convection often dominate flow and create thermal disequilibrium between the water in the borehole and the surrounding media. Preliminary laboratory experiments and the literature suggests that as the polyacrylamide pack is subject to modest compressive stress to the gel media (of order 0.1 ATM), the permeability transitions from of the order of 10 to 7 millidarcys to 0.01 millidarcys, illustrating the remarkable ability to transition from highly permeable to nearly impermeable grouting. Though yet to be confirmed in the field, by locally injecting water at pressure greater than the compressive stress, local voids can be formed which can act as local pump test sources, with all other locations in the borehole hydraulically isolated where local response pressure from the formation can be measured. This arrangement could be valuable for tomographic study of aquifers wherein hundreds of injection zones could be tested by simply pulling an injection pipe vertically through the packed borehole. The gel grains can be of the scale of cm, so do not pass

  10. Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis.

    PubMed

    Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

    2017-01-01

    As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used : SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis : CS, TCMs: Traditional Chinese medicines.

  11. [Preparation of polyacrylamide gel electrophoresis for human chorionic gonadotropin chimeric peptide 12 expressed in E. coli].

    PubMed

    Zou, Yong-Shui; Xu, Wan-Xiang; He, Yuan; Sun, Zhi-Da; Xue, Xiao-Lin

    2002-09-01

    In recent years, development of chimeric peptide (CP) immunogens is a trend in the vaccinological field. The CPs contain a B cell epitope(s) of target antigen and a promiscuous self - or foreign- T cell epitope(s). However, such constructed CPs were all expressed in prokaryotic or eukaryotic systems at lower levels. To purify the human chorionic gonadotropin (hCG) CP12 expressed in E. coli at the level of about 1% of the total cell proteins, an improved method of preparative gel polyacrylamide gel electrophoresis (PAGE) was developed. The important improvement to routine preparative PAGE involves: (1) running reversed electrophoresis by rearranging the gel- carrying plate when the bromophenol blue band arrived at 1-1.5 centimeter from the bottom of the gel; (2) making a collecting trough between the gel and a dialytic membrane that was used to isolate the upper tank buffer. About 8 fractions were collected at regular intervals of 15 minutes after bromophenol blue running out of gel. And then 0.2 ml was taken from each fraction and the protein was precipitated by sequentially adding trichloroacetic acid and acetone. Each sample was dissolved in 20 microL sample buffer and analyzed and identified by SDS-PAGE and Western blotting. As a result, the hCG CP12 expression product with 95% relative homogeneity was harvested at a 50-100 microgram level after a single-step purification of this preparative PAGE, with respect to the sample which contained 3-4 mg of cell proteins.

  12. Quantification of DNA by Agarose Gel Electrophoresis and Analysis of the Topoisomers of Plasmid and M13 DNA Following Treatment with a Restriction Endonuclease or DNA Topoisomerase I

    ERIC Educational Resources Information Center

    Tweedie, John W.; Stowell, Kathryn M.

    2005-01-01

    A two-session laboratory exercise for advanced undergraduate students in biochemistry and molecular biology is described. The first session introduces students to DNA quantification by ultraviolet absorbance and agarose gel electrophoresis followed by ethidium bromide staining. The second session involves treatment of various topological forms of…

  13. Mechanics of a fiber network within a non-fibrillar matrix: model and comparison with collagen-agarose co-gels

    PubMed Central

    Lake, Spencer P.; Hadi, Mohammad F.; Lai, Victor K.; Barocas, Victor H.

    2013-01-01

    While collagen is recognized as the predominant mechanical component of soft connective tissues, the role of the non-fibrillar matrix (NFM) is less well understood. Even model systems, such as the collagen-agarose co-gel, can exhibit complex behavior, making it difficult to identify relative contributions of specific tissue constituents. In the present study, we developed a two-component microscale model of collagen-agarose tissue analogs and used it to elucidate the interaction between collagen and NFM in uniaxial tension. Collagen fibers were represented with Voronoi networks, and the NFM was modeled as a neo-Hookean solid. Model predictions of total normal stress and Poisson’s ratio matched experimental observations well (including high Poisson’s values of ~3), and the addition of NFM led to composition-dependent decreases in volume change and increases in fiber stretch. Because the NFM was more resistant to volume change than the fiber network, extension of the composite led to pressurization of the NFM. Within a specific range of parameter values (low shear modulus and moderate Poisson’s ratio), the magnitude of the reaction force decreased relative to this pressurization component resulting in a negative (compressive) NFM stress in the loading direction, even though the composite tissue was in tension. PMID:22565816

  14. A subtle calculation method for nanoparticle’s molar extinction coefficient: The gift from discrete protein-nanoparticle system on agarose gel electrophoresis

    NASA Astrophysics Data System (ADS)

    Zhong, Ruibo; Yuan, Ming; Gao, Haiyang; Bai, Zhijun; Guo, Jun; Zhao, Xinmin; Zhang, Feng

    2016-03-01

    Discrete biomolecule-nanoparticle (NP) conjugates play paramount roles in nanofabrication, in which the key is to get the precise molar extinction coefficient of NPs. By making best use of the gift from a specific separation phenomenon of agarose gel electrophoresis (GE), amphiphilic polymer coated NP with exact number of bovine serum albumin (BSA) proteins can be extracted and further experimentally employed to precisely calculate the molar extinction coefficient of the NPs. This method could further benefit the evaluation and extraction of any other dual-component NP-containing bio-conjugates.

  15. Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis

    PubMed Central

    Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

    2017-01-01

    Background: As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Objective: Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Materials and Methods: Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). Results: The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Conclusions: Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. SUMMARY The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used: SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis: CS, TCMs: Traditional Chinese medicines PMID:28250651

  16. Tuning mechanical performance of poly(ethylene glycol) and agarose interpenetrating network hydrogels for cartilage tissue engineering.

    PubMed

    Rennerfeldt, Deena A; Renth, Amanda N; Talata, Zsolt; Gehrke, Stevin H; Detamore, Michael S

    2013-11-01

    Hydrogels are attractive for tissue engineering applications due to their incredible versatility, but they can be limited in cartilage tissue engineering applications due to inadequate mechanical performance. In an effort to address this limitation, our team previously reported the drastic improvement in the mechanical performance of interpenetrating networks (IPNs) of poly(ethylene glycol) diacrylate (PEG-DA) and agarose relative to pure PEG-DA and agarose networks. The goal of the current study was specifically to determine the relative importance of PEG-DA concentration, agarose concentration, and PEG-DA molecular weight in controlling mechanical performance, swelling characteristics, and network parameters. IPNs consistently had compressive and shear moduli greater than the additive sum of either single network when compared to pure PEG-DA gels with a similar PEG-DA content. IPNs withstood a maximum stress of up to 4.0 MPa in unconfined compression, with increased PEG-DA molecular weight being the greatest contributing factor to improved failure properties. However, aside from failure properties, PEG-DA concentration was the most influential factor for the large majority of properties. Increasing the agarose and PEG-DA concentrations as well as the PEG-DA molecular weight of agarose/PEG-DA IPNs and pure PEG-DA gels improved moduli and maximum stresses by as much as an order of magnitude or greater compared to pure PEG-DA gels in our previous studies. Although the viability of encapsulated chondrocytes was not significantly affected by IPN formulation, glycosaminoglycan (GAG) content was significantly influenced, with a 12-fold increase over a three-week period in gels with a lower PEG-DA concentration. These results suggest that mechanical performance of IPNs may be tuned with partial but not complete independence from biological performance of encapsulated cells. © 2013 Elsevier Ltd. All rights reserved.

  17. Direct Quantification of Solute Diffusivity in Agarose and Articular Cartilage Using Correlation Spectroscopy.

    PubMed

    Shoga, Janty S; Graham, Brian T; Wang, Liyun; Price, Christopher

    2017-10-01

    Articular cartilage is an avascular tissue; diffusive transport is critical for its homeostasis. While numerous techniques have been used to quantify diffusivity within porous, hydrated tissues and tissue engineered constructs, these techniques have suffered from issues regarding invasiveness and spatial resolution. In the present study, we implemented and compared two separate correlation spectroscopy techniques, fluorescence correlation spectroscopy (FCS) and raster image correlation spectroscopy (RICS), for the direct, and minimally-invasive quantification of fluorescent solute diffusion in agarose and articular cartilage. Specifically, we quantified the diffusional properties of fluorescein and Alexa Fluor 488-conjugated dextrans (3k and 10k) in aqueous solutions, agarose gels of varying concentration (i.e. 1, 3, 5%), and in different zones of juvenile bovine articular cartilage explants (i.e. superficial, middle, and deep). In agarose, properties of solute diffusion obtained via FCS and RICS were inversely related to molecule size, gel concentration, and applied strain. In cartilage, the diffusional properties of solutes were similarly dependent upon solute size, cartilage zone, and compressive strain; findings that agree with work utilizing other quantification techniques. In conclusion, this study established the utility of FCS and RICS as simple and minimally invasive techniques for quantifying microscale solute diffusivity within agarose constructs and articular cartilage explants.

  18. Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment

    NASA Astrophysics Data System (ADS)

    Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E.

    2003-11-01

    Oxidative damage of DNA molecules associated with electron-transfer reactions is an important phenomenon in living cells, which can lead to mutations and contribute to carcinogenesis and the aging processes. This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNA agarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage. A low-cost experimental and computer-interfaced imaging apparatus is described allowing for the digital recording and analysis of the gel electrophoresis results. The first experiment describes the formation of direct strand breaks in double-stranded DNA induced by photoexcitation of the intercalated PF molecules. The second experiment demonstrates that the addition of the well-known electron acceptor, methylviologen, gives rise to a significant enhancement of the photochemical DNA strand cleavage effect. This occurs by an electron transfer step to methylviologen that renders the inital photoinduced charge separation between photoexcited PF and DNA irreversible. The third experiment demonstrates that the action spectrum of the DNA photocleavage matches the absorption spectrum of DNA-bound, intercalated PF molecules, which differs from that of free PF molecules. This result demonstrates that the photoinduced DNA strand cleavage is initiated by intercalated rather than free PF molecules.

  19. Polyacrylamide gel injections for breast augmentation: management of complications in 106 patients, a multicenter study.

    PubMed

    Unukovych, Dmytro; Khrapach, Vasyl; Wickman, Marie; Liljegren, Annelie; Mishalov, Volodymyr; Patlazhan, Gennadiy; Sandelin, Kerstin

    2012-04-01

    Polyacrylamide gel (PAAG) was first manufactured in Ukraine in the late 1980s and introduced as a biomaterial for "breast augmentation without surgery." Since it is prohibited in most countries, PAAG injections are rare nowadays, but their consequences and long-term complications can be crucial. We identified 106 patients consecutively operated on for PAAG complications at three teaching Ukrainian hospitals between 1998 and 2009. All relevant sociodemographic, clinical, and treatment characteristics were collected. Forty-five (42%) patients were available for clinical follow-up. The majority (88%) had had bilateral PAAG injections. The mean volume of injected PAAG was 230 ml/breast (range = 50-400). Mean age at injection was 29 years (range = 17-49) and the mean time from the injection to complications was 6.1 years (SD = 4.1). Symptoms preceding debridement were pain in 85 patients (80%), breast hardening in 79 (74%), breast deformity in 77 (73%), lumps in 57 (54%), gel migration in 39 (37%), fistulas in 17 (16%), and gel leakage in 12 (11%). The surgical interventions in 199 breasts included gel evacuation alone in 107 (54%) or in combination with partial mastectomy in 65 (33%), partial mastectomy and partial pectoralis muscle resection in 12 (6%), or subcutaneous mastectomy in 15 (7%). Of the 199 operated breasts, 86 (43%) immediate and 58 (29%) delayed implant-based breast reconstructions were performed. Injections of PAAG can cause irreversible damage to the breast necessitating complex debridement procedures, even mastectomy and breast reconstruction. Despite numerous surgical interventions, gel remnants are still found on subsequent breast imaging. Although PAAG is prohibited in many countries, different types of injections with unknown long-term effects are currently being used. Making the public aware of the problems of injectables for breast augmentation is warranted.

  20. Hyper alginate gel microbead formation by molecular diffusion at the hydrogel/droplet interface.

    PubMed

    Hirama, Hirotada; Kambe, Taisuke; Aketagawa, Kyouhei; Ota, Taku; Moriguchi, Hiroyuki; Torii, Toru

    2013-01-15

    We report a simple method for forming monodispersed, uniformly shaped gel microbeads with precisely controlled sizes. The basis of our method is the placement of monodispersed sodium alginate droplets, formed by a microfluidic device, on an agarose slab gel containing a high-osmotic-pressure gelation agent (CaCl(2) aq.): (1) the droplets are cross-linked (gelated) due to the diffusion of the gelation agent from the agarose slab gel to the sodium alginate droplets and (2) the droplets simultaneously shrink to a fraction of their original size (<100 μm in diameter) due to the diffusion of water molecules from the sodium alginate droplets to the agarose slab gel. We verified the mass transfer mechanism between the droplet and the agarose slab gel. This method circumvents the limitations of gel microbead formation, such as the need to prepare microchannels of various sizes, microchannel clogging, and the deformation of the produced gel microbeads.

  1. Counterion dye staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and tryptic gel digestion of stained protein for mass spectrometry.

    PubMed

    Cong, Wei-Tao; Wang, Xu; Hwang, Sun-Young; Jin, Li-Tai; Choi, Jung-Kap

    2012-01-01

    A fast and matrix-assisted laser desorption/ionization mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet, to form an ion-pair complex. The protocol, including fixing, staining, and quick washing steps, can be completed in 1-1.5 h, depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

  2. Polygalacturonase from Rhizopus stolonifer, an Elicitor of Casbene Synthetase Activity in Castor Bean (Ricinus communis L.) Seedlings 1

    PubMed Central

    Lee, Sung-Chul; West, Charles A.

    1981-01-01

    Apparently homogeneous polygalacturonase-elicitor purified from the filtrates of Rhizopus stolonifer cultures stimulates germinating castor bean seedlings to produce greatly increased levels of casbene synthetase activity. The purification procedure involved gel-filtration chromatography on Sephadex G-25 and G-75 columns followed by cation-exchange chromatography on a Sephadex CM C-50 column. Homogeneity of the purified preparation was indicated by the results of cationic polyacrylamide disc gel electrophoresis and isoelectric focusing (pI = 8.0). The identity of the casbene elicitor activity and polygalacturonase were indicated by the coincidence of the two activities at all stages of purification, the coincidence of both activities with the single protein-staining band detected on a cationic polyacrylamide disc gel and an isoelectric focusing gel, and the identical behavior of both activities on an agarose gel affinity column. The purified polygalacturonase-elicitor is a glycoprotein with approximately 20% carbohydrate content and an estimated molecular weight of 32,000 by polyacrylamide disc gel electrophoresis. PMID:16661728

  3. QUALITY ASSURANCE CONSIDERATIONS FOR USE OF THE FLUORIMAGER SI AND FRAGMENT ANALYSIS SOFTWARE

    EPA Science Inventory

    The Fluorimager SI (FSI) from Molecular Dynamics is one of several scanning instruments available for the detection of fluorescent emissions associated with DNA samples in a variety of matrices (agarose and polyacrylamide gels, membranes and microplates). In our laboratory, we m...

  4. Mechanism of smectic arrangement of montmorillonite and bentonite clay platelets incorporated in gels of poly(acrylamide) induced by the interaction with cationic surfactants.

    PubMed

    Starodoubtsev, S G; Lavrentyeva, E K; Khokhlov, A R; Allegra, G; Famulari, A; Meille, S V

    2006-01-03

    Structure transitions, induced by the interaction with the cationic surfactant cetylpyridinium chloride in nanocomposite gels of poly(acrylamide) with incorporated suspensions of the two closely related layered clays bentonite and montmorillonite, were studied. Unexpectedly, different behaviors were revealed. X-ray diffraction measurements confirm that, due to the interaction with the surfactant, initially disordered bentonite platelets arrange into highly ordered structures incorporating alternating clay platelets and surfactant bilayers. The formation of these smectic structures also in the cross-linked polymer gels, upon addition of the surfactant, is explained by the existence of preformed, poorly ordered aggregates of the clay platelets in the suspensions before the gel formation. In the case of montmorillonite, smectic ordering of the disordered platelets in the presence of the surfactant is observed only after drying the suspensions and the clay-gel composites. Rheology studies of aqueous suspensions of the two clays, in the absence of both surfactant and gel, evidence a much higher viscosity for bentonite than for montmorillonite, suggesting smaller clay-aggregate size in the latter case. Qualitatively consistent results are obtained from optical micrographs.

  5. In Situ Observations of Thermoreversible Gelation and Phase Separation of Agarose and Methylcellulose Solutions under High Pressure.

    PubMed

    Kometani, Noritsugu; Tanabe, Masahiro; Su, Lei; Yang, Kun; Nishinari, Katsuyoshi

    2015-06-04

    Thermoreversible sol-gel transitions of agarose and methylcellulose (MC) aqueous solutions on isobaric cooling or heating under high pressure up to 400 MPa have been investigated by in situ observations of optical transmittance and falling-ball experiments. For agarose, which undergoes the gelation on cooling, the application of pressure caused a gradual rise in the cloud-point temperature over the whole pressure range examined, which is almost consistent with the pressure dependence of gelling temperature estimated by falling-ball experiments, suggesting that agarose gel is stabilized by compression and that the gelation occurs nearly in parallel with phase separation under ambient and high-pressure conditions. For MC, which undergoes the gelation on heating, the cloud-point temperature showed a slight rise with an initial elevation of pressure up to ∼150 MPa, whereas it showed a marked depression above 200 MPa. In contrast, the gelling temperature of MC, which is nearly identical to the cloud-point temperature at ambient pressure, showed a monotonous rise with increasing pressure up to 350 MPa, which means that MC undergoes phase separation prior to gelation on heating under high pressure above 200 MPa. Similar results were obtained for the melting process of MC gel on cooling. The unique behavior of the sol-gel transition of MC under high pressure has been interpreted in terms of the destruction of hydrophobic hydration by compression.

  6. Urine Collected From Diapers Can Be Used for 2-Dimensional Polyacrylamide Gel Electrophoresis (2D-PAGE) in Infants and Young Children

    PubMed Central

    Kennedy, Mary Jayne; Griffin, Angela; Su, Ruifeng; Merchant, Michael; Klein, Jon

    2011-01-01

    Urinary proteomic profiling has potential to identify candidate biomarkers of renal injury in infants provided an adequate urine sample can be obtained. Although diapers are used to obtain urine for clinical evaluation, their use for proteomic analysis has not been investigated. We therefore performed feasibility studies on the use of diaper-extracted urine for 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Pediatric waste urine (2–20 mL) was applied to gel-containing, non-gel and cotton-gauze diapers and then mechanically expressed. Urine volume and total protein were measured pre- and post-extraction. Proteins were separated via 2D-PAGE following application of urine (20–40 mL) to each matrix. 2D-PAGE was also performed on clinical specimens collected using each diaper type. Differences in the adsorption and retention of urine volume and protein were noted between matrices. Non-gel and cotton-gauze diapers provided the best protein/volume recovery and the lowest interference with the Bradford assay. 2D-PAGE was also successfully completed using urine samples from both cotton fiber matrices. Conversely, samples from low-gel diapers demonstrated poor protein separation and reproducibility. Diapers containing cotton-fiber matrices appear adequate for 2D-PAGE. Qualitative and quantitative analyses of resolved proteins using replicate, high resolution gels will be required, however, before diaper-extracted urine can be applied in proteomic profiling. PMID:21137001

  7. Quantitation of yeast total proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis sample buffer for uniform loading.

    PubMed

    Sheen, Hyukho

    2016-04-01

    Proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) sample buffer are difficult to quantitate due to SDS and reducing agents being in the buffer. Although acetone precipitation has long been used to clean up proteins from detergents and salts, previous studies showed that protein recovery from acetone precipitation varies from 50 to 100% depending on the samples tested. Here, this article shows that acetone precipitates proteins highly efficiently from SDS-PAGE sample buffer and that quantitative recovery is achieved in 5 min at room temperature. Moreover, precipitated proteins are resolubilized with urea/guanidine, rather than with SDS. Thus, the resolubilized samples are readily quantifiable with Bradford reagent without using SDS-compatible assays. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Two-dimensional polyacrylamide gel electrophoresis of bovine semen after cryopreservation in half-milliliter straws.

    PubMed

    Frazer, G S; Bucci, D M; Brooks, C L

    1996-11-01

    One of the problems encountered with two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is the streaking of proteins so that individual spot identification is compromised. This study was conducted to determine whether a low loading dose (50 microg) of protein would permit resolution of more discrete protein spots using megapixel camera technology, and if so, to present a nomenclature for future comparisons of the identified proteins. If the major proteins could be identified in a 50-microg sample we aimed to determine whether they could be identified in the supernatant (seminal plasma plus extender) of cryopreserved semen. Two ejaculates were obtained from each of 6 bulls and bovine seminal plasma (BSP) protein concentration was standardized to 50 microg/10 microl. Isoelectric points (pI) and molecular weights (MWt) of BSP proteins were determined by measuring spot mobility on 2-D PAGE (15% polyacrylamide). Three distinct protein spot constellations (a,b,c) could be readily seen by the naked eye and a faintly stained constellation "d" was identified by the megapixel camera. The image analysis software located 6 protein spots in both constellation "a" (MWt 26 kDa; pI 4.2 to 4.8) and "b" ( MWt 27 kDa; pI 6.6 to 8.0). Constellation "c" contained 13 protein spots distributed in a right-angled triangle with its base towards the acidic end of the gel (MWt 14.7 to 18.8 kDa; pI 5.3 to 7.4). Only spots c(2), c(3), c(5), c(8), and c(13) were present in all 12 samples. Streaking can be eliminated by using 50 microg protein for 2-D PAGE, and the major protein spots are readily identified by megapixel camera technology. Protein spots c(3), c(5), c(13) and constellation "a" appear to correspond with Manjunath's proteins (BSP-A(1), -A(2); -A(3); -30 kDa). Killian's 2 low fertility proteins may lie in the "c" constellation, and 1 of the high fertility proteins may lie in the "b" constellation. The 3 major BSP proteins can be visualized in the supernatant of cryopreserved

  9. Introduction of agarose gel as a green membrane in electromembrane extraction: An efficient procedure for the extraction of basic drugs with a wide range of polarities.

    PubMed

    Tabani, Hadi; Asadi, Sakine; Nojavan, Saeed; Parsa, Mitra

    2017-05-12

    Developing green methods for analyte extraction is one of the most important topics in the field of sample preparation. In this study, for the first time, agarose gel was used as membrane in electromembrane extraction (EME) without using any organic solvent, for the extraction of four model basic drugs (rivastigmine (RIV), verapamil (VER), amlodipine (AML), and morphine (MOR)) with a wide polarity window (log P from 0.43 to 3.7). Different variables playing vital roles in the proposed method were evaluated and optimized. As a driving force, a 25V electrical field was applied to make the analyte migrate from sample solution with pH 7.0, through the agarose gel 3% (w/v) with 5mm thickness, into an acceptor phase (AP) with pH 2.0. The best extraction efficiency was obtained with an extraction duration of 25min. With this new methodology, MOR with high polarity (log P=0.43) was efficiently extracted without using any carrier or ion pair reagents. Limits of detection (LODs) and quantification (LOQs) were in the ranges of 1.5-1.8ngmL -1 and 5.0-6.0ngmL -1 , respectively. Finally, the proposed method was successfully applied to determine concentrations of the model drugs in the wastewater sample. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

    PubMed Central

    Serwer, Philip; Wright, Elena T.

    2012-01-01

    We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

  11. Model creation of moving redox reaction boundary in agarose gel electrophoresis by traditional potassium permanganate method.

    PubMed

    Xie, Hai-Yang; Liu, Qian; Li, Jia-Hao; Fan, Liu-Yin; Cao, Cheng-Xi

    2013-02-21

    A novel moving redox reaction boundary (MRRB) model was developed for studying electrophoretic behaviors of analytes involving redox reaction on the principle of moving reaction boundary (MRB). Traditional potassium permanganate method was used to create the boundary model in agarose gel electrophoresis because of the rapid reaction rate associated with MnO(4)(-) ions and Fe(2+) ions. MRB velocity equation was proposed to describe the general functional relationship between velocity of moving redox reaction boundary (V(MRRB)) and concentration of reactant, and can be extrapolated to similar MRB techniques. Parameters affecting the redox reaction boundary were investigated in detail. Under the selected conditions, good linear relationship between boundary movement distance and time were obtained. The potential application of MRRB in electromigration redox reaction titration was performed in two different concentration levels. The precision of the V(MRRB) was studied and the relative standard deviations were below 8.1%, illustrating the good repeatability achieved in this experiment. The proposed MRRB model enriches the MRB theory and also provides a feasible realization of manual control of redox reaction process in electrophoretic analysis.

  12. DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

    2004-03-24

    Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNAmore » populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.« less

  13. A facile approach to fabricate porous nanocomposite gels based on partially hydrolyzed polyacrylamide and cellulose nanocrystals for adsorbing methylene blue at low concentrations.

    PubMed

    Zhou, Chengjun; Lee, Sunyoung; Dooley, Kerry; Wu, Qinglin

    2013-12-15

    Porous nanocomposite gels were fabricated by a facile method consisting of the electrospinning and subsequent heat treatment based on partially hydrolyzed polyacrylamide (HPAM) of ultra-high molecular weight, with cellulose nanocrystals (CNCs) as crosslinker. The effects of three electrospinning parameters (i.e., solution concentration, composition of solvent mixture, and CNC loading level) on morphology and diameter of electrospun fibers were systematically investigated. The swelling properties of porous gels and their application in the removal of methylene blue dye (as a compound representative of contaminants) were evaluated. Electrospun fiber morphologies without beads, branches, and ribbons were achieved by optimizing the electrospinning solutions. The thermal crosslinking between HPAM and CNCs was realized through esterification, rendering the product nanocomposite membranes insoluble in water. Electrospun fibers of approximately 220 nm in diameter comprised the 3D porous nanocomposite gels, with porosity greater than 50%. The porous nanocomposite gels displayed a rapid swelling rate and an efficient adsorption capacity in removing methylene blue at low concentrations from aqueous solutions. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. [A structural protein study of the influenza A (H1N1) virus by polyacrylamide gel electrophoresis].

    PubMed

    Pérez Guevara, M T; Savón Valdés, C; Rivas Arjona, M; Goyenechea Hernández, A

    1992-01-01

    Influenza is an acute respiratory disease typically appearing as an epidemic. Three immunological types of the influenza virus are known: A, B and C. Continually, antigen changes occur, especially in type A. Therefore, a comparative study was carried out on 4 influenza A(H1N1) virus strains in relation to protein structure (surface antigens), by using polyacrylamide gel electrophoresis by the modified Laemmli method. The objective was to compare the structural proteins of the A/Havana/1292/78 (H1N1) national strain with the proteins of 3 international pattern strains. In all the cases, 6 bands were detected by densitometry. In the 4 strains studied the most abundant protein was M. Great differences between the Cuban strain and the 3 international patterns were not seen.

  15. Blue native polyacrylamide gel electrophoresis and the monitoring of malate- and oxaloacetate-producing enzymes.

    PubMed

    Singh, R; Chénier, D; Bériault, R; Mailloux, R; Hamel, R D; Appanna, V D

    2005-09-30

    We demonstrate a facile blue native polyacrylamide gel electrophoresis (BN-PAGE) technique to detect two malate-generating enzymes, namely fumarase (FUM), malate synthase (MS) and four oxaloacetate-forming enzymes, namely pyruvate carboxylase (PC), phosphoenolpyruvate carboxykinase (PEPCK), citrate lyase (CL) and aspartate aminotransferase (AST). Malate dehydrogenase (MDH) was utilized as a coupling enzyme to detect either malate or oxaloacetate in the presence of their respective substrates and cofactors. The latter four oxaloacetate-forming enzymes were identified by 2,6-dichloroindophenol (DCIP) and p-iodonitrotetrazolium (INT) while the former two malate-producing enzymes were visualized by INT and phenazine methosulfate (PMS) in the reaction mixtures, respectively. The band formed at the site of enzymatic activity was easily quantified, while Coomassie staining provided information on the protein concentration. Hence, the expression and the activity of these enzymes can be readily evaluated. A two-dimensional (2D) BN-PAGE or SDS-PAGE enabled the rapid purification of the enzyme of interest. This technique also provides a quick and inexpensive means of quantifying these enzymatic activities in normal and stressed biological systems.

  16. Electrophoresis gel image processing and analysis using the KODAK 1D software.

    PubMed

    Pizzonia, J

    2001-06-01

    The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

  17. Spring-loaded polymeric gel actuators

    DOEpatents

    Shahinpoor, Mohsen

    1995-01-01

    Spring-loaded electrically controllable polymeric gel actuators are disclosed. The polymeric gels can be polyvinyl alcohol, polyacrylic acid, or polyacrylamide, and are contained in an electrolytic solvent bath such as water plus acetone. The action of the gel is mechanically biased, allowing the expansive and contractile forces to be optimized for specific applications.

  18. Blotting from PhastGel to Membranes by Ultrasound.

    PubMed

    Kost, Joseph; Azagury, Aharon

    2015-01-01

    Ultrasound based approach for enhanced protein blotting is proposed. Three minutes of ultrasound exposure (1 MHz, 2.5 W/cm(2)) was sufficient for a clear transfer of proteins from a polyacrylamide gel (PhastGel) to nitrocellulose or Nylon 66 Biotrans membrane. The proteins evaluated were prestained sodium dodecyl sulfate-polyacrylamide standards (18,500-106,000 Da) and 14C-labeled Rainbow protein molecular weight markers (14,300-200,000 Da).

  19. Blotting from PhastGel to membranes by ultrasound.

    PubMed

    Kost, Joseph

    2009-01-01

    Ultrasound-based approach for enhanced protein blotting is proposed. Three minutes of ultrasound exposure (1 MHz, 2.5 W/cm(2)) was sufficient for a clear transfer of proteins from a polyacrylamide gel (PhastGel) to nitrocellulose or Nylon 66 Biotrans membrane. The proteins evaluated were prestained sodium dodecyl sulfate-polyacrylamide standards (18,500-106,000 Da) and (14)C-labeled Rainbow protein molecular weight markers (14,300-200,000 Da).

  20. Identification of column edges of DNA fragments by using K-means clustering and mean algorithm on lane histograms of DNA agarose gel electrophoresis images

    NASA Astrophysics Data System (ADS)

    Turan, Muhammed K.; Sehirli, Eftal; Elen, Abdullah; Karas, Ismail R.

    2015-07-01

    Gel electrophoresis (GE) is one of the most used method to separate DNA, RNA, protein molecules according to size, weight and quantity parameters in many areas such as genetics, molecular biology, biochemistry, microbiology. The main way to separate each molecule is to find borders of each molecule fragment. This paper presents a software application that show columns edges of DNA fragments in 3 steps. In the first step the application obtains lane histograms of agarose gel electrophoresis images by doing projection based on x-axis. In the second step, it utilizes k-means clustering algorithm to classify point values of lane histogram such as left side values, right side values and undesired values. In the third step, column edges of DNA fragments is shown by using mean algorithm and mathematical processes to separate DNA fragments from the background in a fully automated way. In addition to this, the application presents locations of DNA fragments and how many DNA fragments exist on images captured by a scientific camera.

  1. Spring-loaded polymeric gel actuators

    DOEpatents

    Shahinpoor, M.

    1995-02-14

    Spring-loaded electrically controllable polymeric gel actuators are disclosed. The polymeric gels can be polyvinyl alcohol, polyacrylic acid, or polyacrylamide, and are contained in an electrolytic solvent bath such as water plus acetone. The action of the gel is mechanically biased, allowing the expansive and contractile forces to be optimized for specific applications. 5 figs.

  2. Numerical modelling and experimental study of liquid evaporation during gel formation

    NASA Astrophysics Data System (ADS)

    Pokusaev, B. G.; Khramtsov, D. P.

    2017-11-01

    Gels are promising materials in biotechnology and medicine as a medium for storing cells for bioprinting applications. Gel is a two-phase system consisting of solid medium and liquid phase. Understanding of a gel structure evolution and gel aging during liquid evaporation is a crucial step in developing new additive bioprinting technologies. A numerical and experimental study of liquid evaporation was performed. In experimental study an evaporation process of an agarose gel layer located on Petri dish was observed and mass difference was detected using electronic scales. Numerical model was based on a smoothed particle hydrodynamics method. Gel in a model was represented as a solid-liquid system and liquid evaporation was modelled due to capillary forces and heat transfer. Comparison of experimental data and numerical results demonstrated that model can adequately represent evaporation process in agarose gel.

  3. Evaluation of the friction coefficient, the radial stress, and the damage work during needle insertions into agarose gels.

    PubMed

    Urrea, Fabián A; Casanova, Fernando; Orozco, Gustavo A; García, José J

    2016-03-01

    Agarose hydrogels have been extensively used as a phantom material to mimic the mechanical behavior of soft biological tissues, e.g. in studies aimed to analyze needle insertions into the organs producing tissue damage. To better predict the radial stress and damage during needle insertions, this study was aimed to determine the friction coefficient between the material of commercial catheters and hydrogels. The friction coefficient, the tissue damage and the radial stress were evaluated at 0.2, 1.8, and 10mm/s velocities for 28, 30, and 32 gauge needles of outer diameters equal to 0.36, 0.31, and 0.23mm, respectively. Force measurements during needle insertions and retractions on agarose gel samples were used to analyze damage and radial stress. The static friction coefficient (0.295±0.056) was significantly higher than the dynamic (0.255±0.086). The static and dynamic friction coefficients were significantly smaller for the 0.2mm/s velocity compared to those for the other two velocities, and there was no significant difference between the friction coefficients for 1.8 and 10mm/s. Radial stress averages were 131.2±54.1, 248.3±64.2, and 804.9±164.3Pa for the insertion velocity of 0.2, 1.8, and 10mm/s, respectively. The radial stress presented a tendency to increase at higher insertion velocities and needle size, which is consistent with other studies. However, the damage work did not show to be a good predictor of tissue damage, which appears to be due to simplifications in the analytical model. Differently to other approaches, the method proposed here based on radial stress may be extended in future studies to quantity tissue damage in vivo along the entire needle track. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Formation of composite polyacrylamide and silicone substrates for independent control of stiffness and strain.

    PubMed

    Simmons, Chelsey S; Ribeiro, Alexandre J S; Pruitt, Beth L

    2013-02-21

    Cells that line major tissues in the body such as blood vessels, lungs and gastrointestinal tract experience deformation from mechanical strain with our heartbeat, breathing, and other daily activities. Tissues also remodel in both development and disease, changing their mechanical properties. Taken together, cells can experience vastly different mechanical cues resulting from the combination of these interdependent stimuli. To date, most studies of cellular mechanotransduction have been limited to assays in which variations in substrate stiffness and strain were not combined. Here, we address this technological gap by implementing a method that can simultaneously tune both substrate stiffness and mechanical strain. Substrate stiffness is controlled with different monomer and crosslinker ratios during polyacrylamide gel polymerization, and strain is transferred from the underlying silicone platform when stretched. We demonstrate this platform with polyacrylamide gels with elastic moduli at 6 kPa and 20 kPa in combination with two different silicone formulations. The gels remain attached with up to 50% applied strains. To validate strain transfer through the gels into cells, we employ particle-tracking methods and observe strain transmission via cell morphological changes.

  5. A brief review of other notable protein detection methods on acrylamide gels.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2012-01-01

    Several methods have been described to stain proteins analyzed on acrylamide gels. These include ultrasensitive protein detection in one-dimensional and two-dimensional gel electrophoresis using a fluorescent product from the fungus Epicoccum nigrum; a fluorescence-based Coomassie Blue protein staining; visualization of proteins in acrylamide gels using ultraviolet illumination; fluorescence visualization of proteins in sodium dodecyl sulfate-polyacrylamide gels using environmentally benign, nonfixative, saline solution; and increasing the sensitivity four- to sixfold for detecting trace proteins in dye or silver stained polyacrylamide gels using polyethylene glycol 6000. All these methods are reviewed briefly in this chapter.

  6. One-step separation and purification of hydrolysable tannins from Geranium wilfordii Maxim by adsorption chromatography on cross-linked 12% agarose gel.

    PubMed

    Liu, Dan; Ma, Yan; Wang, Ye; Su, Zhiguo; Gu, Ming; Janson, Jan-Christer

    2011-05-01

    The hydrolysable tannins corilagin and geraniin, the major active components of the traditional Chinese medicine Geranium wilfordii Maxim, have been separated and purified from crude extracts in one step by adsorption chromatography on cross-linked 12% agarose gel (Superose 12 10/300 GL). The separation was achieved by gradient elution using mobile phase A composed of 5% ethanol and 5% acetic acid and mobile phase B composed of 30% ethanol and 30% acetic acid. The gradients were composed as follows: 0-240 mL, 0-25% B; 240-480 mL, 25-40% B; after 480 mL, 100% B. The purities of the collected corilagin and geraniin were 92.4 and 87.2%, and the corresponding yields were 88.0 and 76.8%, respectively. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Transanal submucosal polyacrylamide gel injection treatment of anal incontinence: a randomized controlled trial.

    PubMed

    Altman, Daniel; Hjern, Fredrik; Zetterström, Jan

    2016-05-01

    The efficacious and safe use of transurethral injections of polyacrylamide hydrogel (Bulkamid(®)) in women with stress urinary incontinence suggests that it may be suitable also for treatment of anal incontinence. We aimed to determine the effectiveness and safety of polyacrylamide hydrogel when used as a transanal submucosal bulking agent in women with anal incontinence. Thirty women with a diagnosis of anal incontinence and a Cleveland Clinic Incontinence Score (CCIS) >10 were randomized to three different techniques of transanal submucosal injections using polyacrylamide hydrogel. Follow up was performed at 2, 6 and 12 months using CCIS and the Fecal Incontinence Quality of Life scale (FIQL). In all, 29 of the 30 women completed the follow up. Approximately half of the women requested a re-injection at the 6-month visit. The overall CCIS improved significantly from baseline (14.7. SD 2.5) to 1 year (12.4. SD 3.1) (p = 0.003). There was a significant improvement with regard to the occurrence of loose fecal incontinence (p = 0.014) but not for solid fecal incontinence (p = 0.28). At 1 year the FIQL domains of coping-behavior, depression, and embarrassment showed significant improvements (p = 0.012, p = 0.007 and p = 0.007, respectively). We recorded no adverse events related either to the injection technique or the biomaterial. There were no significant differences between the treatment groups in either CCIS or FIQL scores. Transanal submucosal injection of polyacrylamide hydrogel resulted in a modest although significant overall improvement in anal incontinence symptom scores with corresponding improvements in several domains of quality of life, regardless of injection volume. © 2016 Nordic Federation of Societies of Obstetrics and Gynecology.

  8. 21 CFR 866.4900 - Support gel.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Support gel. 866.4900 Section 866.4900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES...) Identification. A support gel for clinical use is a device that consists of an agar or agarose preparation that...

  9. 21 CFR 866.4900 - Support gel.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Support gel. 866.4900 Section 866.4900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES...) Identification. A support gel for clinical use is a device that consists of an agar or agarose preparation that...

  10. Gel Electrophoresis--The Easy Way for Students

    ERIC Educational Resources Information Center

    VanRooy, Wilhelmina; Sultana, Khalida

    2010-01-01

    This article describes a simple, inexpensive, easy to conduct gel-electrophoresis activity using food dyes. It is an alternative to the more expensive counterparts which require agarose gel, DNA samples, purchased chamber and Tris-borate-EDTA buffer. We suggest some learning activities for senior biology students along with comments on several…

  11. Formation of composite polyacrylamide and silicone substrates for independent control of stiffness and strain

    PubMed Central

    Simmons, Chelsey S.; Ribeiro, Alexandre J. S.; Pruitt, Beth L.

    2013-01-01

    Cells that line major tissues in the body such as blood vessels, lungs and gastrointestinal tract experience deformation from mechanical strain with our heartbeat, breathing, and other daily activities. Tissues also remodel in both development and disease, changing their mechanical properties. Taken together, cells can experience vastly different mechanical cues resulting from the combination of these interdependent stimuli. To date, most studies of cellular mechanotransduction have been limited to assays in which variations in substrate stiffness and strain were not combined. Here, we address this technological gap by implementing a method that can simultaneously tune both substrate stiffness and mechanical strain. Substrate stiffness is controlled with different monomer and crosslinker ratios during polyacrylamide gel polymerization, and strain is transferred from the underlying silicone platform when stretched. We demonstrate this platform with polyacrylamide gels with elastic moduli at 6 kPa and 20 kPa in combination with two different silicone formulations. The gels remain attached with up to 50% applied strains. To validate strain transfer through the gels into cells, we employ particle-tracking methods and observe strain transmission via cell morphological changes. PMID:23287818

  12. Problem-solving test: Southwestern blotting.

    PubMed

    Szeberényi, József

    2014-01-01

    Terms to be familiar with before you start to solve the test: Southern blotting, Western blotting, restriction endonucleases, agarose gel electrophoresis, nitrocellulose filter, molecular hybridization, polyacrylamide gel electrophoresis, proto-oncogene, c-abl, Src-homology domains, tyrosine protein kinase, nuclear localization signal, cDNA, deletion mutants, expression plasmid, transfection, RNA polymerase II, promoter, Shine-Dalgarno sequence, polyadenylation element, affinity chromatography, Northern blotting, immunoprecipitation, sodium dodecylsulfate, autoradiography, tandem repeats. Copyright © 2014 The International Union of Biochemistry and Molecular Biology.

  13. Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex.

    PubMed

    Berggren, K; Chernokalskaya, E; Steinberg, T H; Kemper, C; Lopez, M F; Diwu, Z; Haugland, R P; Patton, W F

    2000-07-01

    SYPRO Ruby dye is a permanent stain comprised of ruthenium as part of an organic complex that interacts noncovalently with proteins. SYPRO Ruby Protein Gel Stain provides a sensitive, gentle, fluorescence-based method for detecting proteins in one-dimensional and two-dimensional sodium dodecyl sulfate-polyacrylamide gels. Proteins are fixed, stained from 3h to overnight and then rinsed in deionized water or dilute methanol/acetic acid solution for 30 min. The stain can be visualized using a wide range of excitation sources commonly used in image analysis systems including a 302 nm UV-B transilluminator, 473 nm second harmonic generation (SHG) laser, 488 nm argon-ion laser, 532 nm yttrium-aluminum-garnet (YAG) laser, xenon arc lamp, blue fluorescent light bulb or blue light-emitting diode (LED). The sensitivity of SYPRO Ruby Protein Gel Stain is superior to colloidal Coomassie Brilliant Blue (CBB) stain or monobromobimane labeling and comparable with the highest sensitivity silver or zinc-imidazole staining procedures available. The linear dynamic range of SYPRO Ruby Protein Gel stain extends over three orders of magnitude, which is vastly superior to silver, zinc-imidazole, monobromobimane and CBB stain. The fluorescent stain does not contain superfluous chemicals (formaldehyde, glutaraldehyde, Tween-20) that frequently interfere with peptide identification in mass spectrometry. While peptide mass profiles are severely altered in protein samples prelabeled with monobromobimane, successful identification of proteins by peptide mass profiling using matrix-assisted laser desorption/ionization mass spectrometry was easily performed after protein detection with SYPRO Ruby Protein Gel stain.

  14. Quantification of AAV particle titers by infrared fluorescence scanning of coomassie-stained sodium dodecyl sulfate-polyacrylamide gels.

    PubMed

    Kohlbrenner, Erik; Henckaerts, Els; Rapti, Kleopatra; Gordon, Ronald E; Linden, R Michael; Hajjar, Roger J; Weber, Thomas

    2012-06-01

    Adeno-associated virus (AAV)-based vectors have gained increasing attention as gene delivery vehicles in basic and preclinical studies as well as in human gene therapy trials. Especially for the latter two-for both safety and therapeutic efficacy reasons-a detailed characterization of all relevant parameters of the vector preparation is essential. Two important parameters that are routinely used to analyze recombinant AAV vectors are (1) the titer of viral particles containing a (recombinant) viral genome and (2) the purity of the vector preparation, most commonly assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by silver staining. An important, third parameter, the titer of total viral particles, that is, the combined titer of both genome-containing and empty viral capsids, is rarely determined. Here, we describe a simple and inexpensive method that allows the simultaneous assessment of both vector purity and the determination of the total viral particle titer. This method, which was validated by comparison with established methods to determine viral particle titers, is based on the fact that Coomassie Brilliant Blue, when bound to proteins, fluoresces in the infrared spectrum. Viral samples are separated by SDS-PAGE followed by Coomassie Brilliant Blue staining and gel analysis with an infrared laser-scanning device. In combination with a protein standard, our method allows the rapid and accurate determination of viral particle titers simultaneously with the assessment of vector purity.

  15. Multichannel microscale system for high throughput preparative separation with comprehensive collection and analysis

    DOEpatents

    Karger, Barry L.; Kotler, Lev; Foret, Frantisek; Minarik, Marek; Kleparnik, Karel

    2003-12-09

    A modular multiple lane or capillary electrophoresis (chromatography) system that permits automated parallel separation and comprehensive collection of all fractions from samples in all lanes or columns, with the option of further on-line automated sample fraction analysis, is disclosed. Preferably, fractions are collected in a multi-well fraction collection unit, or plate (40). The multi-well collection plate (40) is preferably made of a solvent permeable gel, most preferably a hydrophilic, polymeric gel such as agarose or cross-linked polyacrylamide.

  16. A Simple Vertical Slab Gel Electrophoresis Apparatus.

    ERIC Educational Resources Information Center

    Carter, J. B.; And Others

    1983-01-01

    Describes an inexpensive, easily constructed, and safe vertical slab gel kit used routinely for sodium dodecyl sulphate-polyacrylamide gel electrophoresis research and student experiments. Five kits are run from a single transformer. Because toxic solutions are used, students are given plastic gloves and closely supervised during laboratory…

  17. Preparation and flash sintering of MgTiO3 nanopowders obtained by the polyacrylamide gel method

    NASA Astrophysics Data System (ADS)

    Su, Xinghua; Bai, Ge; Zhang, Jing; Zhou, Jie; Jia, Yongjie

    2018-06-01

    Using a polyacrylamide gel method, phase pure and well-dispersed MgTiO3 nanopowders were prepared at 800 °C for 2 h. It was found that a high mole ratio of monomers to precursors resulted in low formation temperature of MgTiO3, due to the highly mixing homogeneity and smaller particle sizes of precursors. Sintering behaviors of MgTiO3 nanopowders under DC electric field from 500 to 800 V/cm were investigated. Nearly full dense MgTiO3 ceramics can be prepared in 30 s. An abrupt and simultaneous increase in current density and power dissipation were observed in sintering process, which are characteristics of flash sintering. The power dissipation for the flash sintering was found to be 82 mW/mm3. The densities and average grain sizes of samples increase with the increase of the electrical field strength. It was suggested that Joule heating was the main mechanism of flash sintering of MgTiO3 ceramics. Our work provides a useful route for the fabrication of dense MgTiO3 ceramics at low temperature in short time.

  18. Organic influences on inorganic patterns of diffusion-controlled precipitation in gels

    NASA Astrophysics Data System (ADS)

    Barge, Laura M.; Nealson, Kenneth H.; Petruska, John

    2010-06-01

    The well-known AgNO 3/K 2CrO 4 reaction-diffusion system produces periodic bands of silver chromate precipitate in gelatin, but only randomly oriented crystals in agarose gel. We show that comparable bands can be produced in agarose gel by adding small amounts of simple organic acids (e.g., acetic acid, N-acetyl glycine, and N-acetyl alanine) that suppress crystal growth and promote formation of rounded particles of precipitate. These results indicate that α-carboxyl groups of amino acids or short peptides in gelatin under mildly acidic conditions can induce periodic band patterns in diffusion-controlled silver chromate precipitates.

  19. Detection of erythrocyte membrane proteins, sialoglycoproteins, and lipids in the same polyacrylamide gel using a double-staining technique.

    PubMed Central

    Dzandu, J K; Deh, M E; Barratt, D L; Wise, G E

    1984-01-01

    A silver/Coomassie brilliant blue R-250 staining technique that permits a color-coded differentiation of erythrocyte membrane proteins, sialoglycoproteins, and lipids in a single one-dimensional NaDodSO4/polyacrylamide gel has been described. Gels stained first with silver stain and then with Coomassie blue (CB) showed the characteristic blue staining of all conventional CB-sensitive membrane polypeptides, whereas periodic acid-Schiff reagent-sensitive sialoglycoproteins and lipids stained yellow. Several yellow Ag-stained bands corresponding to major and minor sialoglycoproteins were detected at Mr X 10(-3) of 88, 72, 65, 41, 35, 31, 28, 24, and 20. Neuraminidase treatment of intact erythrocytes caused shifts in the electrophoretic mobilities of several yellow-stained bands without affecting the CB-stained polypeptide pattern. These observations afforded evidence that the yellow-staining bands were sialoglycoproteins and lipids. The double-staining technique was used in a topological analysis of the membrane surface of the erythrocyte using protease digestion and selective solubilization. Trypsin cleaved the yellow bands at Mr 88,000 and 41,000. Membrane-associated cleavage products were noted at Mr 58,000 and 38,000. Pronase treatment of intact cells gave membrane-associated cleavage products at Mr 38,000 (yellow) and two CB-stained bands at Mr 58,000 and 60,000. These results suggested that the double-staining technique may be applicable in compositional and topological analyses of other biological membranes. Images PMID:6200882

  20. Concentration of acrylamide in a polyacrylamide gel affects VP4 gene coding assignment of group A equine rotavirus strains with P[12] specificity

    PubMed Central

    2010-01-01

    Background It is universally acknowledged that genome segment 4 of group A rotavirus, the major etiologic agent of severe diarrhea in infants and neonatal farm animals, encodes outer capsid neutralization and protective antigen VP4. Results To determine which genome segment of three group A equine rotavirus strains (H-2, FI-14 and FI-23) with P[12] specificity encodes the VP4, we analyzed dsRNAs of strains H-2, FI-14 and FI-23 as well as their reassortants by polyacrylamide gel electrophoresis (PAGE) at varying concentrations of acrylamide. The relative position of the VP4 gene of the three equine P[12] strains varied (either genome segment 3 or 4) depending upon the concentration of acrylamide. The VP4 gene bearing P[3], P[4], P[6], P[7], P[8] or P[18] specificity did not exhibit this phenomenon when the PAGE running conditions were varied. Conclusions The concentration of acrylamide in a PAGE gel affected VP4 gene coding assignment of equine rotavirus strains bearing P[12] specificity. PMID:20573245

  1. Rapid shape memory TEMPO-oxidized cellulose nanofibers/polyacrylamide/gelatin hydrogels with enhanced mechanical strength.

    PubMed

    Li, Nan; Chen, Wei; Chen, Guangxue; Tian, Junfei

    2017-09-01

    TEMPO-oxidized cellulose nanofibers/polyacrylamide/gelatin shape memory hydrogels were successfully fabricated through a facile in-situ free-radical polymerization method, and double network was formed by chemically cross-linked polyacrylamide (PAM) network and physically cross-linked gelatin network. TEMPO-oxidized cellulose nanofibers (TOCNs) were introduced to improve the mechanical properties of the hydrogel. The structure, shape memory behaviors and mechanical properties of the resulting composite gels with varied gel compositions were investigated. The results obtained from those different studies revealed that TOCNs, gelatin, and PAM could mix with each other homogeneously. Due to the thermoreversible nature of the gelatin network, the composite hydrogels exhibited attractive thermo-induced shape memory properties. In addition, good mechanical properties (strength >200kPa, strain >650%) were achieved. Such composite hydrogels with good shape memory behavior and enhanced mechanical strength would be an attractive candidate for a wide variety of applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. [Immobilization of pectawamorine G10x by gel entrapment].

    PubMed

    Bogatskiĭ, A V; Davidenko, T I; Areshidze, I V; Gren', T A; Sevast'ianov, O V

    1979-01-01

    Polyacrylamide gel immobilization of pectawamorine G10x was investigated. Its pectinesterase and polygalacturonase activity and stability in storage were measured. The degree of pectawamorine binding during gel immobilization was 80--90%, 55% of initial activity being retained. Thermal stability of the immobilized and native preparations was equal. Pectinesterase activity of the gel immobilized enzyme increased during storage.

  3. Two-dimensional polyacrylamide gel electrophoresis of equine seminal plasma proteins and their relation with semen freezability.

    PubMed

    Jobim, M I M; Trein, C; Zirkler, H; Gregory, R M; Sieme, H; Mattos, R C

    2011-09-01

    The objective was to evaluate protein profiles of equine seminal plasma using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and to determine whether any of these proteins were related to semen freezability. Seminal plasma was collected from 10 stallions, of high and low semen freezability, housed at the State Stud of Lower Saxony, and routinely used in AI programs. Twenty-five protein spots were identified from the two-dimensional gel (12%), seven of which were present in all samples (all proteins were identified by MALDI-MS). Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been used to generate ion images of samples in one or more mass-to-charge (m/z) values, providing the capability of mapping specific molecules to two-dimensional coordinates of the original sample. Of the 25 proteins identified, two spots had greater relative content (P < 0.05) in seminal plasma samples collected from stallions with high semen freezability: spot 5 (80-85 kDa, isoelectric point [pI] 7.54), identified as CRISP-3; and spot 45 (18.2 kDa, pI 5.0-5.2), identified as HSP-2. Conversely, protein content was greater (P < 0.05) in seminal plasma samples from stallions with low semen freezability: spot 7 (75.4 kDa, pI 6.9-7.4), identified as lactoferrin; spot 15 (26.7 kDa, pI 5.51), identified as kallikrein; spot 25 (25 kDa, pI 7.54), identified as CRISP-3; and spot 35 (13.9 kDa, pI 3.8-4.2), identified as HSP-1. In conclusion, there were differences in the seminal plasma protein profile from stallions with high and low semen freezability. Furthermore, CRISP-3 and HSP-2 were potential seminal plasma markers of high semen freezability. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Nonelectrophoretic bidirectional transfer of a single SDS-PAGE gel with multiple antigens to obtain 12 immunoblots.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2009-01-01

    Protein blotting is an invaluable technique in immunology to detect and characterize proteins of low abundance. Proteins resolved on sodium dodecyl sulfate (SDS) polyacrylamide gels are normally transferred electrophoretically to adsorbent membranes such as nitrocellulose or polyvinylidene diflouride membranes. Here, we describe the nonelectrophroretic transfer of the Ro 60 (or SSA) autoantigen, 220- and 240-kD spectrin antigens, and prestained molecular weight standards from SDS polyacrylamide gels to obtain up to 12 immunoblots from a single gel and multiple sera.

  5. Improved stability and electrophoretic properties of preformed fluorescent cationic dye-DNA complexes in a taps-tetrapentylammonium buffer in agarose slab gels.

    PubMed

    Zeng, Z; Clark, S M; Mathies, R A; Glazer, A N

    1997-10-01

    High-resolution capillary electrophoresis sizing of preformed complexes of bis-intercalating fluorescent dyes with double-stranded DNA has been demonstrated using hydroxyethylcellulose and 3-[tris-(hydroxymethyl) methylamino]-1-propanesulfonic acid-tetrapentylammonium (Taps-NPe+4) buffers (S. M. Clark and R. A. Mathies, Anal. Chem. 69, 1355-1363, 1997). Such capillary electrophoresis separations were unattainable in conventional buffers containing other cations such as Tris+, Na+, and NH+4. We report here the behavior of preformed double-stranded DNA-dye complexes on agarose slab gel electrophoresis in 40 mM Taps-NPe+4, 1 mM H2EDTA, pH 8.2. Upon electrophoresis in this buffer (a) complexes formed at DNA base pairs:dye ratios ranging from 100:1 to 5:1 show the same mobility; (b) the half-lives of DNA-dye complexes with monointercalators are two- to threefold longer than those in commonly used Tris buffers; (c) there is little dye transfer between labeled and unlabeled DNA molecules; and (d) precise two-color sizing of preformed restriction fragment-dye complexes with fluorescent bisintercalators is achieved.

  6. Electrically controlled polymeric gel actuators

    DOEpatents

    Adolf, Douglas B.; Shahinpoor, Mohsen; Segalman, Daniel J.; Witkowski, Walter R.

    1993-01-01

    Electrically controlled polymeric gel actuators or synthetic muscles capable of undergoing substantial expansion and contraction when subjected to changing pH environments, temperature, or solvent. The actuators employ compliant containers for the gels and their solvents. The gels employed may be cylindrical electromechanical gel fibers such as polyacrylamide fibers or a mixture of poly vinyl alcohol-polyacrylic acid arranged in a parallel aggregate and contained in an electrolytic solvent bath such as salt water. The invention includes smart, electrically activated devices exploiting this phenomenon. These devices are capable of being manipulated via active computer control as large displacement actuators for use in adaptive structure such as robots.

  7. Electrically controlled polymeric gel actuators

    DOEpatents

    Adolf, D.B.; Shahinpoor, M.; Segalman, D.J.; Witkowski, W.R.

    1993-10-05

    Electrically controlled polymeric gel actuators or synthetic muscles are described capable of undergoing substantial expansion and contraction when subjected to changing pH environments, temperature, or solvent. The actuators employ compliant containers for the gels and their solvents. The gels employed may be cylindrical electromechanical gel fibers such as polyacrylamide fibers or a mixture of poly vinyl alcohol-polyacrylic acid arranged in a parallel aggregate and contained in an electrolytic solvent bath such as salt water. The invention includes smart, electrically activated devices exploiting this phenomenon. These devices are capable of being manipulated via active computer control as large displacement actuators for use in adaptive structure such as robots. 11 figures.

  8. The preparation of low electroendosmosis agarose and its physico-chemical property

    NASA Astrophysics Data System (ADS)

    Hu, Rugui; Liu, Xiaolei; Liu, Li; Zhang, Quanbin; Zhang, Hong; Niu, Xizhen

    2007-10-01

    Studies on Gelidium amansii agar fractionations were carried out in this paper. Gelidium amansii agar was fractionated on DEAE-Cellulose, and four fractions were obtained sequentially. The fractions were analyzed on physical and chemical properties, and IR and 13C-NMR spectroscopy applied for elucidating the chemical structure. Among the four fractions obtained, water fraction measured up to the standard of low EEO agarose. The sulfate content, ash content, electroendosmosis and gel strength (1%) of water fraction were 0.16%, 0.34%, 0.12 and 1 130g/cm2 respectively, similar to those of the Sigma products.

  9. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis.

    PubMed

    Li, Xingrui; Zhang, Dongfeng; Zhang, Huimin; Guan, Zhichao; Song, Yanling; Liu, Ruochen; Zhu, Zhi; Yang, Chaoyong

    2018-02-20

    Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.

  10. High-resolution gel electrophoresis and sodium dodecyl sulphate-agarose gel electrophoresis on urine samples for qualitative analysis of proteinuria in dogs.

    PubMed

    Giori, Luca; Tricomi, Flavia Marcella; Zatelli, Andrea; Roura, Xavier; Paltrinieri, Saverio

    2011-07-01

    The aims of the current study were to assess whether sodium dodecyl sulphate-agarose gel electrophoresis (SDS-AGE) and high-resolution electrophoresis (HRE) can identify dogs with a urinary protein-to-creatinine ratio (UPC ratio) >0.2 and whether HRE can provide preliminary information about the type of proteinuria, using SDS-AGE as a reference method. HRE and SDS-AGE were conducted on 87 urine samples classified according to the International Renal Interest Society as non-proteinuric (NP; UPC ratio: <0.20; 32/87), borderline proteinuric (BP; UPC ratio: 0.21-0.50; 15/87), or proteinuric (P; UPC ratio: >0.51; 40/87). SDS-AGE and HRE were positive in 14 out of 32 and 3 out of 32 NP samples and in 52 out of 55 and 40 out of 55 samples with a UPC ratio >0.20, respectively. The concordance between HRE or SDS and UPC ratio was comparable (κ = 0.59; κ = 0.55). However, specificity (90%) and positive likelihood ratio (7.76) were higher for HRE than for SDS-AGE (56% and 2.16) while sensitivity was lower (73% vs. 94%). The analysis of HRE results revealed that a percentage of albumin >41.4% and an albumin/α(1)-globulin ratio (alb/α(1) ratio) >1.46 can identify samples classified by SDS-AGE as affected by glomerular proteinuria while a percentage of α(1)-globulin >40.8% and an alb/α(1) ratio <0.84 can identify samples classified by SDS-AGE as affected by tubular proteinuria. In conclusion, both SDS-AGE and HRE could misclassify samples with a UPC ratio higher or lower than 0.20. Therefore, UPC ratio must always be determined before conducting these tests. The percentage of albumin and α(1)-globulin or the alb/α(1) ratio determined by HRE can provide preliminary information about the origin of proteinuria.

  11. The development of simple and sensitive small-molecule fluorescent probes for the detection of serum proteins after native polyacrylamide gel electrophoresis.

    PubMed

    Wang, Fangfang; Huang, Lingyun; Na, Na; He, Dacheng; Sun, Dezhi; Ouyang, Jin

    2012-05-21

    In this paper, a simple and sensitive small-molecule fluorescent probe, 2,5-dihydroxy-4'-dimethylaminochalcone (DHDMAC), was designed and synthesized for the detection of human serum proteins via hydrophobic interactions after polyacrylamide gel electrophoresis (PAGE). This probe produced lower fluorescence emission in the absence of proteins, and the emission intensity was significantly increased after the interaction with serum proteins. To demonstrate the imaging performance of this probe as a fluorescent dye, a series of experiments was conducted that included sensitivity comparison and 2D-PAGE. The results indicated that the sensitivity of DHDMAC staining is comparable to that of the most widely used fluorescent dye, SYPRO Ruby, and more protein spots (including thyroxine-binding globulin, angiotensinogen, afamin, zinc-α-2-glycoprotein and α-1-antichymotrypsin) were detected after 2D-PAGE. Therefore, DHDMAC is a good protein reporter due to its fast staining procedure, low detection limits and high resolution.

  12. Determination of the molecular weight of human gamma-3 chains by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate

    PubMed Central

    Virella, G.; Parkhouse, R. M. E.

    1972-01-01

    The molecular weights (mol. wt) for heavy chains of human IgG were estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. Polyclonal IgG and monoclonal IgG proteins of different subclasses were extensively reduced with 50 mM dithioerythritol, in the presence of 2 per cent sodium dodecyl sulphate, at 100°. Four control proteins of known mol. wt (cytochrome C, chymotrypsinogen A, egg albumin, and serum albumin) were used to construct a linear plot of electrophoretic mobility versus log mol. wt. From this plot, the following mol. wts were calculated: 53,650±700 for polyclonal IgG; 54,200±1065 for γ1, γ2, and γ4 chains, and 60,950±585 for γ3 chains. Those results confirm the larger size of γ3 chains reported by Saluk and Clem (1971). PMID:4346255

  13. Specific capture, recovery and culture of cancer cells using oriented antibody-modified polystyrene chips coated with agarose film.

    PubMed

    Jeong, Jiyun; Lee, Yeolin; Yoo, Yeongeun; Lee, Myung Kyu

    2018-02-01

    Agarose gel can be used for three dimensional (3D) cell culture because it prevents cell attachment. The dried agarose film coated on a culture plate also protected cell attachment and allowed 3D growth of cancer cells. We developed an efficient method for agarose film coating on an oxygen-plasma treated micropost polystyrene chip prepared by an injection molding process. The agarose film was modified to maleimide or Ni-NTA groups for covalent or cleavable attachment of photoactivatable Fc-specific antibody binding proteins (PFcBPs) via their N-terminal cysteine residues or 6xHis tag, respectively. The antibodies photocrosslinked onto the PFcBP-modified chips specifically captured the target cells without nonspecific binding, and the captured cells grew 3D modes on the chips. The captured cells on the cleavable antibody-modified chips were easily recovered by treatment of commercial trypsin-EDTA solution. Under fluidic conditions using an antibody-modified micropost chip, the cells were mainly captured on the micropost walls of the chip rather than on the bottom of it. The presented method will also be applicable for immobilization of oriented antibodies on various microfluidic chips with different structures. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Micro-patterned agarose gel devices for single-cell high-throughput microscopy of E. coli cells.

    PubMed

    Priest, David G; Tanaka, Nobuyuki; Tanaka, Yo; Taniguchi, Yuichi

    2017-12-21

    High-throughput microscopy of bacterial cells elucidated fundamental cellular processes including cellular heterogeneity and cell division homeostasis. Polydimethylsiloxane (PDMS)-based microfluidic devices provide advantages including precise positioning of cells and throughput, however device fabrication is time-consuming and requires specialised skills. Agarose pads are a popular alternative, however cells often clump together, which hinders single cell quantitation. Here, we imprint agarose pads with micro-patterned 'capsules', to trap individual cells and 'lines', to direct cellular growth outwards in a straight line. We implement this micro-patterning into multi-pad devices called CapsuleHotel and LineHotel for high-throughput imaging. CapsuleHotel provides ~65,000 capsule structures per mm 2 that isolate individual Escherichia coli cells. In contrast, LineHotel provides ~300 line structures per mm that direct growth of micro-colonies. With CapsuleHotel, a quantitative single cell dataset of ~10,000 cells across 24 samples can be acquired and analysed in under 1 hour. LineHotel allows tracking growth of > 10 micro-colonies across 24 samples simultaneously for up to 4 generations. These easy-to-use devices can be provided in kit format, and will accelerate discoveries in diverse fields ranging from microbiology to systems and synthetic biology.

  15. Quantification of fetal and total circulatory DNA in maternal plasma samples before and after size fractionation by agarose gel electrophoresis.

    PubMed

    Hromadnikova, I; Zejskova, L; Doucha, J; Codl, D

    2006-11-01

    Fetal extracellular DNA is mainly derived from apoptotic bodies of trophoblast. Recent studies have shown size differences between fetal and maternal extracellular DNA. We have examined the quantification of fetal (SRY gene) and total (GLO gene) extracellular DNA in maternal plasma in different fractions (100-300, 300-500, 500-700, 700-900, and >900 bp) after size fractionation by agarose gel electrophoresis. DNA was extracted from maternal plasma samples from 11 pregnant women carrying male foetuses at the 16th week of gestation. Fetal circulatory DNA was mainly detected in the 100-300 bp fraction with the median concentration being 14.4 GE/ml. A lower median amount of 4.9 GE/ml was also found in the 300-500 bp fraction. Circulatory DNA extracted from the 100-300 bp fraction contained 4.2 times enriched fetal DNA when compared with unseparated DNA sample. Fetal DNA within the 300-500 bp fraction was 2.5 times enriched. Circulatory fetal DNA is predominantly present in a fraction with molecular size <500 bp, which can be used for the detection of paternally inherited alleles. However, the usage of size-separated DNA is not suitable for routine clinical applications because of risk of contamination.

  16. Agarose-based biomaterials for tissue engineering.

    PubMed

    Zarrintaj, Payam; Manouchehri, Saeed; Ahmadi, Zahed; Saeb, Mohammad Reza; Urbanska, Aleksandra M; Kaplan, David L; Mozafari, Masoud

    2018-05-01

    Agarose is a natural polysaccharide polymer having unique characteristics that give reason to consider it for tissue engineering applications. Special characteristics of agarose such as its excellent biocompatibility, thermo-reversible gelation behavior and physiochemical features support its use as a biomaterial for cell growth and/or controlled/localized drug delivery. The resemblance of this natural carbohydrate polymer to the extracellular matrix results in attractive features that bring about a strong interest in its usage in the field. The scope of this review is to summarize the extensive researches addressing agarose-based biomaterials in order to provide an in-depth understanding of its tissue engineering-related applications. Copyright © 2018 Elsevier Ltd. All rights reserved.

  17. Microchannel gel electrophoretic separation systems and methods for preparing and using

    DOEpatents

    Herr, Amy E; Singh, Anup K; Throckmorton, Daniel J

    2015-02-24

    A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

  18. Microchannel gel electrophoretic separation systems and methods for preparing and using

    DOEpatents

    Herr, Amy; Singh, Anup K; Throckmorton, Daniel J

    2013-09-03

    A micro-analytical platform for performing electrophoresis-based immunoassays was developed by integrating photopolymerized cross-linked polyacrylamide gels within a microfluidic device. The microfluidic immunoassays are performed by gel electrophoretic separation and quantifying analyte concentration based upon conventional polyacrylamide gel electrophoresis (PAGE). To retain biological activity of proteins and maintain intact immune complexes, native PAGE conditions were employed. Both direct (non-competitive) and competitive immunoassay formats are demonstrated in microchips for detecting toxins and biomarkers (cytokines, c-reactive protein) in bodily fluids (serum, saliva, oral fluids). Further, a description of gradient gels fabrication is included, in an effort to describe methods we have developed for further optimization of on-chip PAGE immunoassays. The described chip-based PAGE immunoassay method enables immunoassays that are fast (minutes) and require very small amounts of sample (less than a few microliters). Use of microfabricated chips as a platform enables integration, parallel assays, automation and development of portable devices.

  19. A novel superporous agarose medium for high-speed protein chromatography.

    PubMed

    Shi, Qing-Hong; Zhou, Xin; Sun, Yan

    2005-12-05

    A novel superporous agarose (SA) bead characterized by the presence of wide pores has been fabricated by water-in-oil emulsification using solid granules of calcium carbonate as porogenic agent. After cross-linking, the solid granules were removed by dissolving them in hydrochloric acid. Then, the gel was modified with diethylaminoethyl groups to create an anion exchanger, SA-DEAE, for protein adsorption. A homogeneous agarose (HA) bead was also produced and modified with DEAE for comparison. It was found that the porosity of SA-DEAE was about 6% larger than that of HA-DEAE. Moreover, both optical micrographs and confocal laser scanning microscopy (CLSM) of the ion exchangers with adsorbed fluorescein isothiocyanate (FITC) labeled IgG revealed the superporous structure of the SA medium. In addition, the SA-DEAE column had lower backpressure than the HA-DEAE column, confirming the convective flow of mobile phase through the wide pores. Due to the presence of the wide pores, more channels were available for protein transport and, furthermore, more diffusive pores in the agarose network were accessible for the protein approach from different directions. This led to 40% higher protein capacity and two times higher effective pore diffusivity in the SA-DEAE than in HA-DEAE. Moreover, an increase of the efficiency of the SA-DEAE column until a flow rate of 5 cm/min and the independency of the column efficiency at flow rates from 5 to 17.8 cm/min was found, indicating that intraparticle mass transfer was intensified by convective flow at elevated flow rates. Therefore, the chromatographic resolution of IgG and BSA was little affected up to a flow rate of 17.8 cm/min. The results indicate that the SA medium is favorable for high-speed protein chromatography. (c) 2005 Wiley Periodicals, Inc.

  20. Multi-gel casting apparatus for vertical polyacrylamide gels with in-built solution flow system and liquid level detectors.

    PubMed

    Maurye, Praveen; Basu, Arpita; Bandyopadhyay, Tapas Kumar; Biswas, Jayanta Kumar; Mohanty, Bimal Prasana

    2017-08-01

    PAGE is the most widely used technique for the separation and biochemical analysis of biomolecules. The ever growing field of proteomics and genomics necessitates the analysis of many proteins and nucleic acid samples to understand further about the structure and function of cells. Simultaneous analysis of multiple protein samples often requires casting of many PAGE gels. Several variants of multi-gel casting/electrophoresis apparatuses are frequently used in research laboratories. Requirement of supplementary gels to match the growing demand for analyzing additional protein samples sometimes become a cause of concern. Available apparatuses are not amenable to and therefore, not recommended for any modification to accommodate additional gel casting units other than what is prescribed by the manufacturer. A novel apparatus is described here for casting multiple PAGE gels comprising four detachable components that provide enhanced practicability and performance of the apparatus. This newly modified apparatus promises to be a reliable source for making multiple gels in less time without hassle. Synchronized functioning of unique components broaden the possibilities of developing inexpensive, safe, and time-saving multi-gel casting apparatus. This apparatus can be easily fabricated and modified to accommodate desired number of gel casting units. The estimated cost (∼$300) for fabrication of the main apparatus is very competitive and effortless assembly procedure can be completed within ∼30 min. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Analysis of spatial diffusion of ferric ions in PVA-GTA gel dosimeters through magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Marrale, Maurizio; Collura, Giorgio; Gallo, Salvatore; Nici, Stefania; Tranchina, Luigi; Abbate, Boris Federico; Marineo, Sandra; Caracappa, Santo; d'Errico, Francesco

    2017-04-01

    This work focused on the analysis of the temporal diffusion of ferric ions through PVA-GTA gel dosimeters. PVA-GTA gel samples, partly exposed with 6 MV X-rays in order to create an initial steep gradient, were mapped using magnetic resonance imaging on a 7T MRI scanner for small animals. Multiple images of the gels were acquired over several hours after irradiation and were analyzed to quantitatively extract the signal profile. The spatial resolution achieved is 200 μm and this makes this technique particularly suitable for the analysis of steep gradients of ferric ion concentration. The results obtained with PVA-GTA gels were compared with those achieved with agarose gels, which is a standard dosimetric gel formulation. The analysis showed that the diffusion process is much slower (more than five times) for PVA-GTA gels than for agarose ones. Furthermore, it is noteworthy that the diffusion coefficient value obtained through MRI analysis is significantly consistent with that obtained in separate study Marini et al. (Submitted for publication) using a totally independent method such as spectrophotometry. This is a valuable result highlighting that the good dosimetric features of this gel matrix not only can be reproduced but also can be measured through independent experimental techniques based on different physical principles.

  2. Methods and reagents. Degraded DNA and gel tornados.

    PubMed

    Hengen, P N

    1997-04-01

    Methods and reagents is a unique monthly column that highlights current discussions in the newsgroup bionet.molbio.methds-reagnts, available on the Internet. This month's column discusses a case of inexplicable DNA degradation and tornados seen in agarose gels. For details on how to partake in the newsgroup, see the accompanying box.

  3. In vivo biocompatibility evaluation of Cibacron blue-agarose.

    PubMed

    Kao, J M; Rose, R; Yousef, M; Hunter, S K; Rodgers, V G

    1999-12-15

    This study investigated the biocompatibility of Cibacron blue-agarose as a biomaterial for microencapsulation. Cibacron blue-agarose is known to have an affinity for albumin under certain pH conditions and in the proper steric environment. Thus it was postulated that the material's high affinity for host albumin might reduce a secondary immune response and reduce the fibrotic overgrowth that often accompanies transplanted foreign materials. In vivo tests were performed using the Lewis rat model. Both Cibacron blue-agarose and plain agarose disks were prepared, with some disks from each group being pre-exposed to sera from Lewis rats. The disks were transplanted into the peritoneal cavities of Lewis rats. After 115 days the disks were excised. Fibrotic overgrowth was analyzed using light microscopy, and a blind study was used to measure the average growth thickness on each disk. The results demonstrated that all disks developed some fibrotic encapsulation and that the presence of Cibacron blue was not significant in reducing fibrotic overgrowth (p = 0.62). Agarose disks pre-exposed to sera had significantly less average overgrowth than any other group (p = 0. 06). Copyright 1999 John Wiley & Sons, Inc.

  4. 21 CFR 172.255 - Polyacrylamide.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ..., Films and Related Substances § 172.255 Polyacrylamide. Polyacrylamide containing not more than 0.2 percent of acrylamide monomer may be safely used as a film former in the imprinting of soft-shell gelatin...

  5. 21 CFR 172.255 - Polyacrylamide.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., Films and Related Substances § 172.255 Polyacrylamide. Polyacrylamide containing not more than 0.2 percent of acrylamide monomer may be safely used as a film former in the imprinting of soft-shell gelatin...

  6. 21 CFR 172.255 - Polyacrylamide.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ..., Films and Related Substances § 172.255 Polyacrylamide. Polyacrylamide containing not more than 0.2 percent of acrylamide monomer may be safely used as a film former in the imprinting of soft-shell gelatin...

  7. 21 CFR 172.255 - Polyacrylamide.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., Films and Related Substances § 172.255 Polyacrylamide. Polyacrylamide containing not more than 0.2 percent of acrylamide monomer may be safely used as a film former in the imprinting of soft-shell gelatin...

  8. Agarose gels

    NASA Astrophysics Data System (ADS)

    2016-11-01

    Discovered in 17th-century Japan, agar is a jelly-like substance obtained by boiling algae, and it is widely used as a gelling agent for desserts in Japanese, Indian, Philippine and Vietnamese cuisine.

  9. High-quality substrate for fluorescence enhancement using agarose-coated silica opal film.

    PubMed

    Xu, Ming; Li, Juan; Sun, Liguo; Zhao, Yuanjin; Xie, Zhuoying; Lv, Linli; Zhao, Xiangwei; Xiao, Pengfeng; Hu, Jing; Lv, Mei; Gu, Zhongze

    2010-08-01

    To improve the sensitivity of fluorescence detection in biochip, a new kind of substrates was developed by agarose coating on silica opal film. In this study, silica opal film was fabricated on glass substrate using the vertical deposition technique. It can provide stronger fluorescence signals and thus improve the detection sensitivity. After coating with agarose, the hybrid film could provide a 3D support for immobilizing sample. Comparing with agarose-coated glass substrate, the agarose-coated opal substrates could selectively enhance particular fluorescence signals with high sensitivity when the stop band of the silica opal film in the agarose-coated opal substrate overlapped the fluorescence emission wavelength. A DNA hybridization experiment demonstrated that fluorescence intensity of special type of agarose-coated opal substrates was about four times that of agarose-coated glass substrate. These results indicate that the optimized agarose-coated opal substrate can be used for improving the sensitivity of fluorescence detection with high quality and selectivity.

  10. Agarose encapsulated mesoporous carbonated hydroxyapatite nanocomposites powder for drug delivery.

    PubMed

    Kolanthai, Elayaraja; Abinaya Sindu, P; Thanigai Arul, K; Sarath Chandra, V; Manikandan, E; Narayana Kalkura, S

    2017-01-01

    The powder composites are predominantly used for filling of voids in bone and as drug delivery carrier to prevent the infection or inflammatory reaction in the damaged tissues. The objective of this work was to study the synthesis of agarose encapsulation on carbonated hydroxyapatite powder and their biological and drug delivery properties. Mesoporous, nanosized carbonated hydroxyapatite/agarose (CHAp/agarose) powder composites were prepared by solvothermal method and subsequently calcined to study the physico-chemical changes, if it subjected to thermal exposure. The phase of the as-synthesized powder was CHAp/agarose whereas the calcinated samples were non-stoichiometric HAp. The CHAp/agarose nanorods were of length 10-80nm and width 40-190nm for the samples synthesized at temperatures 120°C (ST120) and 150°C (ST150). The calcination process produced spheres (10-50nm) and rods with reduced size (40-120nm length and 20-30nm width). Composites were partially dissolved in SBF solution followed by exhibited better bioactivity than non-stoichiometric HAp confirmed by gravimetric method. Hemo and biocompatibility remained unaffected by presence of agarose or carbonate in the HAp. Specific surface area of the composites was high and exhibited an enhanced amoxicillin and 5-fluorouracil release than the calcined samples. The composites demonstrated a strong antimicrobial activity against E. coli, S. aureus and S. epidermidis. The ST120 showed prolonged drug (AMX and 5-Fcil) release and antimicrobial efficacy than ST150 and calcined samples. This technique would be simple and rapid for composites preparation, to produce high quality crystalline, resorbable, mesoporous and bioactive nanocomposite (CHAp/agarose) powders. This work provides new insight into the role of agarose coated on bioceramics by solvothermal technique and suggests that CHAp/agarose composites powders are promising materials for filling of void in bone and drug delivery applications. Copyright © 2016

  11. Functionalized Agarose Self-Healing Ionogels Suitable for Supercapacitors.

    PubMed

    Trivedi, Tushar J; Bhattacharjya, Dhrubajyoti; Yu, Jong-Sung; Kumar, Arvind

    2015-10-12

    Agarose has been functionalized (acetylated/carbanilated) in an ionic liquid (IL) medium of 1-butyl-3-methylimidazolium acetate at ambient conditions. The acetylated agarose showed a highly hydrophobic nature, whereas the carbanilated agarose could be dissolved in water as well as in the IL medium. Thermoreversible ionogels were obtained by cooling the IL sols of carbanilated agarose at room temperature. The ionogel prepared from a protic-aprotic mixed-IL system (1-butyl-3-methylimidazolium chloride and N-(2-hydroxyethyl)ammonium formate) demonstrated a superior self-healing property, as confirmed from rheological measurements. The superior self-healing property of such an ionogel has been attributed to the unique inter-intra hydrogen-bonding network of functional groups inserted in the agarose. The ionogel was tested as a flexible solid electrolyte for an activated-carbon-based supercapacitor cell. The measured specific capacitance was found to be comparable with that of a liquid electrolyte system at room temperature and was maintained for up to 1000 charge-discharge cycles. Such novel functionalized-biopolymer self-healing ionogels with flexibility and good conductivity are desirable for energy-storage devices and electronic skins with superior lifespans and robustness. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Measurements of Elastic Moduli of Silicone Gel Substrates with a Microfluidic Device

    PubMed Central

    Gutierrez, Edgar; Groisman, Alex

    2011-01-01

    Thin layers of gels with mechanical properties mimicking animal tissues are widely used to study the rigidity sensing of adherent animal cells and to measure forces applied by cells to their substrate with traction force microscopy. The gels are usually based on polyacrylamide and their elastic modulus is measured with an atomic force microscope (AFM). Here we present a simple microfluidic device that generates high shear stresses in a laminar flow above a gel-coated substrate and apply the device to gels with elastic moduli in a range from 0.4 to 300 kPa that are all prepared by mixing two components of a transparent commercial silicone Sylgard 184. The elastic modulus is measured by tracking beads on the gel surface under a wide-field fluorescence microscope without any other specialized equipment. The measurements have small and simple to estimate errors and their results are confirmed by conventional tensile tests. A master curve is obtained relating the mixing ratios of the two components of Sylgard 184 with the resulting elastic moduli of the gels. The rigidity of the silicone gels is less susceptible to effects from drying, swelling, and aging than polyacrylamide gels and can be easily coated with fluorescent tracer particles and with molecules promoting cellular adhesion. This work can lead to broader use of silicone gels in the cell biology laboratory and to improved repeatability and accuracy of cell traction force microscopy and rigidity sensing experiments. PMID:21980487

  13. Steroid receptors analysis in human mammary tumors by isoelectric focusing in agarose.

    PubMed

    Bailleul, S; Gauduchon, P; Malas, J P; Lechevrel, C; Roussel, G; Goussard, J

    1988-08-01

    A high resolution and quantitative method for isoelectric focusing has been developed to separate the isoforms of estrogen and progesterone receptors in human mammary tumor cytosols stabilized by sodium molybdate. Agarose gels (0.5%) were used. Six samples can be analyzed on one gel in about 2 h, and 35-microliters samples are sufficient to determine the estrogen receptor isoform pattern. The constant yields and the reproducibility of data allow a quantitative analysis of these receptors. Four estrogen receptor isoforms have been observed (pI 4.7, 5.5, 6, and 6.5), isoforms with pI 4.7 and 6.5 being present in all tumors. After incubation at 28 degrees C in high ionic strength, the comparison of isoelectric focusing and high-performance size exclusion chromatography patterns of estrogen receptor confirms the oligomeric structure of the pI 4.7 isoform and suggests a monomeric structure for the pI 6.5 isoform. Under the same conditions of analysis, only one progesterone receptor isoform has been detected with pI 4.7.

  14. Pre-labeling of diverse protein samples with a fixed amount of Cy5 for sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis.

    PubMed

    Bjerneld, Erik J; Johansson, Johan D; Laurin, Ylva; Hagner-McWhirter, Åsa; Rönn, Ola; Karlsson, Robert

    2015-09-01

    A pre-labeling protocol based on Cy5 N-hydroxysuccinimide (NHS) ester labeling of proteins has been developed for one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis. We show that a fixed amount of sulfonated Cy5 can be used in the labeling reaction to label proteins over a broad concentration range-more than three orders of magnitude. The optimal amount of Cy5 was found to be 50 to 250pmol in 20μl using a Tris-HCl labeling buffer at pH 8.7. Labeling protein samples with a fixed amount of dye in this range balances the requirements of sub-nanogram detection sensitivity and low dye-to-protein (D/P) ratios for SDS-PAGE. Simulations of the labeling reaction reproduced experimental observations of both labeling kinetics and D/P ratios. Two-dimensional electrophoresis was used to examine the labeling of proteins in a cell lysate using both sulfonated and non-sulfonated Cy5. For both types of Cy5, we observed efficient labeling across a broad range of molecular weights and isoelectric points. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Bio-printing cell-laden Matrigel–agarose constructs

    PubMed Central

    Fan, Rong; Piou, Marine; Darling, Evan; Cormier, Denis; Sun, Jun; Wan, Jiandi

    2017-01-01

    3D printing of biological architectures that mimic the structural and functional features of in vivo tissues is of great interest in tissue engineering and the development of transplantable organ constructs. Printable bio-inks that are compatible with cellular activities play critical roles in the process of 3D bio-printing. Although a variety of hydrogels have been used as bio-inks for 3D bio-printing, they inherit poor mechanical properties and/or the lack of essential protein components that compromise their performance. Here, a hybrid Matrigel–agarose hydrogel system has been demonstrated that possesses both desired rheological properties for bio-printing and biocompatibility for long-term (11 days) cell culture. The agarose component in the hybrid hydrogel system enables the maintenance of 3D-printed structures, whereas Matrigel provides essential microenvironments for cell growth. When human intestinal epithelial HCT116 cells are encapsulated in the printed Matrigel–agarose constructs, high cell viability and proper cell spreading morphology are observed. Given that Matrigel is used extensively for 3D cell culturing, the developed 3D-printable Matrigel–agarose system will open a new way to construct Matrigel-based 3D constructs for cell culture and tissue engineering. PMID:27638155

  16. Investigations on gel forming media use in low gravity bioseparations research

    NASA Technical Reports Server (NTRS)

    Todd, Paul; Szlag, David C.; Plank, Lindsay D.; Delcourt, Scott G.; Kunze, M. Elaine

    1989-01-01

    Research on gelling media and conditions suitable for the preservation of the spatial configuration of cell suspensions and macromolecular solutions after separation in free fluid during low gravity experiments is presented. The examples studied included free electrophoresis of cells in a cylindrical column and two-phase aqueous polymer separation. Microgravity electrophoresis experiments were simulated by separating model cell types (animal or human) in a vertical density gradient containing low-conductivity buffer, 1.7-6.5 percent Ficoll, 6.8-5.0 percent sucrose, and 1 percent SeaPrep low-melting temperature agarose. Upon cooling, a gel formed in the column and cells could be captured at the forming locations. Two-phase extraction experiments were simulated using two-polymer solutions in which phase separation occurs in normal saline at temperatures compatible with cell viability and in which one or both phases form a gel upon cooling. Suitable polymers included commercial agaroses (1-2 percent), maltodextrin (5-7 percent), and gelatin (5-20 percent).

  17. Ultra-deep desulfurization via reactive adsorption on peroxophosphomolybdate/agarose hybrids.

    PubMed

    Xu, Jian; Li, Huacheng; Wang, Shengtian; Luo, Fang; Liu, Yunyu; Wang, Xiaohong; Jiang, Zijiang

    2014-09-01

    A catalyst system composed of peroxophosphomolybdates as catalytic center and agarose as matrix material had been designed. The [C16H33N(CH3)3]3[PO4{MoO(O2)2}4]/agarose (C16PMo(O2)2/agarose) hybrid was found to be active for oxidation desulfurization (ODS) of dibenzothiophene (DBT) or real fuel into corresponding sulfone by H2O2 as an oxidant, while the sulfur content could be reduced to 5ppm. The higher activity comes from its components including [PO4{MoO(O2)2}4] catalytic sites, the hydrophobic quaternary ammonium cation affinity to low polarity substrates, and agarose matrix affinity to H2O2 and sulfone. During the oxidative reaction, the mass transfer resistance between H2O2 and organic sulfurs could be decreased and the reaction rate could increase by the assistance of agarose and hydrophobic tails of [C16H33N(CH3)3]3[PO4{MoO(O2)2}4]. Meanwhile, the oxidative products could be adsorbed by agarose matrix to give clean fuel avoiding the post-treatment. In addition, the hybrid was easily regenerated to be reused. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Investigating the fate of activated sludge extracellular proteins in sludge digestion using sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    PubMed

    Park, Chul; Helm, Richard F; Novak, John T

    2008-12-01

    The fate of activated sludge extracellular proteins in sludge digestion was investigated using three different cation-associated extraction methods and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Extraction methods used were the cation exchange resin (CER) method for extracting calcium (Ca2+) and magnesium (Mg2+), sulfide extraction for removing iron, and base treatment (pH 10.5) for dissolving aluminum. Extracellular polymeric substances extracted were then subjected to SDS-PAGE, and the resultant protein profiles were examined before and after sludge digestion. The SDS-PAGE results showed that three methods led to different SDS-PAGE profiles for both undigested and digested sludges. The results further revealed that CER-extracted proteins remained mainly undegraded in anaerobic digestion, but were degraded in aerobic digestion. While the fate of sulfide- and base-extracted proteins was not clear for aerobic digestion, their changes in anaerobic digestion were elucidated. Most sulfide-extracted proteins were removed by anaerobic digestion, while the increase in protein band intensity and diversity was observed for base-extracted proteins. These results suggest that activated sludge flocs contain different fractions of proteins that are distinguishable by their association with certain cations and that each fraction undergoes different fates in anaerobic and aerobic digestion. The proteins that were resistant to degradation and generated during anaerobic digestion were identified by liquid chromatography tandem mass spectrometry. Protein identification results and their putative roles in activated sludge and anaerobic digestion are discussed in this study.

  19. Separation of Native Allophycocyanin and R-Phycocyanin from Marine Red Macroalga Polysiphonia urceolata by the Polyacrylamide Gel Electrophoresis Performed in Novel Buffer Systems

    PubMed Central

    Wang, Yu; Gong, Xueqin; Wang, Shumei; Chen, Lixue; Sun, Li

    2014-01-01

    Three buffer systems of Imidazole−Acetic acid, HEPES−Imidazole/Bis-tris and Bis-tris−HEPES−MES were designed based on the principle of discontinuous polyacrylamide gel electrophoresis (PAGE) for the native PAGE which could be performed in pH 7.0 and 6.5 in order to analyze and prepare the minor components of allophycocyanin (AP) and R-phycocyanin (R-PC) from marine red macroalga Polysiphonia urceolata. These AP and R-PC phycobiliproteins are easily denatured in alkaline environments. The obtained results demonstrated that the PAGE modes performed in the buffer systems of HEPES−Imidazole/Bis-tris and Bis-tris−HEPES−MES gave the satisfactory resolution and separation of AP and R-PC proteins. The absorption and fluorescence spectra of the AP and R-PC proteins which were prepared by the established PAGE modes proved that they maintained natural spectroscopic characteristics. The established PAGE modes may also provide useful references and selections for some other proteins that are sensitive to alkaline environments or are not effectively separated by the classical PAGE modes performed normally in alkaline buffer systems. PMID:25166028

  20. Lymphocyte receptors for pertussis toxin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Clark, C.G.; Armstrong, G.D.

    1990-12-01

    We have investigated human T-lymphocyte receptors for pertussis toxin by affinity isolation and photoaffinity labeling procedures. T lymphocytes were obtained from peripheral human blood, surface iodinated, and solubilized in Triton X-100. The iodinated mixture was then passed through pertussis toxin-agarose, and the fractions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Autoradiography of the fixed, dried gels revealed several bands in the pertussis toxin-bound fraction that were not observed in fractions obtained from histone or fetuin-agarose. Further investigations employed a photoaffinity labeling reagent, sulfosuccinimidyl 2-(p-azido-salicylamido)-1,3'-dithiopropionate, to identify pertussis toxin receptors in freshly isolated peripheral blood monocytic cells, T lymphocytes, andmore » Jurkat cells. In all three cell systems, the pertussis toxin affinity probe specifically labeled a single protein species with an apparent molecular weight of 70,000 that was not observed when the procedure was performed in the presence of excess unmodified pertussis toxin. A protein comparable in molecular weight to the one detected by the photoaffinity labeling technique was also observed among the species that bound to pertussis toxin-agarose. The results suggest that pertussis toxin may bind to a 70,000-Da receptor in human T lymphocytes.« less

  1. The Morse code effect: A crystal-crystal transformation observed in gel-grown lead (II) oxalate crystals

    NASA Astrophysics Data System (ADS)

    Lisgarten, J. N.; Marks, J. A.

    2018-05-01

    This paper reports on an unusual crystal-crystal transformation phenomenon, which we have called the Morse Code Effect, based on the change in appearance of lead(II) oxalate crystals grown in agarose gels.

  2. Fundamentals of Polymer Gel Dosimeters

    NASA Astrophysics Data System (ADS)

    McAuley, Kim B.

    2006-12-01

    The recent literature on polymer gel dosimetry contains application papers and basic experimental studies involving polymethacrylic-acid-based and polyacrylamide-based gel dosimeters. The basic studies assess the relative merits of these two most commonly used dosimeters, and explore the effects of tetrakis hydroxymethyl phosphonium chloride (THPC) antioxidant on dosimeter performance. Polymer gel dosimeters that contain THPC or other oxygen scavengers are called normoxic dosimeters, because they can be prepared under normal atmospheric conditions, rather than in a glove box that excludes oxygen. In this review, an effort is made to explain some of the underlying chemical phenomena that affect dosimeter performance using THPC, and that lead to differences in behaviour between dosimeters made using the two types of monomer systems. Progress on the development of new more effective and less toxic dosimeters is also reported.

  3. Development of bufferless gel electrophoresis chip for easy preparation and rapid DNA separation.

    PubMed

    Oleksandrov, Sergiy; Aman, Abdurazak; Lim, Wanyoung; Kim, Younghee; Bae, Nam Ho; Lee, Kyoung G; Lee, Seok Jae; Park, Sungsu

    2018-02-01

    This work presents a handy, fast, and compact bufferless gel electrophoresis chip (BGEC), which consists of precast agarose gel confined in a disposable plastic body with electrodes. It does not require large volumes of buffer to fill reservoirs, or the process of immersing the gel in the buffer. It withstands voltages up to 28.4 V/cm, thereby allowing DNA separation within 10 min with a similar separation capability to the standard gel electrophoresis. The results suggest that our BGEC is highly suitable for in situ gel electrophoresis in forensic, epidemiological settings and crime scenes where standard gel electrophoresis equipment cannot be brought in while quick results are needed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Macrosorb Kieselguhr-agarose composite adsorbents. New tools for downstream process design and scale up. Scientific note.

    PubMed

    Bite, M G; Berezenko, S; Reed, F J; Derry, L

    1988-08-01

    Incompressible Macrosorb composite adsorbents, while retaining all the desirable properties of traditional agarose-based hydrogel media, overcome the operational limitations imposed by the use of soft hydrogels: They permit useful application of fast flow rates without restrictions on bed depth and they can be used in fluidized bed mode. Considerations which are important when contemplating scaled-up processing are discussed. A comparative cost estimate for a production process for extracting albumin from bovine serum in column equipment illustrates the various advantages which may be exploited when using a composite adsorbent in place of a conventional soft gel equivalent.

  5. A motor-driven syringe-type gradient maker for forming immobilized pH gradient gels.

    PubMed

    Fawcett, J S; Sullivan, J V; Chidakel, B E; Chrambach, A

    1988-05-01

    A motor driven gradient maker based on the commercial model (Jule Inc., Trumbull, CT) was designed for immobilized pH gradient gels to provide small volumes, rapid stirring and delivery, strict volume and temperature control and air exclusion. The device was constructed and by a convenient procedure yields highly reproducible gradients either in solution or on polyacrylamide gels.

  6. Use of Two Dimensional Semi-denaturing Detergent Agarose Gel Electrophoresis to Confirm Size Heterogeneity of Amyloid or Amyloid-like Fibers.

    PubMed

    Hanna-Addams, Sarah; Wang, Zhigao

    2018-04-26

    Amyloid or amyloid-like fibers have been associated with many human diseases, and are now being discovered to be important for many signaling pathways. The ability to readily detect the formation of these fibers under various experimental conditions is essential for understanding their potential function. Many methods have been used to detect the fibers, but not without some drawbacks. For example, electron microscopy (EM), or staining with Congo Red or Thioflavin T often requires purification of the fibers. On the other hand, semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) allows detection of the SDS-resistant amyloid-like fibers in the cell extracts without purification. In addition, it allows the comparison of the size difference of the fibers. More importantly, it can be used to identify specific proteins within the fibers by Western blotting. It is less time consuming and more easily accessible to a wider number of labs. SDD-AGE results often show variable degree of heterogeneity. It raises the question whether part of the heterogeneity results from the dissociation of the protein complex during the electrophoresis in the presence of SDS. For this reason, we have employed a second dimension of SDD-AGE to determine if the size heterogeneity seen in SDD-AGE is truly a result of fiber heterogeneity in vivo and not a result of either degradation or dissociation of some of the proteins during electrophoresis. This method allows fast, qualitative confirmation that the amyloid or amyloid-like fibers are not partially dissociating during the SDD-AGE process.

  7. Antioxidant effect of green tea on polymer gel dosimeter

    NASA Astrophysics Data System (ADS)

    Samuel, E. J. J.; Sathiyaraj, P.; Deena, T.; Kumar, D. S.

    2015-01-01

    Extract from Green Tea (GTE) acts as an antioxidant in acrylamide based polymer gel dosimeter. In this work, PAGAT gel was used for investigation of antioxidant effect of GTE.PAGAT was called PAGTEG (Polyacrylamide green tea extract gel dosimeter) after adding GTE. Free radicals in water cause pre polymerization of polymer gel before irradiation. Polyphenols from GTE are highly effective to absorb the free radicals in water. THPC is used as an antioxidant in polymer gel dosimeter but here we were replaced it by GTE and investigated its effect by spectrophotometer. GTE added PAGAT samples response was lower compared to THPC added sample. To increase the sensitivity of the PAGTEG, sugar was added. This study confirmed that THPC was a good antioxidant for polymer gel dosimeter. However, GTE also can be used as an antioxidant in polymer gel if use less quantity (GTE) and add sugar as sensitivity enhancer.

  8. Markers of Developmentally Regulated Programmed Cell Death and Their Analysis in Cereal Seeds.

    PubMed

    Domínguez, Fernando; Cejudo, Francisco Javier

    2018-01-01

    Programmed cell death (PCD) is a key process for the development and differentiation of multicellular organisms, which is characterized by well-defined morphological and biochemical features. These include chromatin condensation, DNA degradation and nuclear fragmentation, with nucleases and proteases playing a relevant function in these processes. In this chapter we describe methods routinely used for the analysis of hallmarks of developmentally regulated PCD in cereal seed tissues, which are based on agarose and polyacrylamide gel electrophoresis, in situ staining of DNA fragmentation, and cell-free assays of relevant enzymatic activities.

  9. Preparation of tritium-labeled optical isomers of amino acids by ligand exchange chromatography on polyacrylamide sorbent containing L-phenylalanine groupings

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zolotarev, Yu.A.; Penkina, V.I.; Dostavalov, I.N.

    Tritium-labeled optically active amino acids are obtained by resolving racemates of the corresponding amino acids by chromatography on a chiral polyacrylamide sorbent, filled with copper ions. The chiral sorbent is obtained by the action of formaldehyde and L-phenylalanine on a Biogel P-4 polyacrylamide gel in an alkaline medium. Data are given on the ligand exchange chromatography of amino acids on this sorbent, depending on the degree of filling of the sorbent by copper ions and the concentration of the eluent. Conditions were selected for the quantitative resolution of racemates of amino acids and examples are given of a preparative obtainingmore » of tritium labeled optical isomers of amino acids.« less

  10. Modeling the Dynamics of Gel Electrophorresis in the High School Classroom

    ERIC Educational Resources Information Center

    Saucedo, Skyler R.

    2013-01-01

    Gel electrophoresis, used by geneticists and forensic experts alike, is an immensely popular technique that utilizes an electric field to separate molecules and proteins by size and charge. At the microscopic level, a dye or complex protein like DNA is passed through agarose, a gelatinous three-dimensional matrix of pores and nano-sized tunnels.…

  11. Modified Terminal Restriction Fragment Analysis for Quantifying Telomere Length Using In-gel Hybridization.

    PubMed

    Jenkins, Frank J; Kerr, Charles M; Fouquerel, Elise; Bovbjerg, Dana H; Opresko, Patricia L

    2017-07-10

    There are several different techniques for measuring telomere length, each with their own advantages and disadvantages. The traditional approach, Telomere Restriction Fragment (TRF) analysis, utilizes a DNA hybridization technique whereby genomic DNA samples are digested with restriction enzymes, leaving behind telomere DNA repeats and some sub-telomeric DNA. These are separated by agarose gel electrophoresis, transferred to a filter membrane and hybridized to oligonucleotide probes tagged with either chemiluminescence or radioactivity to visualize telomere restriction fragments. This approach, while requiring a larger quantity of DNA than other techniques such as PCR, can measure the telomere length distribution of a population of cells and allows measurement expressed in absolute kilobases. This manuscript demonstrates a modified DNA hybridization procedure for determining telomere length. Genomic DNA is first digested with restriction enzymes (that do not cut telomeres) and separated by agarose gel electrophoresis. The gel is then dried and the DNA is denatured and hybridized in situ to a radiolabeled oligonucleotide probe. This in situ hybridization avoids loss of telomere DNA and improves signal intensity. Following hybridization, the gels are imaged utilizing phosphor screens and the telomere length is quantified using a graphing program. This procedure was developed by the laboratories of Drs. Woodring Wright and Jerry Shay at the University of Texas Southwestern 1 , 2 . Here, we present a detailed description of this procedure, with some modifications.

  12. Modification of a neuronal network direction using stepwise photo-thermal etching of an agarose architecture.

    PubMed

    Suzuki, Ikurou; Sugio, Yoshihiro; Moriguchi, Hiroyuki; Jimbo, Yasuhiko; Yasuda, Kenji

    2004-07-01

    Control over spatial distribution of individual neurons and the pattern of neural network provides an important tool for studying information processing pathways during neural network formation. Moreover, the knowledge of the direction of synaptic connections between cells in each neural network can provide detailed information on the relationship between the forward and feedback signaling. We have developed a method for topographical control of the direction of synaptic connections within a living neuronal network using a new type of individual-cell-based on-chip cell-cultivation system with an agarose microchamber array (AMCA). The advantages of this system include the possibility to control positions and number of cultured cells as well as flexible control of the direction of elongation of axons through stepwise melting of narrow grooves. Such micrometer-order microchannels are obtained by photo-thermal etching of agarose where a portion of the gel is melted with a 1064-nm infrared laser beam. Using this system, we created neural network from individual Rat hippocampal cells. We were able to control elongation of individual axons during cultivation (from cells contained within the AMCA) by non-destructive stepwise photo-thermal etching. We have demonstrated the potential of our on-chip AMCA cell cultivation system for the controlled development of individual cell-based neural networks.

  13. Beverage-Agarose Gel Electrophoresis: An Inquiry-Based Laboratory Exercise with Virtual Adaptation

    ERIC Educational Resources Information Center

    Cunningham, Steven C.; McNear, Brad; Pearlman, Rebecca S.; Kern, Scott E.

    2006-01-01

    A wide range of literature and experience has shown that teaching methods that promote active learning, such as inquiry-based approaches, are more effective than those that rely on passive learning. Gel electrophoresis, one of the most common laboratory techniques in molecular biology, has a wide range of applications in the life sciences. As…

  14. Gadolinium-loaded gel scintillators for neutron and antineutrino detection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Riddle, Catherine Lynn; Akers, Douglas William; Demmer, Ricky Lynn

    A gadolinium (Gd) loaded scintillation gel (Gd-ScintGel) compound allows for neutron and gamma-ray detection. The unique gel scintillator encompasses some of the best features of both liquid and solid scintillators, yet without many of the disadvantages associated therewith. Preferably, the gel scintillator is a water soluble Gd-DTPA compound and water soluble fluorophores such as: CdSe/ZnS (or ZnS) quantum dot (Q-dot) nanoparticles, coumarin derivatives 7-hydroxy-4-methylcoumarin, 7-hydroxy-4-methylcoumarin-3-acetic acid, 7-hydroxycoumarin-3-carboxylic acid, and Alexa Fluor 350 as well as a carbostyril compound, carbostyril 124 in a stable water-based gel, such as methylcellulose or polyacrylamide polymers. The Gd-loaded ScintGel allows for a homogenious distribution ofmore » the Gd-DTPA and the fluorophores, and yields clean fluorescent emission peaks. A moderator, such as deuterium or a water-based clear polymer, can be incorporated in the Gd-ScintGel. The gel scintillators can be used in compact detectors, including neutron and antineutrino detectors.« less

  15. Polymer gel dosimeters with reduced toxicity: a preliminary investigation of the NMR and optical dose response using different monomers

    NASA Astrophysics Data System (ADS)

    Senden, R. J.; DeJean, P.; McAuley, K. B.; Schreiner, L. J.

    2006-07-01

    In this work, three new polymer gel dosimeter recipes were investigated that may be more suitable for widespread applications than polyacrylamide gel dosimeters, since the extremely toxic acrylamide has been replaced with the less harmful monomers N-isopropylacrylamide (NIPAM), diacetone acrylamide and N-vinylformamide. The new gel dosimeters studied contained gelatin (5 wt%), monomer (3 wt%), N,N'-methylene-bis-acrylamide crosslinker (3 wt%) and tetrakis (hydroxymethyl) phosphonium chloride antioxidant (10 mM). The NMR response (R2) of the dosimeters was analysed for conditions of varying dose, dose rate, time post-irradiation, and temperature during irradiation and scanning. It was shown that the dose-response behaviour of the NIPAM/Bis gel dosimeter is comparable to that of normoxic polyacrylamide gel (PAGAT) in terms of high dose-sensitivity and low dependence on dose rate and irradiation temperature, within the ranges considered. The dose-response (R2) of NIPAM/Bis appears to be linear over a greater dose range than the PAGAT gel dosimeter. The effects of time post-irradiation (temporal instability) and temperature during NMR scanning on the R2 response were more significant for NIPAM/Bis dosimeters. Diacetone acrylamide and N-vinylformamide gel dosimeters possessed considerably lower dose-sensitivities. The optical dose-response, measured in terms of the attenuation coefficient for each polymer gel dosimeter, showed potential for the use of optical imaging techniques in future studies.

  16. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis

    PubMed Central

    Choi, Hoseok; Choi, Bomi; Seo, Ju Tae; Lee, Kyung Jin; Gye, Myung Chan; Kim, Young-Pil

    2016-01-01

    Assaying the glycogen synthase kinase-3 (GSK3) activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed) peptide substrate for GSK3 was employed, a distinct mobility shift in the fluorescent bands on the agarose was observed by GSK3-induced phosphorylation of the primed peptides. The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts. PMID:27092510

  17. Automated Genotyping of a Highly Informative Panel of 40 Short Insertion-Deletion Polymorphisms Resolved in Polyacrylamide Gels for Forensic Identification and Kinship Analysis

    PubMed Central

    Pena, Heloisa B.; Pena, Sérgio D. J.

    2012-01-01

    Objective Short insertion-deletion polymorphisms (indels) are the second most abundant form of genetic variations in humans after SNPs. Since indel alleles differ in size, they can be typed using the same methodological approaches and equipment currently utilized for microsatellite genotyping, which is already operational in forensic laboratories. We have previously shown that a panel of 40 carefully chosen indels has excellent potential for forensic identification, with combined probability of identity (match probability) of 7.09 × 10–17 for Europeans. Methods We describe the successful development of a multiplex system for genotyping the 40-indel panel in long thin denaturing polyacrylamide gels with silver staining. We also demonstrate that the system can be easily fully automated with a simple large scanner and commercial software. Results and Conclusion The great advantage of the new system of typing is its very low cost. The total price for laboratory equipment is less than EUR 10,000.-, and genotyping of an individual patient will cost less than EUR 10.- in supplies. Thus, the 40-indel panel described here and the newly developed ‘low-tech’ analysis platform represent useful new tools for forensic identification and kinship analysis in laboratories with limited budgets, especially in developing countries. PMID:22851937

  18. Gel electrophoresis of linear and star-branched DNA

    NASA Astrophysics Data System (ADS)

    Lau, Henry W.; Archer, Lynden A.

    2011-12-01

    The electrophoretic mobility of double-stranded DNA in polyacrylamide gel is investigated using an activated hopping model for the transport of a charged object within a heterogeneous medium. The model is premised upon a representation of the DNA path through the gel matrix as a series of traps with alternating large and small cross sections. Calculations of the trap dimensions from gel data show that the path imposes varying degrees of confinement upon migrating analytes, which retard their forward motion in a size-dependent manner. An expression derived for DNA mobility is shown to provide accurate predictions for the dynamics of linear DNA (67-622 bp) in gels of multiple concentrations. For star-branched DNA, the incorporation within the model of a length scale previously proposed to account for analyte architecture [Yuan , Anal. Chem.ANCHAM0003-270010.1021/ac060414w 78, 6179 (2006)] leads to mobility predictions that compare well with experimental results for a wide range of DNA shapes and molecular weights.

  19. A noda-like virus isolated from the sweetpotato pest spodoptera eridania (Cramer) (Lep.; noctuidae)

    PubMed

    Zeddam; Rodriguez; Ravallec; Lagnaoui

    1999-11-01

    A small isometric virus has been isolated from larvae of the sweetpotato pest Spodoptera eridania (Cramer) collected near Pariacoto, Ancash province, Peru. It is designated the Pariacoto virus (PaV). In addition to its high pathogenicity on its natural host Spodoptera eridania, PaV was found to replicate in Spodoptera ochrea (Hampson) larvae but not in Spodoptera frugiperda (Smith) larvae. The size of the viral particle was estimated to be about 30 nm in diameter. Polyacrylamide gel electrophoresis showed a protein of approximately 40.5 kDa. After agarose gel electrophoresis, the viral genome appeared to be bipartite RNA. Gel immunodiffusion tests showed no serological relationship between PaV and Nodamura virus, the type species for insect nodaviruses. Electron microscopy confirmed that viral replication occurs in the cytoplasm. These properties are similar to those of other members of family Nodaviridae, to which the virus is currently assigned. Copyright 1999 Academic Press.

  20. Development of a highly sensitive three-dimensional gel electrophoresis method for characterization of monoclonal protein heterogeneity.

    PubMed

    Nakano, Keiichi; Tamura, Shogo; Otuka, Kohei; Niizeki, Noriyasu; Shigemura, Masahiko; Shimizu, Chikara; Matsuno, Kazuhiko; Kobayashi, Seiichi; Moriyama, Takanori

    2013-07-15

    Three-dimensional gel electrophoresis (3-DE), which combines agarose gel electrophoresis and isoelectric focusing/SDS-PAGE, was developed to characterize monoclonal proteins (M-proteins). However, the original 3-DE method has not been optimized and its specificity has not been demonstrated. The main goal of this study was to optimize the 3-DE procedure and then compare it with 2-DE. We developed a highly sensitive 3-DE method in which M-proteins are extracted from a first-dimension agarose gel, by diffusing into 150 mM NaCl, and the recovery of M-proteins was 90.6%. To validate the utility of the highly sensitive 3-DE, we compared it with the original 3-DE method. We found that highly sensitive 3-DE provided for greater M-protein recovery and was more effective in terms of detecting spots on SDS-PAGE gels than the original 3-DE. Moreover, highly sensitive 3-DE separates residual normal IgG from M-proteins, which could not be done by 2-DE. Applying the highly sensitive 3-DE to clinical samples, we found that the characteristics of M-proteins vary tremendously between individuals. We believe that our highly sensitive 3-DE method described here will prove useful in further studies of the heterogeneity of M-proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Polyacrylamide polymer (modified cationic) denture... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended to...

  2. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Polyacrylamide polymer (modified cationic) denture... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended to...

  3. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Polyacrylamide polymer (modified cationic) denture... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended to...

  4. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Polyacrylamide polymer (modified cationic) denture... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended to...

  5. 21 CFR 872.3480 - Polyacrylamide polymer (modified cationic) denture adhesive.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Polyacrylamide polymer (modified cationic) denture... polymer (modified cationic) denture adhesive. (a) Identification. A polyacrylamide polymer (modified cationic) denture adhesive is a device composed of polyacrylamide polymer (modified cationic) intended to...

  6. A pneumatic device for rapid loading of DNA sequencing gels.

    PubMed

    Panussis, D A; Cook, M W; Rifkin, L L; Snider, J E; Strong, J T; McGrane, R M; Wilson, R K; Mardis, E R

    1998-05-01

    This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and 377 DNA sequencing instruments. The device is mounted onto the existing gel cassettes and makes the process of loading high-density gels less cumbersome while the associated time and errors are reduced. The principle of operation includes the simultaneous transfer of the entire batch of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling their insertion in the gel wells once the device is securely mounted. Gel-loading devices capable of simultaneously transferring 72 samples onto the PE/ABI 373 and 377 are currently being used in our production sequencing groups while a 96-sample transfer prototype undergoes testing.

  7. Use of PCR and Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis Techniques for Differentiation of Prevotella intermedia Sensu Stricto and Prevotella nigrescens

    PubMed Central

    Premaraj, Thyagaseely; Kato, Naoki; Fukui, Katsuhito; Kato, Haru; Watanabe, Kunitomo

    1999-01-01

    Primers were designed from 16S rRNA sequences of Prevotella intermedia sensu stricto and Prevotella nigrescens and were used to discriminate these two species by PCR. The results were compared with those from the PCR technique using primers designed from arbitrarily primed PCR products by Guillot and Mouton (E. Guillot and C. Mouton, J. Clin. Microbiol. 35:1876–1882, 1997). The specificities of both assays were studied by using P. intermedia ATCC 25611, P. nigrescens ATCC 33563, 174 clinical isolates of P. intermedia sensu lato, and 59 reference strains and 58 clinical isolates of other Prevotella species and/or common oral flora. In addition, the usefulness and reliability of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the differentiation of the two species were examined by comparing the results with those from PCR assays. The controversial lipase test for distinguishing these species was also carried out. Unambiguous differentiation was made by both PCR assays, and the results matched each other. The SDS-PAGE assay was found to misidentify a few strains tested, compared with the results of PCR assays. The lipase test was positive for both species, including the reference strains of P. intermedia and P. nigrescens. We conclude that both PCR assays are simple, rapid, reliable, and specific methods which could be used in clinical studies and that the lipase test is not valuable in the differentiation. The reliable discrimination of the two species by SDS-PAGE is questionable. PMID:10074526

  8. Temporal effect of inertial cavitation with and without microbubbles on surface deformation of agarose S gel in the presence of 1-MHz focused ultrasound.

    PubMed

    Tomita, Y; Matsuura, T; Kodama, T

    2015-01-01

    Sonoporation has the potential to deliver extraneous molecules into a target tissue non-invasively. There have been numerous investigations of cell membrane permeabilization induced by microbubbles, but very few studies have been carried out to investigate sonoporation by inertial cavitation, especially from a temporal perspective. In the present paper, we show the temporal variations in nano/micro-pit formations following the collapse of inertial cavitation bubbles, with and without Sonazoid® microbubbles. Using agarose S gel as a target material, erosion experiments were conducted in the presence of 1-MHz focused ultrasound applied for various exposure times, Tex (0.002-60 s). Conventional microscopy was used to measure temporal variations in micrometer-scale pit numbers, and atomic force microscopy utilized to detect surface roughness on a nanometer scale. The results demonstrated that nanometer-scale erosion was predominantly caused by Sonazoid® microbubbles and C4F10 gas bubbles for 0.002 s

  9. Southern blotting.

    PubMed

    Brown, T

    2001-05-01

    the second alternate protocol is therefore more rapid than the basic protocol and can result in more complete transfer. Although the ease and reliability of capillary transfer methods makes this far and away the most popular system for Southern blotting with agarose gels, it unfortunately does not work with polyacrylamide gels, whose smaller pore size impedes the transverse movement of the DNA molecules. The third alternate protocol describes an electroblotting procedure that is currently the most reliable method for transfer of DNA from a polyacrylamide gel. Dot and slot blotting are also described.

  10. Native gel analysis for RISC assembly.

    PubMed

    Kawamata, Tomoko; Tomari, Yukihide

    2011-01-01

    Small-interfering RNAs (siRNAs) and microRNAs (miRNAs) regulate expression of their target mRNAs via the RNA-induced silencing complex (RISC). A core component of RISC is the Argonaute (Ago) protein, which dictates the RISC function. In Drosophila, miRNAs and siRNAs are generally loaded into Ago1-containing RISC (Ago1-RISC) and Ago2-containing RISC (Ago2-RISC), respectively. We developed a native agarose gel system to directly detect Ago1-RISC, Ago2-RISC, and their precursor complexes. Methods presented here will provide powerful tools to biochemically dissect the RISC assembly pathways.

  11. Cyclic compression maintains viability and induces chondrogenesis of human mesenchymal stem cells in fibrin gel scaffolds.

    PubMed

    Pelaez, Daniel; Huang, Chun-Yuh Charles; Cheung, Herman S

    2009-01-01

    Mechanical loading has long been shown to modulate cartilage-specific extracellular matrix synthesis. With joint motion, cartilage can experience mechanical loading in the form of compressive, tensile or shearing load, and hydrostatic pressure. Recent studies have demonstrated the capacity of unconfined cyclic compression to induce chondrogenic differentiation of human mesenchymal stem cell (hMSC) in agarose culture. However, the use of a nonbiodegradable material such as agarose limits the applicability of these constructs. Of the possible biocompatible materials available for tissue engineering, fibrin is a natural regenerative scaffold, which possesses several desired characteristics including a controllable degradation rate and low immunogenicity. The objective of the present study was to determine the capability of fibrin gels for supporting chondrogenesis of hMSCs under cyclic compression. To optimize the system, three concentrations of fibrin gel (40, 60, and 80 mg/mL) and three different stimulus frequencies (0.1, 0.5, and 1.0 Hz) were used to examine the effects of cyclic compression on viability, proliferation and chondrogenic differentiation of hMSCs. Our results show that cyclic compression (10% strain) at frequencies >0.5 Hz and gel concentration of 40 mg/mL fibrinogen appears to maintain cellular viability within scaffolds. Similarly, variations in gel component concentration and stimulus frequency can be modified such that a significant chondrogenic response can be achieved by hMSC in fibrin constructs after 8 h of compression spread out over 2 days. This study demonstrates the suitability of fibrin gel for supporting the cyclic compression-induced chondrogenesis of mesenchymal stem cells.

  12. In-gel multiple displacement amplification of long DNA fragments diluted to the single molecule level.

    PubMed

    Michikawa, Yuichi; Sugahara, Keisuke; Suga, Tomo; Ohtsuka, Yoshimi; Ishikawa, Kenichi; Ishikawa, Atsuko; Shiomi, Naoko; Shiomi, Tadahiro; Iwakawa, Mayumi; Imai, Takashi

    2008-12-15

    The isolation and multiple genotyping of long individual DNA fragments are needed to obtain haplotype information for diploid organisms. Limiting dilution of sample DNA followed by multiple displacement amplification is a useful technique but is restricted to short (<5 kb) DNA fragments. In the current study, a novel modification was applied to overcome these problems. A limited amount of cellular DNA was carefully released from intact cells into a mildly heated alkaline agarose solution and mixed thoroughly. The solution was then gently aliquoted and allowed to solidify while maintaining the integrity of the diluted DNA. Exogenously provided Phi29 DNA polymerase was used to perform consistent genomic amplification with random hexameric oligonucleotides within the agarose gels. Simple heat melting of the gel allowed recovery of the amplified materials in a solution of the polymerase chain reaction (PCR)-ready form. The haplotypes of seven SNPs spanning 240 kb of the DNA surrounding the human ATM gene region on chromosome 11 were determined for 10 individuals, demonstrating the feasibility of this new method.

  13. Interaction of electromagnetic fields with chondrocytes in gel culture

    NASA Astrophysics Data System (ADS)

    Grodzinsky, Alan J.; Buschmann, Michael D.; Gluzband, Yehezkiel A.

    1992-01-01

    The specific objectives of this research period were: (1) to quantify the effect of applied electric fields on chondrocyte metabolism, using a range of stimulation frequencies and amplitudes; (2) to compare the chondrocyte biosynthetic response to applied fields at early times in agarose gel culture before an extracellular matrix has accumulated and at later times after significant deposition of matrix around and between the cells; and (3) to begin to interpret the biosynthetic response to applied fields in terms of models of physical mechanisms. The results of these studies suggest that electric fields applied to chondrocytes in agarose can modulate the synthesis of proteoglycans and protein constituents. Biosynthesis may be inhibited or stimulated depending on the amplitude of the applied current density. In addition, the presence of extracellular matrix may enhance the ability of normal chondrocytes and cells in intact cartilage to respond to electric fields, although the presence of matrix was not required for the stimulatory response to be observed with Swarm rat chondrosarcoma cells.

  14. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    NASA Astrophysics Data System (ADS)

    Zhang, Junfang; Rivero, Mayela; Choi, S. K.

    2007-02-01

    We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

  15. Crosslinking of agarose bioplastic using citric acid.

    PubMed

    Awadhiya, Ankur; Kumar, David; Verma, Vivek

    2016-10-20

    We report chemical crosslinking of agarose bioplastic using citric acid. Crosslinking was confirmed using Fourier transform infrared (FTIR) spectroscopy. The effects of crosslinking on the tensile strength, swelling, thermal stability, and degradability of the bioplastic were studied in detail. The tensile strength of the bioplastic films increased from 25.1MPa for control films up to a maximum of 52.7MPa for citric acid crosslinked films. At 37°C, the amount of water absorbed by crosslinked agarose bioplastic was only 11.5% of the amount absorbed by non-crosslinked controls. Thermogravimetric results showed that the crosslinked samples retain greater mass at high temperature (>450°C) than control samples. Moreover, while the crosslinked films were completely degradable, the rate of degradation was lower compared to non-crosslinked controls. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Triton-polyacrylamide gel electrophoresis and leucine aminopeptidase activity staining detect Triton-slowed bands including high-molecular-mass aminopeptidase N (CD13) isoform in cholestatic patient sera.

    PubMed

    Kawai, Makoto; Hara, Yukichi

    2006-02-01

    Western blotting of aminopeptidase N (APN) detects a high-molecular-mass isoform (260 kDa) [M. Kawai, Y. Otake, Y. Hara High-molecular-mass isoform of aminopeptidase N/CD13 in serum from cholestatic patients. Clin Chim Acta 330 (2003) 141-149] in cholestatic patient serum but is time-consuming. Human sera were electrophoresed on polyacrylamide gel containing Triton-X100 (Triton-PAGE) and stained with leucine-B-naphthylamide (LAP-staining). The stained bands were eluted from the gel, treated with N- and O-glycosidase if necessary, and analyzed by Western blotting [M. Kawai, Y. Otake, Y. Hara High-molecular-mass isoform of aminopeptidase N/CD13 in serum from cholestatic patients. Clin Chim Acta 330 (2003) 141-149]. Triton-PAGE and LAP-staining clearly detected fast bands in all the sera examined. Almost parallel with leucine aminopeptidase activity, slow bands were strongly stained in all 11 cholestatic patients but clearly stained in 3 out of 14 patients with hepatobiliary diseases other than cholestasis. PAGE with various concentrations of Triton showed that Triton slows down slow bands but not fast bands. Western blotting showed that Triton-PAGE-slow bands of cholestasis contained 140 and 260-kDa APN and that fast bands were slightly smaller than monomer-size slow bands after glycosidase treatment. Less time-consuming than Western blotting, Triton-PAGE and LAP-staining detect novel APN bands slowed by Triton and partly composed of the high-molecular-mass isoform in cholestasis. The slow bands seem to be homodimers of APN with transmembrane anchors. The polypeptide of the fast band seems to be processed differently from that of the slow band.

  17. A gel probe equilibrium sampler for measuring arsenic porewater profiles and sorption gradients in sediments: I. Laboratory development

    USGS Publications Warehouse

    Campbell, K.M.; Root, R.; O'Day, P. A.; Hering, J.G.

    2008-01-01

    A gel probe equilibrium sampler has been developed to study arsenic (As) geochemistry and sorption behavior in sediment porewater. The gels consist of a hydrated polyacrylamide polymer, which has a 92% water content. Two types of gels were used in this study. Undoped (clear) gels were used to measure concentrations of As and other elements in sediment porewater. The polyacrylamide gel was also doped with hydrous ferric oxide (HFO), an amorphous iron (Fe) oxyhydroxide. When deployed in the field, HFO-doped gels introduce a fresh sorbent into the subsurface thus allowing assessment of in situ sorption. In this study, clear and HFO-doped gels were tested under laboratory conditions to constrain the gel behavior prior to field deployment. Both types of gels were allowed to equilibrate with solutions of varying composition and re-equilibrated in acid for analysis. Clear gels accurately measured solution concentrations (??1%), and As was completely recovered from HFO-doped gels (??4%). Arsenic speciation was determined in clear gels through chromatographic separation of the re-equilibrated solution. For comparison to speciation in solution, mixtures of As(III) and As(V) adsorbed on HFO embedded in gel were measured in situ using X-ray absorption spectroscopy (XAS). Sorption densities for As(III) and As(V) on HFO embedded in gel were obtained from sorption isotherms at pH 7.1. When As and phosphate were simultaneously equilibrated (in up to 50-fold excess of As) with HFO-doped gels, phosphate inhibited As sorption by up to 85% and had a stronger inhibitory effect on As(V) than As(III). Natural organic matter (>200 ppm) decreased As adsorption by up to 50%, and had similar effects on As(V) and As(III). The laboratory results provide a basis for interpreting results obtained by deploying the gel probe in the field and elucidating the mechanisms controlling As partitioning between solid and dissolved phases in the environment. ?? 2008 American Chemical Society.

  18. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics.

    PubMed

    Lohnes, Karen; Quebbemann, Neil R; Liu, Kate; Kobzeff, Fred; Loo, Joseph A; Ogorzalek Loo, Rachel R

    2016-07-15

    The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. The effects of treatment on lipoprotein subfractions evaluated by polyacrylamide gel electrophoresis in patients with autoimmune hypothyroidism and hyperthyroidism.

    PubMed

    Minarikova, Zuzana; Gaspar, Ludovit; Kruzliak, Peter; Celecová, Zuzana; Oravec, Stanislav

    2014-10-10

    Atherogenic dyslipoproteinemia is one of the most important risk factor for atherosclerotic changes development. Hypothyroidism is one of the most common causes of secondary dyslipidemias which results from reduced LDL clearance and therefore raised levels of LDL and apoB. Association between small dense LDL (sdLDL) presentation and thyroid status has been examinated using polyacrylamide gel electrophoresis for lipoprotein subfractions evaluation. 40 patients with diagnosed autoimmune hypothyroidism and 30 patients with autoimmune hyperthyroidism were treated with thyroxine replacement or thyreo-suppressive treatment. In both groups lipid profiles, LDL subractions, apolipoproteins (apoA1, apoB), apoA1/apoB ratio and atherogenic index of plazma (AIP) were examined before treatment and in state of euthyreosis. Thyroxine replacement therapy significantly reduced levels of total cholesterol (TC), LDL, triglycerides (TG) and also decreased levels of sdLDL (8,55±11,671 vs 0,83±1,693mg/dl; p<0,001), apoB and AIP. For estimation of atherogenic lipoprotein profile existence an AIP evaluation seems to be better than apoB measurement because of the more evident relationship with sdLDL (r=0,538; p<0,01). Thyreo-suppressive therapy significantly increased levels of TC, LDL, TG and apoB. The sdLDL was not found in hyperthyroid patients. Atherogenic lipoprotein profile was present in 52.5% of hypothyroid subjects, which is higher prevalence than in normal, age-related population. Substitution treatment leads to an improvement of the lipid levels, TG, apoB, AIP and LDL subclasses. It significantly changed the presentation of sdLDL - we noticed shift to large, less atherogenic LDL particles. Significantly positive correlation between sdLDL and TAG; sdLDL and VLDL alerts to hypertriglyceridemia as a major cardiovascular risk factor.

  20. A cost-effective device for the rapid transfer of gel-separated proteins onto membranes.

    PubMed

    Tam, Hann W; Huang, Yu-Chen; Tam, Ming F

    2009-03-01

    We describe here the fabrication of a cost-effective semi-dry blotting apparatus for the transfer of proteins onto membranes. Graphite sheets were used as electrodes. Protein mixtures were separated on NuPAGE 4% to 12% polyacrylamide gradient gels. With a Tris-bicine buffer, we demonstrated that close to 80% of the proteins with apparent molecular mass of 80kDa or less were removed from the gels after 8min of blotting. The process is much faster than the techniques reported previously in the literature.

  1. Microfluidic device having an immobilized pH gradient and PAGE gels for protein separation and analysis

    DOEpatents

    Sommer, Gregory J.; Hatch, Anson V.; Singh, Anup K.; Wang, Ying-Chih

    2012-12-11

    Disclosed is a novel microfluidic device enabling on-chip implementation of a two-dimensional separation methodology. Previously disclosed microscale immobilized pH gradients (IPG) are combined with perpendicular polyacrylamide gel electrophoresis (PAGE) microchannels to achieve orthogonal separations of biological samples. Device modifications enable inclusion of sodium dodecyl sulfate (SDS) in the second dimension. The device can be fabricated to use either continuous IPG gels, or the microscale isoelectric fractionation membranes we have also previously disclosed, for the first dimension. The invention represents the first all-gel two-dimensional separation microdevice, with significantly higher resolution power over existing devices.

  2. Microfluidic device having an immobilized pH gradient and page gels for protein separation and analysis

    DOEpatents

    Sommer, Gregory J; Hatch, Anson V; Singh, Anup K; Wang, Ying-Chih

    2014-05-20

    Disclosed is a novel microfluidic device enabling on-chip implementation of a two-dimensional separation methodology. Previously disclosed microscale immobilized pH gradients (IPG) are combined with perpendicular polyacrylamide gel electrophoresis (PAGE) microchannels to achieve orthogonal separations of biological samples. Device modifications enable inclusion of sodium dodecyl sulfate (SDS) in the second dimension. The device can be fabricated to use either continuous IPG gels, or the microscale isoelectric fractionation membranes we have also previously disclosed, for the first dimension. The invention represents the first all-gel two-dimensional separation microdevice, with significantly higher resolution power over existing devices.

  3. Network Confinement and Heterogeneity Slows Nanoparticle Diffusion in Polymer Gels

    NASA Astrophysics Data System (ADS)

    Parrish, Emmabeth; Caporizzo, Matthew; Composto, Russell

    Nanoparticle (NP) diffusion was measured in polyacrylamide gels (PAG) with a mesh size comparable to NP size, 20nm. The confinement ratio (CR), NP diameter/mesh, increased from 0.4 to 3.8 by increasing crosslinker density and 0.4 to 2 by adding acetone, which collapsed PAG. In all gels, NPs either became localized (<200nm) or diffused microns, as measured by single particle tracking. Mean squared displacements (MSD) of mobile NPs decreased as CR increased. In collapsed gels, the localized NP population increased and MSD of mobile NPs decreased compared to crosslinked PAG. For all CRs, van Hove distributions exhibited non-Gaussian displacements consistent with intermittent localization of NPs. The non-Gaussian parameter increased from a maximum of 1.5 for crosslinked PAG to 5 for collapsed PAG, consistent with greater network heterogeneity. Diffusion coefficients, D, decreased exponentially as CR increased for crosslinked gels, but in collapsed gels D decreased more strongly, suggesting CR alone was insufficient to capture diffusion. Collapsing the gel resulted in an increasingly tortuous pathway for NPs, slowing diffusion at a given CR. Understanding how gel structure affects NP mobility will allow the design of gels with improved ability to separate and release molecules. ACS/PRF 54028-ND7, NSF/MWN DMR-1210379.

  4. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... polyacrylamide polymer denture adhesive. 872.3420 Section 872.3420 Food and Drugs FOOD AND DRUG ADMINISTRATION....3420 Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive. (a) Identification. A carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive is a device...

  5. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... polyacrylamide polymer denture adhesive. 872.3420 Section 872.3420 Food and Drugs FOOD AND DRUG ADMINISTRATION....3420 Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive. (a) Identification. A carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive is a device...

  6. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... polyacrylamide polymer denture adhesive. 872.3420 Section 872.3420 Food and Drugs FOOD AND DRUG ADMINISTRATION....3420 Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive. (a) Identification. A carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive is a device...

  7. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... polyacrylamide polymer denture adhesive. 872.3420 Section 872.3420 Food and Drugs FOOD AND DRUG ADMINISTRATION....3420 Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive. (a) Identification. A carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive is a device...

  8. 21 CFR 872.3420 - Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... polyacrylamide polymer denture adhesive. 872.3420 Section 872.3420 Food and Drugs FOOD AND DRUG ADMINISTRATION....3420 Carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive. (a) Identification. A carboxymethylcellulose sodium and cationic polyacrylamide polymer denture adhesive is a device...

  9. Simple and Rapid System for Two-Dimensional Gel Electrophoresis Technique: A Laboratory Exercise for High School Students

    ERIC Educational Resources Information Center

    Maurye, Praveen; Basu, Arpita; Biswas, Jayanta Kumar; Bandyopadhyay, Tapas Kumar; Naskar, Malay

    2018-01-01

    Polyacrylamide gel electrophoresis (PAGE) is the most classical technique favored worldwide for resolution of macromolecules in many biochemistry laboratories due to its incessant advanced developments and wide modifications. These ever-growing advancements in the basic laboratory equipments lead to emergence of many expensive, complex, and tricky…

  10. Network confinement and heterogeneity slows nanoparticle diffusion in polymer gels

    NASA Astrophysics Data System (ADS)

    Parrish, Emmabeth; Caporizzo, Matthew A.; Composto, Russell J.

    2017-05-01

    Nanoparticle (NP) diffusion was measured in polyacrylamide gels (PAGs) with a mesh size comparable to the NP size, 21 nm. The confinement ratio (CR), NP diameter/mesh size, increased from 0.4 to 3.8 by increasing crosslinker density and from 0.4 to 2.1 by adding acetone, which collapsed the PAGs. In all gels, NPs either became localized, moving less than 200 nm, diffused microns, or exhibited a combination of these behaviors, as measured by single particle tracking. Mean squared displacements (MSDs) of mobile NPs decreased as CR increased. In collapsed gels, the localized NP population increased and MSD of mobile NPs decreased compared to crosslinked PAGs. For all CRs, van Hove distributions exhibited non-Gaussian displacements, consistent with intermittent localization of NPs. The non-Gaussian parameter increased from a maximum of 1.5 for crosslinked PAG to 5 for collapsed PAG, consistent with greater network heterogeneity in these gels. Diffusion coefficients decreased exponentially as CR increased for crosslinked gels; however, in collapsed gels, the diffusion coefficients decreased more strongly, which was attributed to network heterogeneity. Collapsing the gel resulted in an increasingly tortuous pathway for NPs, slowing diffusion at a given CR. Understanding how gel structure affects NP mobility will allow the design and enhanced performance of gels that separate and release molecules in membranes and drug delivery platforms.

  11. Analysis of splicing complexes on native gels.

    PubMed

    Ares, Manuel

    2013-10-01

    Splicing requires a complex set of ATP-dependent macromolecular associations that lead to the rearrangement of just a few covalent bonds in the pre-mRNA substrate. Seeing only the covalent bonds breaking and forming is seeing only a very small part of the process. Analysis of native splicing complexes into which the radiolabeled substrate has been assembled, but not necessarily completely reacted, has provided a good understanding of the process. This protocol describes a gel method for detecting and analyzing yeast splicing complexes formed in vitro on a radiolabeled pre-mRNA substrate. Complexes formed during the splicing reaction are quenched by dilution and addition of an excess of RNA, which is thought to strip nonspecifically bound proteins from the labeled substrate RNA. After loading on a low-percentage, low-cross-linking ratio composite agarose-acrylamide gel (in 10% glycerol), labeled bands are detected. These can be extracted and shown to contain small nuclear RNAs (snRNAs) and partly reacted pre-mRNA.

  12. Detection of proteolytic activity by covalent tethering of fluorogenic substrates in zymogram gels.

    PubMed

    Deshmukh, Ameya A; Weist, Jessica L; Leight, Jennifer L

    2018-05-01

    Current zymographic techniques detect only a subset of known proteases due to the limited number of native proteins that have been optimized for incorporation into polyacrylamide gels. To address this limitation, we have developed a technique to covalently incorporate fluorescently labeled, protease-sensitive peptides using an azido-PEG3-maleimide crosslinker. Peptides incorporated into gels enabled measurement of MMP-2, -9, -14, and bacterial collagenase. Sensitivity analysis demonstrated that use of peptide functionalized gels could surpass detection limits of current techniques. Finally, electrophoresis of conditioned media from cultured cells resulted in the appearance of several proteolytic bands, some of which were undetectable by gelatin zymography. Taken together, these results demonstrate that covalent incorporation of fluorescent substrates can greatly expand the library of detectable proteases using zymographic techniques.

  13. Performance and biocompatibility of extremely tough alginate/polyacrylamide hydrogels.

    PubMed

    Darnell, Max C; Sun, Jeong-Yun; Mehta, Manav; Johnson, Christopher; Arany, Praveen R; Suo, Zhigang; Mooney, David J

    2013-11-01

    Although hydrogels now see widespread use in a host of applications, low fracture toughness and brittleness have limited their more broad use. As a recently described interpenetrating network (IPN) of alginate and polyacrylamide demonstrated a fracture toughness of ≈ 9000 J/m(2), we sought to explore the biocompatibility and maintenance of mechanical properties of these hydrogels in cell culture and in vivo conditions. These hydrogels can sustain a compressive strain of over 90% with minimal loss of Young's Modulus as well as minimal swelling for up to 50 days of soaking in culture conditions. Mouse mesenchymal stem cells exposed to the IPN gel-conditioned media maintain high viability, and although cells exposed to conditioned media demonstrate slight reductions in proliferation and metabolic activity (WST assay), these effects are abrogated in a dose-dependent manner. Implantation of these IPN hydrogels into subcutaneous tissue of rats for 8 weeks led to mild fibrotic encapsulation and minimal inflammatory response. These results suggest the further exploration of extremely tough alginate/PAAM IPN hydrogels as biomaterials. © 2013 Elsevier Ltd. All rights reserved.

  14. One-pot synthesis of fluorescent polysaccharides: adenine grafted agarose and carrageenan.

    PubMed

    Oza, Mihir D; Prasad, Kamalesh; Siddhanta, A K

    2012-08-01

    New fluorescent polysaccharides were synthesized by grafting the nucleobase adenine on to the backbones of agarose and κ-carrageenan, which were characterized by FT-IR, (13)C NMR, TGA, XRD, UV, and fluorescence properties. The synthesis involved a rapid water based potassium persulfate (KPS) initiated method under microwave irradiation. The emission spectra of adenine grafted agarose and κ-carrageenan were recorded in aqueous (5×10(-5) M) solution, exhibiting λ(em,max) 347 nm by excitation at 261 nm, affording ca. 30% and 40% enhanced emission intensities, respectively compared to that of pure adenine solution in the same concentration. Similar emission intensity was recorded in the pure adenine solution at its molar equivalent concentrations present in the 5×10(-5) M solution of the agarose and carrageenan grafted products, that is, 3.28×10(-5) M and 4.5×10(-5) M respectively. These fluorescent adenine grafted products may have potential utility in various sensor applications. Copyright © 2012. Published by Elsevier Ltd.

  15. Modeling the Dynamics of Gel Electrophorresis in the High School Classroom

    NASA Astrophysics Data System (ADS)

    Saucedo, Skyler R.

    2013-01-01

    Gel electrophoresis, used by geneticists and forensic experts alike, is an immensely popular technique that utilizes an electric field to separate molecules and proteins by size and charge. At the microscopic level, a dye or complex protein like DNA is passed through agarose, a gelatinous three-dimensional matrix of pores and nano-sized tunnels. When forced through a maze of holes, the molecule unravels, forming a long chain, slithering through the field of pores in a process colloquially coined "reputation." As a result, the smaller molecules travel farther through the gel when compared to molecules of larger molecular weight. This highly effective "molecular sieve" provides consistent data and allows scientists to compare similar sequences of DNA base pairs in a routine fashion.2 When performed at the high school level, gel electrophoresis provides students the opportunity to learn about a contemporary lab technique of great scientific relevance. Doing real science certainly excites students and motivates them to learn more.

  16. Detection of xanthine oxidase and immunologically related proteins in fractions from bovine mammary tissue and milk after electrophoresis in polyacrylamide gels containing sodium dodecyl sulphate.

    PubMed Central

    Mather, I H; Sullivan, C H; Madara, P J

    1982-01-01

    A solid-phase immunoassay was used to detect xanthine oxidase in fractions from bovine mammary glands after electrophoresis in polyacrylamide gels containing sodium dodecyl sulphate. Under these conditions the major proportion of xanthine oxidase in either mammary tissue or mild could be recovered as a protein of mol.wt. 150 000. In mammary tissue approx. 80% of the enzyme was in a soluble form and the remainder was accounted for in either 'mitochondrial' or microsomal fractions after tissue homogenization and fractionation. Affinity chromatography of either detergent-solubilized microsomal membranes or postmicrosomal supernatants on immobilized antibody to xanthine oxidase yielded a single protein that cross-reacted with antibody to the enzyme. In milk presumptive degradation products of the enzyme were detected in minor quantities with mol.wts. of 43 000 in the whey fraction and 90 000 in fat-globule membrane. Only the undegraded enzyme was present in the skim-milk membrane fraction. Xanthine oxidase is therefore synthesized and secreted as a protein with a monomeric mol.wt. of 150 000 and is not subjected to extensive proteolytic degradation during the storage of milk in mammary alveoli. The significance of the results is discussed in relation to the overall protein composition of the membranes of milk-fat globules and skim milk. Images Fig. 1. Fig. 2. Fig. 3. PMID:7046730

  17. Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic Acid Interactions

    PubMed Central

    Hellman, Lance M.; Fried, Michael G.

    2009-01-01

    The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. After electrophoresis, the distribution of species containing nucleic acid is determined, usually by autoradiography of 32P-labeled nucleic acid. In general, protein-nucleic acid complexes migrate more slowly than the corresponding free nucleic acid. In this article, we identify the most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions. A representative protocol is provided and commonly used variants are discussed. Expected outcomes are briefly described. References to extensions of the method and a troubleshooting guide are provided. PMID:17703195

  18. Massively parallel single-molecule and single-cell emulsion reverse transcription polymerase chain reaction using agarose droplet microfluidics.

    PubMed

    Zhang, Huifa; Jenkins, Gareth; Zou, Yuan; Zhu, Zhi; Yang, Chaoyong James

    2012-04-17

    A microfluidic device for performing single copy, emulsion Reverse Transcription Polymerase Chain Reaction (RT-PCR) within agarose droplets is presented. A two-aqueous-inlet emulsion droplet generator was designed and fabricated to produce highly uniform monodisperse picoliter agarose emulsion droplets with RT-PCR reagents in carrier oil. Template RNA or cells were delivered from one inlet with RT-PCR reagents/cell lysis buffer delivered separately from the other. Efficient RNA/cell encapsulation and RT-PCR at the single copy level was achieved in agarose-in-oil droplets, which, after amplification, can be solidified into agarose beads for further analysis. A simple and efficient method to graft primer to the polymer matrix using 5'-acrydite primer was developed to ensure highly efficient trapping of RT-PCR products in agarose. High-throughput single RNA molecule/cell RT-PCR was demonstrated in stochastically diluted solutions. Our results indicate that single-molecule RT-PCR can be efficiently carried out in agarose matrix. Single-cell RT-PCR was successfully performed which showed a clear difference in gene expression level of EpCAM, a cancer biomarker gene, at the single-cell level between different types of cancer cells. This work clearly demonstrates for the first time, single-copy RT-PCR in agarose droplets. We believe this will open up new possibilities for viral RNA detection and single-cell transcription analysis.

  19. Agarose electrophoresis of DNA in discontinuous buffers, using a horizontal slab apparatus and a buffer system with improved properties.

    PubMed

    Zsolnai, A; Orbán, L; Chrambach, A

    1993-03-01

    Using a horizontal slab apparatus with a buffer in the reservoirs at the level of the gel ("sea-level electrophoresis"), the retrograde discontinuous buffer system reported by Wiltfang et al. for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of proteins was applied to DNA electrophoresis. This application yielded the advantages of an increased displacement rate of the moving boundary front and a decrease in the concentration of the counterion base in the resolving phase, which yielded reduced relative mobility values at equivalent gel concentrations and practicable low buffer concentrations. The change of relative mobilities (Rf) with a variation of field strength is decreased compared to that of the migration rate in the continuous Tris-boric-acid-EDTA (TBE) buffer and thus the robustness of the system is improved, as well as the efficiency of separation. The system of Wiltfang et al. has in common with previously described discontinuous DNA system, that it is able to stack DNA from dilute samples and is insensitive to sample components with lower net mobilities than DNA, such as acetate. However, the variance of Rf at constant current density in the discontinuous buffer system is not improved over that of the migration rate at constant field strength in the continuous TBE buffer.

  20. Lupus autoantibodies target ribosomal P proteins

    PubMed Central

    1985-01-01

    All nine SLE (systemic lupus erythematosus) sera with antiribosomal antibody activity targeted the same three ribosomal protein antigens, of molecular masses 38 and 17/19 kD when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. One serum reacted with an additional protein of approximately kD. Ribosomal subunit fractionation by composite gel electrophoresis and sucrose density ultracentrifugation showed that these proteins were part of the large subunit. Isoelectric focusing in agarose, and two-dimensional polyacrylamide gel electrophoresis revealed that the antigens had pI between 4.5 and 6.5, but that the 17/19 kD antigens were more acidic than the 38 kD antigen. Similarities in the molecular masses, charges, as well as the presence of highly conserved crossreactive epitopes, failure to bind to carboxymethylcellulose at pH 4.2, and extractability of the 17/19 kD proteins by 400 mM NH4Cl-ethanol at 0 degrees C indicated that these antigens were analogous to the proteins P0 (38 kD) and P1/P2 (17/19 kD) described previously (25, 36). Co-identity was confirmed using reference antibodies and antigen. Although antibodies to these proteins were only found in 5-10% of more than 50 sera screened by radioimmunoassay or Western blotting, the selective production of antibodies to epitopes on three (out of a total of more than 80) ribosomal proteins may provide further clues to autoantibody induction of SLE. PMID:2410526

  1. Polyacrylamide Gel-Contained Zinc Finger Peptide as the "Lock" and Zinc Ions as the "Key" for Construction of Ultrasensitive Prostate-Specific Antigen SERS Immunosensor.

    PubMed

    Xie, Linglin; Yang, Xia; He, Yi; Yuan, Ruo; Chai, Yaqin

    2018-05-02

    In this work, we adopted polyacrylamide gel-contained zinc finger peptide (PZF) as a "lock" of Raman signal and zinc ions (Zn 2+ ) as a sensitive "key", which was converted from target-captured ZnO NPs, to achieve the measurement of prostate-specific antigen (PSA). Owing to the lock effect from PZF, the surface-enhanced Raman scattering (SERS) tag toluidine blue (TB) connected on Ag NP-coating silica wafer was sheltered leading to low Raman response. Meanwhile, target PSA can specifically connect with antibody 2-coupled ZnO nanocomplexes (ZnO@Au@Ab 2 ) and antibody 1-coupled magnetic (CoFe 2 O 4 @Au@Ab 1 ) nanocomposite through sandwich immunoassay. In the presence of HCl, the ZnO NPs would convert into Zn 2+ to open the PZF because Zn 2+ can specifically react with zinc finger peptide to destroy the PZF structure forming abundant pores. In this way, Zn 2+ could act as the key of Raman signal to open the PZF structure obtaining a strong Raman signal of TB. The proposed SERS sensor can have a quantitative detection of PSA within the range of 1 pg mL -1 to 10 ng mL -1 with a detection limit of 0.65 pg mL -1 . The interaction between zinc finger peptide and Zn 2+ was firstly applied in SERS sensor for the sensitive detection of PSA. These results demonstrated that the new designed SERS biosensor could be a promising tool in biomarker diagnosis.

  2. Development of a bi-functional silica monolith for electro-osmotic pumping and DNA clean-up/extraction using gel-supported reagents in a microfluidic device.

    PubMed

    Oakley, Jennifer A; Shaw, Kirsty J; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

    2009-06-07

    A silica monolith used to support both electro-osmotic pumping (EOP) and the extraction/elution of DNA coupled with gel-supported reagents is described. The benefits of the combined EOP extraction/elution system were illustrated by combining DNA extraction and gene amplification using the polymerase chain reaction (PCR) process. All the reagents necessary for both processes were supported within pre-loaded gels that allow the reagents to be stored at 4 degrees C for up to four weeks in the microfluidic device. When carrying out an analysis the crude sample only needed to be hydrodynamically introduced into the device which was connected to an external computer controlled power supply via platinum wire electrodes. DNA was extracted with 65% efficiency after loading lysed cells onto a silica monolith. Ethanol contained within an agarose gel matrix was then used to wash unwanted debris away from the sample by EOP (100 V cm(-1) for 5 min). The retained DNA was subsequently eluted from the monolith by water contained in a second agarose gel, again by EOP using an electric field of 100 V cm(-1) for 5 min, and transferred into the PCR reagent containing gel. The eluted DNA in solution was successfully amplified by PCR, confirming that the concept of a complete self-contained microfluidic device could be realised for DNA sample clean up and amplification, using a simple pumping and on-chip reagent storage methodology.

  3. Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

    PubMed Central

    Murphy, Sandra; Dowling, Paul; Ohlendieck, Kay

    2016-01-01

    The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry 1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins. PMID:28248237

  4. Enhancing purification efficiency of affinity functionalized composite agarose micro beads using Fe3O4 nanoparticles.

    PubMed

    Amiri, S; Mehrnia, M R; Roudsari, F Pourasgharian

    2017-01-15

    In this work, a series of magnetic and nonmagnetic agarose matrices were fabricated for protein purification. Certain amounts of Fe 3 O 4 nanoparticles were encapsulated in agarose beads to form composite magnetic matrices with enhanced purification efficiency. Structure and morphology of prepared matrices were studied by optical and scanning electron microscopes, FT-IR, and BET-BJH analysis. The prepared matrices had regular spherical shape, followed by a uniform size distribution. By nanoparticles addition, the number of mesopores decreased while population of pores with radius ≤10nm increased; thus, higher specific area achieved. According to VSM results, magnetization degree was one of the characteristics affected by agarose content of the beads. A dye ligand, Cibacron Blue F3GA (CB), was covalently bound to beads to adsorb Bovine serum albumin. CB concentration was determined by elemental analysis. It was shown that magnetic beads hold higher CB concentrations than nonmagnetic ones due to higher specific area. As a result, magnetic 8%-agarose beads had the highest affinity adsorption capacity in static experiments. Moreover, breakthrough curves were monitored to calculate dynamic binding capacity. And, it was shown that magnetic 4%-agarose had the highest adsorbing amount (6.00mg/mL). It was implied that pore diffusion in magnetic 4%-agarose may be the reason for higher dynamic capacity. Plus, column efficiency was evaluated. It was revealed that all magnetic beads had lower HETP (0.11, 0.12 and 0.11cm for magnetic 4, 6, and 8%-agarose beads) than nonmagnetic ones (P-value<0.05). Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

    PubMed Central

    2011-01-01

    Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well

  6. Minimizing inhibition of PCR-STR typing using digital agarose droplet microfluidics.

    PubMed

    Geng, Tao; Mathies, Richard A

    2015-01-01

    The presence of PCR inhibitors in forensic and other biological samples reduces the amplification efficiency, sometimes resulting in complete PCR failure. Here we demonstrate a high-performance digital agarose droplet microfluidics technique for single-cell and single-molecule forensic short tandem repeat (STR) typing of samples contaminated with high concentrations of PCR inhibitors. In our multifaceted strategy, the mitigation of inhibitory effects is achieved by the efficient removal of inhibitors from the porous agarose microgel droplets carrying the DNA template through washing and by the significant dilution of targets and remaining inhibitors to the stochastic limit within the ultralow nL volume droplet reactors. Compared to conventional tube-based bulk PCR, our technique shows enhanced (20 ×, 10 ×, and 16 ×) tolerance of urea, tannic acid, and humic acid, respectively, in STR typing of GM09948 human lymphoid cells. STR profiling of single cells is not affected by small soluble molecules like urea and tannic acid because of their effective elimination from the agarose droplets; however, higher molecular weight humic acid still partially inhibits single-cell PCR when the concentration is higher than 200 ng/μL. Nevertheless, the full STR profile of 9948 male genomic DNA contaminated with 500 ng/μL humic acid was generated by pooling and amplifying beads carrying single-molecule 9948 DNA PCR products in a single secondary reaction. This superior performance suggests that our digital agarose droplet microfluidics technology is a promising approach for analyzing low-abundance DNA targets in the presence of inhibitors. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  7. Novel diffusive gradients in thin films technique to assess labile sulfate in soil.

    PubMed

    Hanousek, Ondrej; Mason, Sean; Santner, Jakob; Chowdhury, Md Mobaroqul Ahsan; Berger, Torsten W; Prohaska, Thomas

    2016-09-01

    A novel diffusive gradients in thin films (DGT) technique for sampling labile soil sulfate was developed, based on a strong basic anion exchange resin (Amberlite IRA-400) for sulfate immobilization on the binding gel. For reducing the sulfate background on the resin gels, photopolymerization was applied instead of ammonium persulfate-induced polymerization. Agarose cross-linked polyacrylamide (APA) hydrogels were used as diffusive layer. The sulfate diffusion coefficient in APA gel was determined as 9.83 × 10(-6) ± 0.35 × 10(-6) cm(2) s(-1) at 25 °C. The accumulated sulfate was eluted in 1 mol L(-1) HNO3 with a recovery of 90.9 ± 1.6 %. The developed method was tested against two standard extraction methods for soil sulfate measurement. The obtained low correlation coefficients indicate that DGT and conventional soil test methods assess differential soil sulfate pools, rendering DGT a potentially important tool for measuring labile soil sulfate.

  8. Acute toxicity of polyacrylamide flocculants to early life stages of freshwater mussels

    USGS Publications Warehouse

    Buczek, Sean B.; Cope, W. Gregory; McLaughlin, Richard A.; Kwak, Thomas J.

    2017-01-01

    Polyacrylamide has become an effective tool for reducing construction-related suspended sediment and turbidity, which are considered to have significant adverse impacts on aquatic ecosystems and are a leading cause of the degradation of North American streams and rivers. However, little is known about the effects of polyacrylamide on many freshwater organisms, and prior to the present study, no information existed on the toxicity of polyacrylamide compounds to native freshwater mussels (family Unionidae), one of the most imperiled faunal groups globally. Following standard test guidelines, we exposed juvenile mussels (test duration 96 h) and glochidia larvae (test duration 24 h) to 5 different anionic polyacrylamide compounds and 1 non-ionic compound. Species tested included the yellow lampmussel (Lampsilis cariosa), an Atlantic Slope species that is listed as endangered in North Carolina; the Appalachian elktoe (Alasmidonta raveneliana), a federally endangered Interior Basin species; and the washboard (Megalonaias nervosa), a common Interior Basin species. We found that median lethal concentrations (LC50s) of polyacrylamide ranged from 411.7 to >1000 mg/L for glochidia and from 126.8 to >1000 mg/L for juveniles. All LC50s were orders of magnitude greater (2–3) than concentrations typically recommended for turbidity control (1–5 mg/L), regardless of their molecular weight or charge density. The results demonstrate that the polyacrylamide compounds tested were not acutely toxic to the mussel species and life stages tested, indicating minimal risk of short-term exposure from polyacrylamide applications in the environment. However, other potential uses of polyacrylamide in the environment (e.g., wastewater treatment, paper processing, mining, algae removal) and their chronic or sublethal effects remain uncertain and warrant additional investigation.

  9. Coupling the Alkaline-Surfactant-Polymer Technology and the Gelation Technology to Maximize Oil Production

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malcolm Pitts; Jie Qi; Dan Wilson

    2005-12-01

    Gelation technologies have been developed to provide more efficient vertical sweep efficiencies for flooding naturally fractured oil reservoirs or reservoirs with different sand lenses with high permeability contrast. The field proven alkaline-surfactant-polymer technology economically recovers 15% to 25% OOIP more crude oil than waterflooding froin swept pore space of an oil reservoir. However, alkaline-surfactant-polymer technology is not amenable to naturally fractured reservoirs or reservoirs with high permeability contrast zones because much of injected solution bypasses target pore space containing oil. This work investigates whether combining these two technologies could broaden applicability of alkaline-surfactant-polymer flooding into these reservoirs. Fluid-fluid interaction withmore » different gel chemical compositions and alkaline-surfactant-polymer solution with pH values ranging from 9.2 to 12.9 have been tested. Aluminum-polyacrylamide gels are not stable to alkaline-surfactant-polymer solutions at any pH. Chromium-polyacrylamide gels with polymer to chromium ion ratios of 25 or greater were stable to alkaline-surfactant-polymer solutions if solution pH was 10.6 or less. When the polymer to chromium ion was 15 or less, chromium-polyacrylamide gels were stable to alkaline-surfactant-polymer solutions with pH values up to 12.9. Chromium-xanthan gum gels were stable to alkaline-surfactant-polymer solutions with pH values of 12.9 at the polymer to chromium ion ratios tested. Silicate-polyacrylamide, resorcinol-formaldehyde, and sulfomethylated resorcinol-formaldehyde gels were also stable to alkaline-surfactant-polymer solutions with pH values ranging from 9.2 to 12.9. Iron-polyacrylamide gels were immediately destroyed when contacted with any of the alkaline-surfactant-polymer solutions with pH values ranging from 9.2 to 12.9. Gel solutions under dynamic conditions of linear corefloods showed similar stability to alkaline-surfactant-polymer solutions

  10. Nanoscale supramolecular ordering in gel-surfactant complexes: Sodium alkyl sulfates in poly(diallyldimethylammonium chloride)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sokolov, E.L.; Yeh, F.; Khokhlov, A.

    1996-12-25

    Studies of slightly cross-linked polycationic gels interacting with anionic surfactants have been performed by using random copolymers of poly(diallyldimethylammonium chloride) (PDADMACl) and polyacrylamide (PAAm) with varying content of PDADMACl and degree of cross-linking. Gel samples which had been fully swollen in water were placed in aqueous solutions of sodium alkyl sulfates (octyl(SOS), decyl-(SDCS), dodecyl (SDS), tetradecyl (STS), and hexyl (SHS) sulfates). The degree of the sample volume contraction depends on the PDADMACl content. The collapsed gel-surfactant complexes were studied using synchrotron small-angle X-ray scattering. All studied samples containing PDADMACl exhibited pronounced supramolecular nanostructures. The gel-SDCS complex exhibited a cubic structuremore » with a periodicity (7.75 nm) of approximately 4 times the surfactant molecular length, while the gel-SDS, gel-STS, and gel-SHS complexes showed hexagonal supramolecular ordering with a periodicity of approximately 2 times the surfactant molecular length. The d spacing of the longest periodicity in the complexes was dependent on the PDADMACl content and the surfactant. The d spacing generally increased with decreasing PDADMACl (charge) content and increasing number of carbon atoms in the surfactant alkyl chain. 20 refs., 11 figs., 5 tabs.« less

  11. The influence of ionic strength on DNA diffusion in gel networks

    NASA Astrophysics Data System (ADS)

    Fu, Yuanxi; Jee, Ah-Young; Kim, Hyeong-Ju; Granick, Steve

    Cations are known to reduce the rigidity of the DNA molecules by screening the negative charge along the sugar phosphate backbone. This was established by optical tweezer pulling experiment of immobilized DNA strands. However, little is known regarding the influence of ions on the motion of DNA molecules as they thread through network meshes. We imaged in real time the Brownian diffusion of fluorescent labeled lambda-DNA in an agarose gel network in the presence of salt with monovalent or multivalent cations. Each movie was analyzed using home-written program to yield a trajectory of center of the mass and the accompanying history of the shape fluctuations. One preliminary finding is that ionic strength has a profound influence on the slope of the trace of mean square displacement (MSD) versus time. The influence of ionic strength on DNA diffusion in gel networks.

  12. High performance gel imaging with a commercial single lens reflex camera

    NASA Astrophysics Data System (ADS)

    Slobodan, J.; Corbett, R.; Wye, N.; Schein, J. E.; Marra, M. A.; Coope, R. J. N.

    2011-03-01

    A high performance gel imaging system was constructed using a digital single lens reflex camera with epi-illumination to image 19 × 23 cm agarose gels with up to 10,000 DNA bands each. It was found to give equivalent performance to a laser scanner in this high throughput DNA fingerprinting application using the fluorophore SYBR Green®. The specificity and sensitivity of the imager and scanner were within 1% using the same band identification software. Low and high cost color filters were also compared and it was found that with care, good results could be obtained with inexpensive dyed acrylic filters in combination with more costly dielectric interference filters, but that very poor combinations were also possible. Methods for determining resolution, dynamic range, and optical efficiency for imagers are also proposed to facilitate comparison between systems.

  13. System and method of infrared matrix-assisted laser desorption/ionization mass spectrometry in polyacrylamide gels

    DOEpatents

    Haglund, Jr., Richard F.; Ermer, David R.; Baltz-Knorr, Michelle Lee

    2004-11-30

    A system and method for desorption and ionization of analytes in an ablation medium. In one embodiment, the method includes the steps of preparing a sample having analytes in a medium including at least one component, freezing the sample at a sufficiently low temperature so that at least part of the sample has a phase transition, and irradiating the frozen sample with short-pulse radiation to cause medium ablation and desorption and ionization of the analytes. The method further includes the steps of selecting a resonant vibrational mode of at least one component of the medium and selecting an energy source tuned to emit radiation substantially at the wavelength of the selected resonant vibrational mode. The medium is an electrophoresis medium having polyacrylamide. In one embodiment, the energy source is a laser, where the laser can be a free electron laser tunable to generate short-pulse radiation. Alternatively, the laser can be a solid state laser tunable to generate short-pulse radiation. The laser can emit light at various ranges of wavelength.

  14. Retention of gene expression in porcine islets after agarose encapsulation and long-term culture

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dumpala, Pradeep R., E-mail: pdumpala@rixd.org; Holdcraft, Robert W.; Martis, Prithy C.

    Agarose encapsulation of porcine islets allows extended in vitro culture, providing ample time to determine the functional capacity of the islets and conduct comprehensive microbiological safety testing prior to implantation as a treatment for type 1 diabetes mellitus. However, the effect that agarose encapsulation and long-term culture may have on porcine islet gene expression is unknown. The aim of the present study was to compare the transcriptome of encapsulated porcine islets following long-term in vitro culture against free islets cultured overnight. Global gene expression analysis revealed no significant change in the expression of 98.47% of genes. This indicates that the gene expressionmore » profile of free islets is highly conserved following encapsulation and long-term culture. Importantly, the expression levels of genes that code for critical hormones secreted by islets (insulin, glucagon, and somatostatin) as well as transcripts encoding proteins involved in their packaging and secretion are unchanged. While a small number of genes known to play roles in the insulin secretion and insulin signaling pathways are differentially expressed, our results show that overall gene expression is retained following islet isolation, agarose encapsulation, and long-term culture. - Highlights: • Effect of agarose encapsulation and 8 week culture on porcine islets was analyzed. • Transcriptome analysis revealed no significant change in a majority (98%) of genes. • Agarose encapsulation allows for long-term culture of porcine islets. • Islet culture allows for functional and microbial testing prior to clinical use.« less

  15. Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

    PubMed

    Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

    2017-06-23

    The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

  16. Non-toxic agarose/gelatin-based microencapsulation system containing gallic acid for antifungal application.

    PubMed

    Lam, P-L; Gambari, R; Kok, S H-L; Lam, K-H; Tang, J C-O; Bian, Z-X; Lee, K K-H; Chui, C-H

    2015-02-01

    Aspergillus niger (A. niger) is a common species of Aspergillus molds. Cutaneous aspergillosis usually occurs in skin sites near intravenous injection and approximately 6% of cutaneous aspergillosis cases which do not involve burn or HIV-infected patients are caused by A. niger. Biomaterials and biopharmaceuticals produced from microparticle-based drug delivery systems have received much attention as microencapsulated drugs offer an improvement in therapeutic efficacy due to better human absorption. The frequently used crosslinker, glutaraldehyde, in gelatin-based microencapsulation systems is considered harmful to human beings. In order to tackle the potential risks, agarose has become an alternative polymer to be used with gelatin as wall matrix materials of microcapsules. In the present study, we report the eco-friendly use of an agarose/gelatin-based microencapsulation system to enhance the antifungal activity of gallic acid and reduce its potential cytotoxic effects towards human skin keratinocytes. We used optimal parameter combinations, such as an agarose/gelatin ratio of 1:1, a polymer/oil ratio of 1:60, a surfactant volume of 1% w/w and a stirring speed of 900 rpm. The minimum inhibitory concentration of microencapsulated gallic acid (62.5 µg/ml) was significantly improved when compared with that of the original drug (>750 µg/ml). The anti-A. niger activity of gallic acid -containing microcapsules was much stronger than that of the original drug. Following 48 h of treatment, skin cell survival was approximately 90% with agarose/gelatin microcapsules containing gallic acid, whereas cell viability was only 25-35% with free gallic acid. Our results demonstrate that agarose/gelatin-based microcapsules containing gallic acid may prove to be helpful in the treatment of A. niger-induced skin infections near intravenous injection sites.

  17. Comparison of genome size and synthesis of structural proteins of Hirame Rhabdovirus, infectious hematopoietic necrosis virus, and viral hemorrhagic Septicemia virus

    USGS Publications Warehouse

    Nishizawa, Toyohiko; Yoshimizu, Mamoru; Winton, James R.; Kimura, Takahisa

    1991-01-01

    Genomic RNA was extracted from purified virions of hirame rhabdovirus (HRV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The full-length RNA was analyzed using formaldehyde agarose gel electrophoresis followed by ethidium bromide staining. Compared with an internal RNA size standard, all three viral genomic RNAs appeared to have identical relative mobilities and were estimated to be approximately 10.7 kilobases in length or about 3.7 megadaltons in molecular mass. Structural protein synthesis of HRV, IHNV, and VHSV was studied using cell cultures treated with actinomycin D. At 2 h intervals, proteins were labeled with 35S-methionine, extracted, and analyzed by SDS-polyacrylamide gel electrophoresis and autoradiography. The five structural proteins of each of the three viruses appeared in the following order : nucleoprotein (N), matrix protein 1 (M1), matrix protein 2 (M2), glycoprotein (G), and polymerase (L) reflecting both the approximate relative abundance of each protein within infected cells and the gene order within the viral genome.

  18. The effect of solute concentration on hindered gradient diffusion in polymeric gels

    NASA Astrophysics Data System (ADS)

    Buck, Kristan K. S.; Dungan, Stephanie R.; Phillips, Ronald J.

    1999-10-01

    The effect of solute concentration on hindered diffusion of sphere-like colloidal solutes in stiff polymer hydrogels is examined theoretically and experimentally. In the theoretical development, it is shown that the presence of the gel fibres enhances the effect of concentration on the thermodynamic driving force for gradient diffusion, while simultaneously reducing the effect of concentration on the hydrodynamic drag. The result is that gradient diffusion depends more strongly on solute concentration in gels than it does in pure solution, by an amount that depends on the partition coefficient and hydraulic permeability of the gel solute system. Quantitative calculations are made to determine the concentration-dependent diffusivity correct to first order in solute concentration. In order to compare the theoretical predictions with experimental data, rates of diffusion have been measured for nonionic micelles and globular proteins in solution and agarose hydrogels at two gel concentrations. The measurements were performed by using holographic interferometry, through which one monitors changes in refractive index as gradient diffusion takes place within a transparent gel. If the solutes are modelled as spheres with short-range repulsive interactions, then the experimentally measured concentration dependence of the diffusivities of both the protein and micelles is in good agreement with the theoretical predictions.

  19. [Discrimination of types of polyacrylamide based on near infrared spectroscopy coupled with least square support vector machine].

    PubMed

    Zhang, Hong-Guang; Yang, Qin-Min; Lu, Jian-Gang

    2014-04-01

    In this paper, a novel discriminant methodology based on near infrared spectroscopic analysis technique and least square support vector machine was proposed for rapid and nondestructive discrimination of different types of Polyacrylamide. The diffuse reflectance spectra of samples of Non-ionic Polyacrylamide, Anionic Polyacrylamide and Cationic Polyacrylamide were measured. Then principal component analysis method was applied to reduce the dimension of the spectral data and extract of the principal compnents. The first three principal components were used for cluster analysis of the three different types of Polyacrylamide. Then those principal components were also used as inputs of least square support vector machine model. The optimization of the parameters and the number of principal components used as inputs of least square support vector machine model was performed through cross validation based on grid search. 60 samples of each type of Polyacrylamide were collected. Thus a total of 180 samples were obtained. 135 samples, 45 samples for each type of Polyacrylamide, were randomly split into a training set to build calibration model and the rest 45 samples were used as test set to evaluate the performance of the developed model. In addition, 5 Cationic Polyacrylamide samples and 5 Anionic Polyacrylamide samples adulterated with different proportion of Non-ionic Polyacrylamide were also prepared to show the feasibilty of the proposed method to discriminate the adulterated Polyacrylamide samples. The prediction error threshold for each type of Polyacrylamide was determined by F statistical significance test method based on the prediction error of the training set of corresponding type of Polyacrylamide in cross validation. The discrimination accuracy of the built model was 100% for prediction of the test set. The prediction of the model for the 10 mixing samples was also presented, and all mixing samples were accurately discriminated as adulterated samples. The

  20. Ink-native electrophoresis: an alternative to blue-native electrophoresis more suitable for in-gel detection of enzymatic activity.

    PubMed

    Kaneko, Keisuke; Sueyoshi, Noriyuki; Kameshita, Isamu; Ishida, Atsuhiko

    2013-09-15

    Blue-native electrophoresis (BNE) is a useful technique for analyzing protein complexes, but the Coomassie brilliant blue (CBB) dye used in BNE often hampers in-gel detection of enzymatic activity. Here we report an improved method, termed ink-native electrophoresis (INE), in which Pelikan 4001 fountain pen ink is used as a charge-shifting agent instead of CBB. INE is more suitable than BNE for in-gel detection of protein kinase activity after polyacrylamide gel electrophoresis (PAGE), and its performance in protein complex separation is comparable to that of conventional BNE. INE may provide a powerful tool to isolate and analyze various protein complexes. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Northern blots: capillary transfer of RNA from agarose gels and filter hybridization using standard stringency conditions.

    PubMed

    Rio, Donald C

    2015-03-02

    In this protocol, an RNA sample, fractionated by gel electrophoresis, is transferred from the gel onto a membrane by capillary transfer. Short-wave UV light is used to fix the transferred RNA to the membrane. The membrane is then pretreated to block nonspecific probe-binding sites, and hybridization of the immobilized RNA to a (32)P-labeled DNA or RNA probe specific for the mRNA of interest is performed. Finally, the membrane is washed and subjected to autoradiography or phosphorimaging. Because exposure to UV cross-links the RNA to the membrane, the membrane can be stripped and hybridized with other probes. The procedure is suitable for detecting poly(A)(+)-selected mRNA or mRNA in total cellular RNA if the target transcript is relatively abundant. Using DNA or RNA probes labeled to 1 × 10(8)-10 × 10(8) cpm/µg, it should be possible to detect ∼5 pg of a specific RNA. © 2015 Cold Spring Harbor Laboratory Press.

  2. Novel hydrophobic interaction chromatography matrix for specific isolation and simple elution of immunoglobulins (A, G, and M) from porcine serum.

    PubMed

    Ramos-Clamont, Gabriela; del Carmen Candia-Plata, Maria; Zamudio, Roberto Guzman; Vazquez-Moreno, Luz

    2006-07-28

    A new, highly acetylated agarose matrix (HA-Sepharose) was synthesized and used as a hydrophobic interaction chromatography (HIC) medium to specifically isolate immunoglobulins (Igs) from porcine serum. Recovery of Igs was in a single step and under mild conditions. HA-Sepharose adsorption was studied in terms of salt, gel acetylation time, flow rate, and protein concentration on the loading buffer. At 0.5 M Na2SO4, control with unmodified Sepharose retained a small fraction (0.70 mg/mL of matrix) of serum albumin. On the contrary HA-Sepharose retained primary Igs (IgA, IgG, and 53% of IgM) as revealed by sodium dodecyl sulphate 10% polyacrylamide gel electrophoresis (SDS-PAGE), quantitative radial immunodiffusion and immunodetection. At a flow rate of 1 mL/min, the HA-Sepharose column capacity (3.9 mg/mL of matrix) was similar to the reported capacity for the commercial thiophilic T-gel. However, HA-Sepharose showed higher recovery of IgA and IgM than the T-gel in the same salt conditions, clearly an advantage in terms of immunoglobulin recovery strategies. Acetylation changed the matrix adsorption from albumin to immunoglobulins; thus, the highly acetylated gel rendered recoveries of Igs from unprocessed porcine serum practically free of albumin.

  3. Characterization of Novel Gel Casting System to Make Complex Shaped Aluminum Oxide (Al2O3) Parts

    DTIC Science & Technology

    2016-03-01

    investigated including systems based on starch , gelatin, protein, and agarose. Generally, all systems are too expensive for high-volume casting.13 While gel...was determined by measuring the resistance force in uniaxial compression. Therefore, the specimen was considered gelled when the resistance force was...used to lower the indenter tip at a rate of 30 mm/min by a distance of 6 mm while measuring the maximum resistance force during the indentation. At the

  4. Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis.

    PubMed

    Robinson, Nicholas P

    2013-01-01

    Branched DNA molecules are generated by the essential processes of replication and recombination. Owing to their distinctive extended shapes, these intermediates migrate differently from linear double-stranded DNA under certain electrophoretic conditions. However, these branched species exist in the cell at much low abundance than the bulk linear DNA. Consequently, branched molecules cannot be visualized by conventional electrophoresis and ethidium bromide staining. Two-dimensional native-native agarose electrophoresis has therefore been developed as a method to facilitate the separation and visualization of branched replication and recombination intermediates. A wide variety of studies have employed this technique to examine branched molecules in eukaryotic, archaeal, and bacterial cells, providing valuable insights into how DNA is duplicated and repaired in all three domains of life.

  5. Gel electrophoretic isolation, in the hundred microgram range, of recombinant SDS-syntaxin from sea urchin egg cortical vesicles.

    PubMed

    Li, Y M; Chrambach, A

    2001-11-01

    Recombinant urchin syntaxin [Xa cut], electrophoresed at pH 9.0 (25 degrees C) or 10.2 (0 degrees C) in a discontinuous Tris-chloride-glycinate buffer system in the presence of 0.03% SDS in the catholyte, exhibits a multicomponent pattern in gels of a polyacrylamide concentration of 12% and 3% crosslinking. The position in the pattern of the syntaxin band was identified by reference to electropherograms of a previous study (P. Backlund, pers. comm.). The complexity of the protein composition of the preparation was reduced by selective stacking of proteins with mobilities greater than that of syntaxin. This provides a gel pattern consisting of two bands with mobilities close to that identified as syntaxin, as well as a minor, more slowly migrating, contaminant. The two major components are designated as S1 and S2, the latter being the larger species. In the absence of SDS, the preparation exhibits two pairs of protein components. Three of the proteins are charge isomers, i.e., of equal size, differing only in net charge, assumed to be forms of S1, while the fourth component is larger and is assumed to be S2. Aliquots of the preparation, containing 150 microg of protein were loaded on a cylindrical polyacrylamide gel of 18 mm diameter, and separated S1 and S2 were excised in a position defined by their characteristic values of relative mobility (Rf). Two or three gel slices, corresponding in Rf to S1 or S2, were pooled and loaded onto a Stacking Gel (5% polyacrylamide, 20% cross-linked) of 18 mm diameter, equipped with a collection chamber of 200 microL volume. The protein was electroeluted from the gel slices and concentrated into a stack by electrophoresis. The stack, marked by bromphenolblue, was allowed to migrate into the collection chamber, was collected and analyzed by protein assay and re-electrophoresis. Re-electrophoresis of S1 shows that it consists of at least three components. Recovered S1 constitutes 47% of the preparation, based on protein assay, S2 4

  6. Monte Carlo modeling of a conventional X-ray computed tomography scanner for gel dosimetry purposes.

    PubMed

    Hayati, Homa; Mesbahi, Asghar; Nazarpoor, Mahmood

    2016-01-01

    Our purpose in the current study was to model an X-ray CT scanner with the Monte Carlo (MC) method for gel dosimetry. In this study, a conventional CT scanner with one array detector was modeled with use of the MCNPX MC code. The MC calculated photon fluence in detector arrays was used for image reconstruction of a simple water phantom as well as polyacrylamide polymer gel (PAG) used for radiation therapy. Image reconstruction was performed with the filtered back-projection method with a Hann filter and the Spline interpolation method. Using MC results, we obtained the dose-response curve for images of irradiated gel at different absorbed doses. A spatial resolution of about 2 mm was found for our simulated MC model. The MC-based CT images of the PAG gel showed a reliable increase in the CT number with increasing absorbed dose for the studied gel. Also, our results showed that the current MC model of a CT scanner can be used for further studies on the parameters that influence the usability and reliability of results, such as the photon energy spectra and exposure techniques in X-ray CT gel dosimetry.

  7. Capillary sample introduction of polymerase chain reaction (PCR) products separated in ultrathin slab gels.

    PubMed

    Bullard, K M; Hietpas, P B; Ewing, A G

    1998-01-01

    Polymerase chain reaction (PCR) amplified short tandem repeat (STR) samples from the HUMVWF locus have been analyzed using a unique sample introduction and separation technique. A single capillary is used to transfer samples onto an ultrathin slab gel (57 microm thin). This ultrathin nondenaturing polyacrylamide gel is used to separate the amplified fragments, and laser-induced fluorescence with ethidium bromide is used for detection. The feasibility of performing STR analysis using this system has been investigated by examining the reproducibility for repeated samples. Reproducibility is examined by comparing the migration of the 14 and 17 HUMVWF alleles on three consecutive separations on the ultrathin slab gel. Using one locus, separations match in migration time with the two alleles 42 s apart for each of the three consecutive separations. This technique shows potential to increase sample throughput in STR analysis techniques although separation resolution still needs to be improved.

  8. Transfer in SDS of biotinylated proteins from acrylamide gels to an avidin-coated membrane filter.

    PubMed

    Karlin, Arthur; Wang, Chaojian; Li, Jing; Xu, Qiang

    2004-06-01

    Avidin was covalently linked to aldehyde-derivatized polyethersulfone membrane filters. These filters were used in Western blot analysis of proteins reacted with biotinylation reagents and electrophoresed in sodium dodecyl sulfate (SDS) on polyacrylamide gels. Electrophoretic transfer from the gels to these filters was in 0.1% SDS, in which the covalently bound avidin retained its biotin-binding capacity. We compared Western blots on avidin-coated membrane filters of biotinylated and nonbiotinylated forms of mouse immunoglobulin G (IgG), mouse IgG heavy chain, muscle-type acetylcholine receptor alpha subunit, and fused alpha and beta subunits of receptor. Biotinylated proteins were captured with high specificity compared to their nonbiotinylated counterparts and sensitively detected on the avidin-coated membranes.

  9. New visible and selective DNA staining method in gels with tetrazolium salts.

    PubMed

    Paredes, Aaron J; Naranjo-Palma, Tatiana; Alfaro-Valdés, Hilda M; Barriga, Andrés; Babul, Jorge; Wilson, Christian A M

    2017-01-15

    DNA staining in gels has historically been carried out using silver staining and fluorescent dyes like ethidium bromide and SYBR Green I (SGI). Using fluorescent dyes allows recovery of the analyte, but requires instruments such as a transilluminator or fluorimeter to visualize the DNA. Here we described a new and simple method that allows DNA visualization to the naked eye by generating a colored precipitate. It works by soaking the acrylamide or agarose DNA gel in SGI and nitro blue tetrazolium (NBT) solution that, when exposed to sunlight, produces a purple insoluble formazan precipitate that remains in the gel after exposure to light. A calibration curve made with a DNA standard established a detection limit of approximately 180 pg/band at 500 bp. Selectivity of this assay was determined using different biomolecules, demonstrating a high selectivity for DNA. Integrity and functionality of the DNA recovered from gels was determined by enzymatic cutting with a restriction enzyme and by transforming competent cells after the different staining methods, respectively. Our method showed the best performance among the dyes employed. Based on its specificity, low cost and its adequacy for field work, this new methodology has enormous potential benefits to research and industry. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. A comparative in vitro study of the digestibility of heat- and high pressure-induced gels prepared from industrial milk whey proteins

    NASA Astrophysics Data System (ADS)

    He, Jin-Song; Mu, Tai-Hua; Wang, Juan

    2013-06-01

    We undertook this study to compare the digestibility of heat- and high pressure-induced gels produced from whey protein isolate (WPI). To simulate in vivo gastrointestinal digestion of WPI gels, a pepsin-trypsin digestion system was used. The in vitro protein digestibility of WPI gels induced by high pressure (400 MPa and 30 min; P-gel) and those induced by heat (80°C and 30 min; H-gel) was compared using a protein concentration of 0.14 g mL-1. The in vitro protein digestibility of P-gels was significantly greater than that of H-gels (p<0.05). The size-exclusion chromatography profiles of the hydrolysates showed that the P-gel generated more and smaller peptides than natural WPI and H-gels. Furthermore, Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed some soluble disulfide-mediated aggregation in the P-gel, while there was more insoluble aggregation in the H-gel than the P-gel. The P-gel was more sensitive to proteinase than the H-gel, which was related to the content of S-S bonds, and this in turn could be attributed to the differences in the gelation mechanism between the H-gel and P-gel.

  11. Coupling the Alkaline-Surfactant-Polymer Technology and The Gelation Technology to Maximize Oil Production

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malcolm Pitts; Jie Qi; Dan Wilson

    2005-12-01

    Gelation technologies have been developed to provide more efficient vertical sweep efficiencies for flooding naturally fractured oil reservoirs or reservoirs with different sand lenses with high permeability contrast. The field proven alkaline-surfactant-polymer technology economically recovers 15% to 25% OOIP more crude oil than waterflooding from swept pore space of an oil reservoir. However, alkaline-surfactant-polymer technology is not amenable to naturally fractured reservoirs or reservoirs with high permeability contrast zones because much of injected solution bypasses target pore space containing oil. This work investigates whether combining these two technologies could broaden applicability of alkaline-surfactant-polymer flooding into these reservoirs. Fluid-fluid interaction withmore » different gel chemical compositions and alkaline-surfactant-polymer solution with pH values ranging from 9.2 to 12.9 have been tested. Aluminum-polyacrylamide gels are not stable to alkaline-surfactant-polymer solutions at any pH. Chromium-polyacrylamide gels with polymer to chromium ion ratios of 25 or greater were stable to alkaline-surfactant-polymer solutions if solution pH was 10.6 or less. When the polymer to chromium ion was 15 or less, chromium-polyacrylamide gels were stable to alkaline-surfactant-polymer solutions with pH values up to 12.9. Chromium-xanthan gum gels were stable to alkaline-surfactant-polymer solutions with pH values of 12.9 at the polymer to chromium ion ratios tested. Silicate-polyacrylamide, resorcinol-formaldehyde, and sulfomethylated resorcinol-formaldehyde gels were also stable to alkaline-surfactant-polymer solutions with pH values ranging from 9.2 to 12.9. Iron-polyacrylamide gels were immediately destroyed when contacted with any of the alkaline-surfactant-polymer solutions with pH values ranging from 9.2 to 12.9. Gel solutions under dynamic conditions of linear corefloods showed similar stability to alkaline-surfactant-polymer solutions

  12. Pulsed-field gel electrophoresis (PFGE): application in population structure studies of bovine mastitis-causing streptococci.

    PubMed

    Santos-Sanches, Ilda; Chambel, Lélia; Tenreiro, Rogério

    2015-01-01

    Pulsed-field gel electrophoresis (PFGE) separates large DNA molecules by the use of an alternating electrical field, such that greater size resolution can be obtained when compared to normal agarose gel electrophoresis. PFGE is often employed to track pathogens and is a valuable typing scheme to detect and differentiate strains. Particularly, the contour-clamped homogeneous electric field (CHEF) PFGE system is considered to be the gold standard for use in epidemiological studies of many bacterial pathogens. Here we describe a PFGE protocol that was applicable to the study of bovine streptococci, namely, Streptococcus agalactiae (group B Streptococcus, GBS), Streptococcus dysgalactiae subsp. dysgalactiae (group C Streptococcus, GCS), and Streptococcus uberis-which are relevant pathogens causing mastitis, a highly prevalent and costly disease in dairy industry due to antibiotherapy and loss in milk production.

  13. Purification of brain D2 dopamine receptor.

    PubMed Central

    Williamson, R A; Worrall, S; Chazot, P L; Strange, P G

    1988-01-01

    D2 dopamine receptors have been extracted from bovine brain using the detergent cholate and purified approximately 20,000-fold by affinity chromatography on haloperidol-sepharose and wheat germ agglutinin-agarose columns. The purified preparation contains D2 dopamine receptors as judged by the pharmacological specificity of [3H]spiperone binding to the purified material. The sp. act. of [3H]spiperone binding in the purified preparation is 2.5 nmol/mg protein. The purified preparation shows a major diffuse band at Mr 95,000 upon SDS-polyacrylamide gel electrophoresis and there is evidence for microheterogeneity either at the protein or glycosylation level. Photoaffinity labelling of D2 dopamine receptors also shows a species of Mr 95,000. The D2 dopamine receptor therefore is a glycoprotein of Mr 95,000. Images PMID:3243275

  14. Strategies for the crystallization of viruses: using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus.

    PubMed

    Schellenberger, Pascale; Demangeat, Gérard; Lemaire, Olivier; Ritzenthaler, Christophe; Bergdoll, Marc; Oliéric, Vincent; Sauter, Claude; Lorber, Bernard

    2011-05-01

    The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and viral proteins synthesized upon infection, the wild type GFLV strain F13 and a natural mutant (GFLV-TD) carrying a Gly₂₉₇Asp mutation were purified, characterized and crystallized. Subsequently, the geometry and volume of their crystals was optimized by establishing phase diagrams. GFLV-TD was twice as soluble as the parent virus in the crystallization solution and its crystals diffracted X-rays to a resolution of 2.7 Å. The diffraction limit of GFLV-F13 crystals was extended from 5.5 to 3 Å by growth in agarose gel. Preliminary crystallographic analyses indicate that both types of crystals are suitable for structure determination. Keys for the successful production of GFLV crystals include the rigorous quality control of virus preparations, crystal quality improvement using phase diagrams, and crystal lattice reinforcement by growth in agarose gel. These strategies are applicable to the production of well-diffracting crystals of other viruses and macromolecular assemblies. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments.

    PubMed Central

    Gray, A J; Beecher, D E; Olson, M V

    1984-01-01

    A stand-alone, interactive computer system has been developed that automates the analysis of ethidium bromide-stained agarose and acrylamide gels on which DNA restriction fragments have been separated by size. High-resolution digital images of the gels are obtained using a camera that contains a one-dimensional, 2048-pixel photodiode array that is mechanically translated through 2048 discrete steps in a direction perpendicular to the gel lanes. An automatic band-detection algorithm is used to establish the positions of the gel bands. A color-video graphics system, on which both the gel image and a variety of operator-controlled overlays are displayed, allows the operator to visualize and interact with critical stages of the analysis. The principal interactive steps involve defining the regions of the image that are to be analyzed and editing the results of the band-detection process. The system produces a machine-readable output file that contains the positions, intensities, and descriptive classifications of all the bands, as well as documentary information about the experiment. This file is normally further processed on a larger computer to obtain fragment-size assignments. Images PMID:6320097

  16. Comparative proteomic analysis of the ribosomes in 5-fluorouracil resistance of a human colon cancer cell line using the radical-free and highly reducing method of two-dimensional polyacrylamide gel electrophoresis.

    PubMed

    Kimura, Kosei; Wada, Akira; Ueta, Masami; Ogata, Akihiko; Tanaka, Satoru; Sakai, Akiko; Yoshida, Hideji; Fushitani, Hideo; Miyamoto, Akiko; Fukushima, Masakazu; Uchiumi, Toshio; Tanigawa, Nobuhiko

    2010-11-01

    Many auxiliary functions of ribosomal proteins (r-proteins) have received considerable attention in recent years. However, human r-proteins have hardly been examined by proteomic analysis. In this study, we isolated ribosomal particles and subsequently compared the proteome of r-proteins between the DLD-1 human colon cancer cell line and its 5-fluorouracil (5-FU)-resistant sub-line, DLD-1/5-FU, using the radical-free and highly reducing method of two-dimensional polyacrylamide gel electrophoresis, which has a superior ability to separate basic proteins, and we discuss the role of r-proteins in 5-FU resistance. Densitometric analysis was performed to quantify modulated proteins, and protein spots showing significant changes were identified by employing matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Three basic proteins (L15, L37 and prohibitin) which were significantly modulated between DLD-1 and DLD-1/5-FU were identified. Two proteins, L15 and L37, showed down-regulated expression in DLD-1/5-FU in comparison to DLD-1. Prohibitin, which is not an r-protein and is known to be localized in the mitochondria, showed up-regulated expression in DLD-1/5-FU. These 3 proteins may be related to 5-FU resistance.

  17. Analysis of the response of PVA-GTA Fricke-gel dosimeters with clinical magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Collura, Giorgio; Gallo, Salvatore; Tranchina, Luigi; Abbate, Boris Federico; Bartolotta, Antonio; d'Errico, Francesco; Marrale, Maurizio

    2018-01-01

    Fricke gel dosimeters produced with a matrix of Poly-vinyl alcohol (PVA) cross-linked with glutaraldehyde (GTA) were analyzed with magnetic resonance imaging (MRI). Previous studies based on spectrophotometry showed valuable dosimetric features of these gels in terms of X-ray sensitivity and diffusion of the ferric ions produced after irradiation. In this study, MRI was performed on the gels at 1.5 T with a clinical scanner in order to optimize the acquisition parameters and obtain high contrast between irradiated and non-irradiated samples. The PVA gels were found to offer good linearity in the range of 0-10 Gy and a stable signal for several hours after irradiation. The sensitivity was about 40% higher compared to gels produced with agarose as gelling agent. The effect of xylenol orange (XO) on the MRI signal was also investigated: gel dosimeters made without XO show higher sensitivity to x-rays than those made with XO. The dosimetric accuracy of the 3D gels was investigated by comparing their MRI response to percentage depth dose and transversal dose profile measurements made with an ionization chamber in a water phantom. The comparison of PVA-GTA gels with and without XO showed that the chelating agent reduces the MRI sensitivity of the gels. Depth-dose and transversal dose profiles acquired by PVA-GTA gels without XO are more accurate and consistent with the ionization chamber data. However, diffusion effects hinder accurate measurements in the steep dose gradient regions and they should be further reduced by modifying the gel matrix and/or by minimizing the delay between irradiation and imaging.

  18. Molecular interactions in a surfactant-water-polyacrylamide system, according to densimetry, viscometry, conductometry, and spectroscopy data

    NASA Astrophysics Data System (ADS)

    Harutyunyan, R. S.

    2013-08-01

    Molecular interactions in a surfactant-polyacrylamide-water system are investigated. It is established that the interactions affect such physicochemical parameters of the system as viscosity, density, surface tension, conductivity, and critical micelle concentration. It is shown that in a polyacrylamide-water system, raising the polyacrylamide concentration to 0.02% causes conformational changes in its macromolecule.

  19. Simple and rapid system for two-dimensional gel electrophoresis technique: A laboratory exercise for high school students.

    PubMed

    Maurye, Praveen; Basu, Arpita; Biswas, Jayanta Kumar; Bandyopadhyay, Tapas Kumar; Naskar, Malay

    2018-02-28

    Polyacrylamide gel electrophoresis (PAGE) is the most classical technique favored worldwide for resolution of macromolecules in many biochemistry laboratories due to its incessant advanced developments and wide modifications. These ever-growing advancements in the basic laboratory equipments lead to emergence of many expensive, complex, and tricky laboratory equipments. Practical courses of biochemistry at high school or undergraduate levels are often affected by these complications. Two dimensional gel electrophoresis technique (2D-PAGE) used for resolving thousands of proteins in a gel is a combination of isoelectric focusing (first dimension gel electrophoresis technique) and sodium-dodecylsulphate PAGE (second dimension gel electrophoresis technique or SDS-PAGE). Two different laboratory equipments are needed to carry out effective 2D-PAGE technique, which also invites extra burden to the school laboratory. Here, we describe a low cost, time saving and simple gel cassette for protein 2D-PAGE technique that uses easily fabricated components and routine off-the-shelf materials. The performance of the apparatus was verified in a practical exercise by a group of high school students with positive outcomes. © 2018 by The International Union of Biochemistry and Molecular Biology, 2018. © 2018 The International Union of Biochemistry and Molecular Biology.

  20. Drying techniques for the visualisation of agarose-based chromatography media by scanning electron microscopy.

    PubMed

    Nweke, Mauryn C; Turmaine, Mark; McCartney, R Graham; Bracewell, Daniel G

    2017-03-01

    The drying of chromatography resins prior to scanning electron microscopy is critical to image resolution and hence understanding of the bead structure at sub-micron level. Achieving suitable drying conditions is especially important with agarose-based chromatography resins, as over-drying may cause artefact formation, bead damage and alterations to ultrastructural properties; and under-drying does not provide sufficient resolution for visualization under SEM. This paper compares and contrasts the effects of two drying techniques, critical point drying and freeze drying, on the morphology of two agarose based resins (MabSelect™/d w ≈85 µm and Capto™ Adhere/d w ≈75 µm) and provides a complete method for both. The results show that critical point drying provides better drying and subsequently clearer ultrastructural visualization of both resins under SEM. Under this protocol both the polymer fibers (thickness ≈20 nm) and the pore sizes (diameter ≈100 nm) are clearly visible. Freeze drying is shown to cause bead damage to both resins, but to different extents. MabSelect resin encounters extensive bead fragmentation, whilst Capto Adhere resin undergoes partial bead disintegration, corresponding with the greater extent of agarose crosslinking and strength of this resin. While freeze drying appears to be the less favorable option for ultrastructural visualization of chromatography resin, it should be noted that the extent of fracturing caused by the freeze drying process may provide some insight into the mechanical properties of agarose-based chromatography media. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Use of Competitive PCR to Detect and Quantify Haplosporidium nelsoni Infection (MSX disease) in the Eastern Oyster (Crassostrea virginica).

    PubMed

    Day, J Michael; Franklin, Dean E.; Brown, Bonnie L.

    2000-09-01

    This study was undertaken to develop a quantitative polymerase chain reaction assay that would improve the utility of PCR for detecting Haplosporidium nelsoni (MSX), a serious parasite of the eastern oyster Crassostrea virginica. A competitive PCR sequence was generated from the H. nelsoni small subunit ribosomal DNA fragment, originally described by Stokes and colleagues, that was amplified by the same PCR primers and had similar amplification performance. Assays performed using competitor dilutions ranging from 0.05 to 500 pg/µl DNA were used to test oyster samples designated using histological techniques as having "light" or "heavy" MSX infections. Visual diagnoses were confirmed equally well with three methods: densitometry of ethidium-bromide-stained agarose, densitometry of SYBRGreen-stained polyacrylamide gels, and analysis by GeneScan 3.0 of fluorescent products detected in ultrathin gels. Oysters diagnosed as negative for MSX tested as negative or light by PCR. Oysters with light MSX infections generally had less than 5 pg/µl infectious DNA. Oysters with heavy infections generally corresponded to 5 pg/µl or greater competitor dilutions.

  2. The pPSU Plasmids for Generating DNA Molecular Weight Markers.

    PubMed

    Henrici, Ryan C; Pecen, Turner J; Johnston, James L; Tan, Song

    2017-05-26

    Visualizing nucleic acids by gel electrophoresis is one of the most common techniques in molecular biology, and reference molecular weight markers or ladders are commonly used for size estimation. We have created the pPSU1 & pPSU2 pair of molecular weight marker plasmids which produce both 100 bp and 1 kb DNA ladders when digested with two common restriction enzymes. The 100 bp ladder fragments have been optimized to migrate appropriately on both agarose and native polyacrylamide, unlike many currently available DNA ladders. Sufficient plasmid DNA can be isolated from 100 ml E. coli cultures for the two plasmids to produce 100 bp or 1 kb ladders for 1000 gels. As such, the pPSU1 and pPSU2 plasmids provide reference fragments from 50 to 10000 bp at a fraction of the cost of commercial DNA ladders. The pPSU1 and pPSU2 plasmids are available without licensing restrictions to nonprofit academic users, affording freely available high-quality, low-cost molecular weight standards for molecular biology applications.

  3. Purification and Characterization of the Crown Gall-specific Enzyme, Octopine Synthase 1

    PubMed Central

    Hack, Ethan; Kemp, John D.

    1980-01-01

    A single enzyme catalyzes the synthesis of all four N2-(1-carboxyethyl)-amino acid derivatives found in a crown gall tumor tissue induced by Agrobacterium tumefaciens (E. F. Sm. and Town.) Conn strain B6 on sunflower (Helianthus annuus L.). This enzyme, octopine synthase, has been purified by ammonium sulfate fractionation and chromatography on diethylaminoethylcellulose, blue agarose, and hydroxylapatite. The purified enzyme has all the N2-(1-carboxyethyl)-amino acid synthesizing activities found in crude preparations, and the relative activities with six amino acids remain nearly constant during purification. Although the maximum velocities (V) and Michaelis constants (Km) differ, the ratio V/Km is the same for all amino acid substrates. Thus an equimolar mixture of amino acids will give rise to an equimolar mixture of products. The kinetic properties of the enzyme are consistent with a partially ordered mechanism with arginine (NADPH, then arginine or pyruvate). Octopine synthase is a monomeric enzyme with a molecular weight of 39,000 by gel filtration and 38,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Images PMID:16661312

  4. Molecular Understanding and Structural-Based Design of Polyacrylamides and Polyacrylates as Antifouling Materials.

    PubMed

    Chen, Hong; Zhao, Chao; Zhang, Mingzhen; Chen, Qiang; Ma, Jie; Zheng, Jie

    2016-04-12

    Design and synthesis of highly bioinert and biocompatible antifouling materials are crucial for a broad range of biomedical and engineering applications. Among antifouling materials, polyacrylamides and polyacrylates have proved so promising because of cheap raw materials, ease of synthesis and applicability, and abundant functional groups. The strong surface hydration and the high surface packing density of polyacrylamides and polyacrylates are considered to be the key contributors to their antifouling property. In this article, we review our studies on the design and synthesis of a series of polyacrylamides and polyacrylates with different molecular structures. These polymers can be fabricated into different architectural forms (brushes, nanoparticles, nanogels, and hydrogels), all of which are highly resistant to the attachment of proteins, cells, and bacteria. We find that small structural changes in the polymers can lead to large enhancement in surface hydration and antifouling performance, both showing a positive correlation. This reveals a general design rule for effective antifouling materials. Furthermore, polyacrylamides and polyacrylates are readily functionalized with other bioactive compounds to achieve different new multifunctionalities.

  5. Development in electrophoresis: instrumentation for two-dimensional gel electrophoresis of protein separation and application of capillary electrophoresis in micro-bioanalysis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Xu, Aoshuang

    2008-01-01

    This dissertation begins with a general introduction of topics related to this work. The following chapters contain three scientific manuscripts, each presented in a separate chapter with accompanying tables, figures, and literature citations. The final chapter summarizes the work and provides some prospective on this work. This introduction starts with a brief treatment of the basic principles of electrophoresis separation, followed by a discussion of gel electrophoresis and particularly polyacrylamide gel electrophoresis for protein separation, a summary of common capillary electrophoresis separation modes, and a brief treatment of micro-bioanalysis application of capillary electrophoresis, and ends with an overview of proteinmore » conformation and dynamics.« less

  6. Effects of Gel Thickness on Microscopic Indentation Measurements of Gel Modulus

    PubMed Central

    Long, Rong; Hall, Matthew S.; Wu, Mingming; Hui, Chung-Yuen

    2011-01-01

    In vitro, animal cells are mostly cultured on a gel substrate. It was recently shown that substrate stiffness affects cellular behaviors in a significant way, including adhesion, differentiation, and migration. Therefore, an accurate method is needed to characterize the modulus of the substrate. In situ microscopic measurements of the gel substrate modulus are based on Hertz contact mechanics, where Young's modulus is derived from the indentation force and displacement measurements. In Hertz theory, the substrate is modeled as a linear elastic half-space with an infinite depth, whereas in practice, the thickness of the substrate, h, can be comparable to the contact radius and other relevant dimensions such as the radius of the indenter or steel ball, R. As a result, measurements based on Hertz theory overestimate the Young's modulus. In this work, we discuss the limitations of Hertz theory and then modify it, taking into consideration the nonlinearity of the material and large deformation using a finite-element method. We present our results in a simple correction factor, ψ, the ratio of the corrected Young's modulus and the Hertz modulus in the parameter regime of δ/h ≤ min (0.6, R/h) and 0.3 ≤ R/h ≤ 12.7. The ψ factor depends on two dimensionless parameters, R/h and δ/h (where δ is the indentation depth), both of which are easily accessible to experiments. This correction factor agrees with experimental observations obtained with the use of polyacrylamide gel and a microsphere indentation method in the parameter range of 0.1 ≤ δ/h ≤ 0.4 and 0.3 ≤ R/h ≤ 6.2. The effect of adhesion on the use of Hertz theory for small indentation depth is also discussed. PMID:21806932

  7. COUPLING THE ALKALINE-SURFACTANT-POLYMER TECHNOLOGY AND THE GELATION TECHNOLOGY TO MAXIMIZE OIL PRODUCTION

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malcolm Pitts; Jie Qi; Dan Wilson

    2005-04-01

    Gelation technologies have been developed to provide more efficient vertical sweep efficiencies for flooding naturally fractured oil reservoirs or more efficient areal sweep efficiency for those with high permeability contrast ''thief zones''. The field proven alkaline-surfactant-polymer technology economically recovers 15% to 25% OOIP more oil than waterflooding from swept pore space of an oil reservoir. However, alkaline-surfactant-polymer technology is not amenable to naturally fractured reservoirs or those with thief zones because much of injected solution bypasses target pore space containing oil. This work investigates whether combining these two technologies could broaden applicability of alkaline-surfactant-polymer flooding into these reservoirs. A priormore » fluid-fluid report discussed interaction of different gel chemical compositions and alkaline-surfactant-polymer solutions. Gel solutions under dynamic conditions of linear corefloods showed similar stability to alkaline-surfactant-polymer solutions as in the fluid-fluid analyses. Aluminum-polyacrylamide, flowing gels are not stable to alkaline-surfactant-polymer solutions of either pH 10.5 or 12.9. Chromium acetate-polyacrylamide flowing and rigid flowing gels are stable to subsequent alkaline-surfactant-polymer solution injection. Rigid flowing chromium acetate-polyacrylamide gels maintained permeability reduction better than flowing chromium acetate-polyacrylamide gels. Silicate-polyacrylamide gels are not stable with subsequent injection of either a pH 10.5 or a 12.9 alkaline-surfactant-polymer solution. Chromium acetate-xanthan gum rigid gels are not stable to subsequent alkaline-surfactant-polymer solution injection. Resorcinol-formaldehyde gels were stable to subsequent alkaline-surfactant-polymer solution injection. When evaluated in a dual core configuration, injected fluid flows into the core with the greatest effective permeability to the injected fluid. The same gel stability trends to

  8. Effect of carbon fiber addition on the electromagnetic shielding properties of carbon fiber/polyacrylamide/wood based fiberboards

    NASA Astrophysics Data System (ADS)

    Dang, Baokang; Chen, Yipeng; Yang, Ning; Chen, Bo; Sun, Qingfeng

    2018-05-01

    Carbon fiber (CF) reinforced polyacrylamide/wood fiber composite boards are fabricated by mechanical grind-assisted hot-pressing, and are used for electromagnetic interference (EMI) shielding. CF with an average diameter of 150 nm is distributed on wood fiber, which is then encased by polyacrylamide. The CF/polyacrylamide/wood fiber (CPW) composite exhibits an optimal EMI shielding effectiveness (SE) of 41.03 dB compared to that of polyacrylamide/wood fiber composite (0.41 dB), which meets the requirements of commercial merchandise. Meanwhile, the CPW composite also shows high mechanical strength. The maximum modulus of rupture (MOR) and modulus of elasticity (MOE) of CPW composites are 39.52 MPa and 5823.15 MPa, respectively. The MOR and MOE of CPW composites increased by 38% and 96%, respectively, compared to that of polyacrylamide/wood fiber composite (28.64 and 2967.35 MPa).

  9. Effect of carbon fiber addition on the electromagnetic shielding properties of carbon fiber/polyacrylamide/wood based fiberboards.

    PubMed

    Dang, Baokang; Chen, Yipeng; Yang, Ning; Chen, Bo; Sun, Qingfeng

    2018-05-11

    Carbon fiber (CF) reinforced polyacrylamide/wood fiber composite boards are fabricated by mechanical grind-assisted hot-pressing, and are used for electromagnetic interference (EMI) shielding. CF with an average diameter of 150 nm is distributed on wood fiber, which is then encased by polyacrylamide. The CF/polyacrylamide/wood fiber (CPW) composite exhibits an optimal EMI shielding effectiveness (SE) of 41.03 dB compared to that of polyacrylamide/wood fiber composite (0.41 dB), which meets the requirements of commercial merchandise. Meanwhile, the CPW composite also shows high mechanical strength. The maximum modulus of rupture (MOR) and modulus of elasticity (MOE) of CPW composites are 39.52 MPa and 5823.15 MPa, respectively. The MOR and MOE of CPW composites increased by 38% and 96%, respectively, compared to that of polyacrylamide/wood fiber composite (28.64 and 2967.35 MPa).

  10. Ultrasensitivity by Molecular Titration in Spatially Propagating Enzymatic Reactions

    PubMed Central

    Semenov, Sergey N.; Markvoort, Albert J.; Gevers, Wouter B.L.; Piruska, Aigars; de Greef, Tom F.A.; Huck, Wilhelm T.S.

    2013-01-01

    Delineating design principles of biological systems by reconstitution of purified components offers a platform to gauge the influence of critical physicochemical parameters on minimal biological systems of reduced complexity. Here we unravel the effect of strong reversible inhibitors on the spatiotemporal propagation of enzymatic reactions in a confined environment in vitro. We use micropatterned, enzyme-laden agarose gels which are stamped on polyacrylamide films containing immobilized substrates and reversible inhibitors. Quantitative fluorescence imaging combined with detailed numerical simulations of the reaction-diffusion process reveal that a shallow gradient of enzyme is converted into a steep product gradient by addition of strong inhibitors, consistent with a mathematical model of molecular titration. The results confirm that ultrasensitive and threshold effects at the molecular level can convert a graded input signal to a steep spatial response at macroscopic length scales. PMID:23972857

  11. Diffusive transfer to membranes as an effective interface between gel electrophoresis and mass spectrometry

    NASA Astrophysics Data System (ADS)

    Ogorzalek Loo, Rachel R.; Mitchell, Charles; Stevenson, Tracy I.; Loo, Joseph A.; Andrews, Philip C.

    1997-12-01

    Diffusive transfer was examined as a blotting method to transfer proteins from polyacrylamide gels to membranes for ultraviolet matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The method is well-suited for transfers from isoelectric focusing (IEF) gels. Spectra have been obtained for 11 pmol of 66 kDa albumin loaded onto an IEF gel and subsequently blotted to polyethylene. Similarly, masses of intact carbonic anhydrase and hemoglobin were obtained from 14 and 20 pmol loadings. This methodology is also compatible with blotting high molecular weight proteins, as seen for 6 pmol of the 150 kDa monoclonal antibody anti-[beta]-galactosidase transferred to Goretex. Polypropylene, Teflon, Nafion and polyvinylidene difluoride (PVDF) also produced good spectra following diffusive transfer. Only analysis from PVDF required that the membrane be kept wet prior to application of matrix. Considerations in mass accuracy for analysis from large-area membranes with continuous extraction and delayed extraction were explored, as were remedies for surface charging. Vapor phase CNBr cleavage was applied to membrane-bound samples for peptide mapping.

  12. Fluorescence detection of proteins in sodium dodecyl sulfate-polyacrylamide gels using environmentally benign, nonfixative, saline solution.

    PubMed

    Steinberg, T H; Lauber, W M; Berggren, K; Kemper, C; Yue, S; Patton, W F

    2000-02-01

    SYPRO Tangerine stain is an environmentally benign alternative to conventional protein stains that does not require solvents such as methanol or acetic acid for effective protein visualization. Instead, proteins can be stained in a wide range of buffers, including phosphate-buffered saline or simply 150 mM NaCl using an easy, one-step procedure that does not require destaining. Stained proteins can be excited by ultraviolet light of about 300 nm or with visible light of about 490 nm. The fluorescence emission maximum of the dye is approximately 640 nm. Noncovalent binding of SYPRO Tangerine dye is mediated by sodium dodecyl sulfate (SDS) and to a lesser extent by hydrophobic amino acid residues in proteins. This is in stark contrast to acidic silver nitrate staining, which interacts predominantly with lysine residues or Coomassie Blue R, which in turn interacts primarily with arginine and lysine residues. The sensitivity of SYPRO Tangerine stain is similar to that of the SYPRO Red and SYPRO Orange stains - about 4-10 ng per protein band. This detection sensitivity is comparable to colloidal Coomassie blue staining and rapid silver staining procedures. Since proteins stained with SYPRO Tangerine dye are not fixed, they can easily be eluted from gels or utilized in zymographic assays, provided that SDS does not inactivate the protein of interest. This is demonstrated with in-gel detection of rabbit liver esterase activity using alpha-naphthyl acetate and Fast Blue BB dye as well as Escherichia coli beta-glucuronidase activity using ELF-97 beta-D-glucuronide. The dye is also suitable for staining proteins in gels prior to their transfer to membranes by electroblotting. Gentle staining conditions are expected to improve protein recovery after electroelution and to reduce the potential for artifactual protein modifications such as the alkylation of lysine and esterification of glutamate residues, which complicate interpretation of peptide fragment profiles generated by

  13. Evaluation of the electroosmotic medium pump system for preparative disk gel electrophoresis.

    PubMed

    Hayakawa, M; Hosogi, Y; Takiguchi, H; Saito, S; Shiroza, T; Shibata, Y; Hiratsuka, K; Kiyama-Kishikawa, M; Abiko, Y

    2001-01-15

    This paper describes an improved electroosmotic elution system for preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) based on the epochal idea of H. V. Tan et al. (Nucleic Acids Res. 1988, 16, 1921-1930). In this elution system, a semipermeable membrane, mounted under the gel terminal end, works as the elution pump as well as the partition of the elution chamber. We refer to this system as the "electroosmotic medium pump system." Operation of the constructed apparatus (3.6 cm i.d. disk gel column) and resolution of the protein bands were examined by separation of the model protein mixture (bovine serum albumin (BSA), ovalbumin, bovine carbonic anhydrase, soybean trypsin inhibitor) and purification of the membrane protein, dipeptidyl peptidase IV (DPP IV). The Spectra/Por 7 dialysis membrane provided a better flow profile for the elution buffer. The four model proteins of the protein mixture were able to be completely separated from each other and recovered without dilution. The maximum protein concentration of eluate achieved was 93 mg/ml, when applying a single component, BSA fraction V, as a sample. Furthermore, the multifunctional ectoenzyme, DPP IV, was purified in a single step. Copyright 2001 Academic Press.

  14. Study on pre-irradiation grafting of BSA⧸NASI conjugates on agarose and its application

    NASA Astrophysics Data System (ADS)

    Min, Yi; Baolin, Zhang; Hongfei, Ha

    1993-10-01

    In this work we used N-acryloxysuccinimide (NASI) with a function group as the intermediate to graft the Bovine Serum Albumin (BSA), passthrough BSA / NASI conjugates, onto agarose which has been pre-irradiated in Co-60 γ-source. Preparation of BSA / NASI conjugates was carried out at 37°C for 2h, the molar ratio of BSA and NASI in reaction is 1:6. Pre-irradiation of agarose sample was carried out at room temperature in air and grafting was performed below 37°C for 5h under bubbling nitrogen. The total dose used was lower than 7 kGy. This technique is applicable to immobilize BSA and other proteins or separate the tryptophans enantiomer as well.

  15. Increase in local protein concentration by field-inversion gel electrophoresis.

    PubMed

    Tsai, Henghang; Low, Teck Yew; Freeby, Steve; Paulus, Aran; Ramnarayanan, Kalpana; Cheng, Chung-Pui Paul; Leung, Hon-Chiu Eastwood

    2007-09-26

    Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and non-specific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein separation efficiency. Enhancement of protein separation efficiency was investigated by implementing pulsed field-inversion gel electrophoresis (FIGE). Separation of model protein species and large protein complexes was compared between FIGE and constant field electrophoresis (CFE) in different percentages of PAGs. Band intensities of proteins in FIGE with appropriate ratios of forward and backward pulse times were superior to CFE despite longer running times. These results revealed an increase in band intensity per defined gel volume. A biphasic protein relative mobility shift was observed in percentages of PAGs up to 14%. However, the effect of FIGE on protein separation was stochastic at higher PAG percentage. Rat liver lysates subjected to FIGE in the second-dimension separation of two-dimensional polyarcylamide gel electrophoresis (2D PAGE) showed a 20% increase in the number of discernible spots compared with CFE. Nine common spots from both FIGE and CFE were selected for peptide sequencing by mass spectrometry (MS), which revealed higher final ion scores of all nine protein spots from FIGE. Native protein complexes ranging from 800 kDa to larger than 2000 kDa became apparent using FIGE compared with CFE. The present investigation suggests that FIGE under appropriate conditions improves protein separation efficiency during PAGE as a result of increased local protein concentration. FIGE can be implemented with minimal additional instrumentation in any laboratory setting. Despite the tradeoff of longer running times, FIGE can be a powerful protein separation tool.

  16. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry.

    PubMed

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-11

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  17. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    PubMed Central

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide. PMID:26865351

  18. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Wenyang; Yuan, Zhiwei; Huang, Lulu; Kang, Jie; Jiang, Ruowei; Zhong, Hongying

    2016-02-01

    Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.

  19. Rapid in vitro labeling procedures for two-dimensional gel fingerprinting

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Y.F.; Fowlks, E.R.

    1982-01-15

    Improvements of existing in vitro procedures for labeling RNA radioactively, and modifications of the two-dimensional polyacrylamide gel electrophoresis system for making RNA fingerprints are described. These improvements are (a) inactivation of phosphatase with nitric acid at pH 2.0 eliminated the phenol-cholorform extraction step during 5'-end labeling with polynucleotide kinase and (..gamma..-/sup 32/P)ATP; (b) ZnSO/sub 4/ inactivation of R Nase T/sub 1/ results in a highly efficient procedure for 3'-end labeling with T4 ligase and (5'-/sup 32/P)pCp; and (c) a rapid 4-min procedure for variable quantity range of /sup 125/I and RNA results in a qualitative and quantitative sample for high-molecularmore » weight RNA fingerprinting. Thus, these in vitro procedures become rapid and reproducible when combined with two-dimensional gel electrophoresis which eliminates simultaneously labeled impurities. Each labeling procedure is compared, using tobacco mosaic virus, Brome mosaic virus, and polio RNA. A series of Ap-rich oligonucleotides was discovered in the inner genome of Brome mosaic Virus RNA-3.« less

  20. Role of carbohydrate in multimeric structure of factor VIII/von Willebrand factor protein.

    PubMed Central

    Gralnick, H R; Williams, S B; Rick, M E

    1983-01-01

    The carbohydrate moiety of the factor VIII/von Willebrand (vW) factor protein is important in the expression of vW factor activity and the intravascular survival of the protein. Studies of normal human factor VIII/vW factor protein indicate that there is a requirement of a full complement of penultimate galactose for the maintenance of a normal multimeric structure. Release of penultimate galactose by beta-galactosidase or modification by galactose oxidase results in loss of the largest molecular weight multimers and increased numbers of intermediate and smaller multimers. In contrast, terminal galactose on the factor VIII/vW factor protein does not appear to play a significant role in the maintenance of the multimer organization. The abnormalities in multimeric structure and molecular size were demonstrated by NaDodSO4/polyacrylamide/agarose gel electrophoresis, NaDodSO4/glyoxyl-agarose electrophoresis, and sucrose density ultracentrifugation. These studies indicate that the penultimate galactose plays a role in the maintenance of the largest multimers of the factor VIII/vW factor protein. This may explain why, in some patients with variant forms of vW disease, a carbohydrate abnormality also may affect the multimeric structure of the plasma factor VIII/vW factor protein. Images PMID:6601805

  1. Purification and Characterization of Caffeine Synthase from Tea Leaves1

    PubMed Central

    Kato, Misako; Mizuno, Kouichi; Fujimura, Tatsuhito; Iwama, Masanori; Irie, Masachika; Crozier, Alan; Ashihara, Hiroshi

    1999-01-01

    Caffeine synthase (CS), the S-adenosylmethionine-dependent N-methyltransferase involved in the last two steps of caffeine biosynthesis, was extracted from young tea (Camellia sinensis) leaves; the CS was purified 520-fold to apparent homogeneity and a final specific activity of 5.7 nkat mg−1 protein by ammonium sulfate fractionation and hydroxyapatite, anion-exchange, adenosine-agarose, and gel-filtration chromatography. The native enzyme was monomeric with an apparent molecular mass of 61 kD as estimated by gel-filtration chromatography and 41 kD as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme displayed a sharp pH optimum of 8.5. The final preparation exhibited 3- and 1-N-methyltransferase activity with a broad substrate specificity, showing high activity toward paraxanthine, 7-methylxanthine, and theobromine and low activity with 3-methylxanthine and 1-methylxanthine. However, the enzyme had no 7-N-methyltransferase activity toward xanthosine and xanthosine 5′-monophosphate. The Km values of CS for paraxanthine, theobromine, 7-methylxanthine, and S-adenosylmethionine were 24, 186, 344, and 21 μm, respectively. The possible role and regulation of CS in purine alkaloid biosynthesis in tea leaves are discussed. The 20-amino acid N-terminal sequence for CS showed little homology with other methyltransferases. PMID:10364410

  2. Purification and characterization of caffeine synthase from tea leaves.

    PubMed

    Kato, M; Mizuno, K; Fujimura, T; Iwama, M; Irie, M; Crozier, A; Ashihara, H

    1999-06-01

    Caffeine synthase (CS), the S-adenosylmethionine-dependent N-methyltransferase involved in the last two steps of caffeine biosynthesis, was extracted from young tea (Camellia sinensis) leaves; the CS was purified 520-fold to apparent homogeneity and a final specific activity of 5.7 nkat mg-1 protein by ammonium sulfate fractionation and hydroxyapatite, anion-exchange, adenosine-agarose, and gel-filtration chromatography. The native enzyme was monomeric with an apparent molecular mass of 61 kD as estimated by gel-filtration chromatography and 41 kD as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme displayed a sharp pH optimum of 8.5. The final preparation exhibited 3- and 1-N-methyltransferase activity with a broad substrate specificity, showing high activity toward paraxanthine, 7-methylxanthine, and theobromine and low activity with 3-methylxanthine and 1-methylxanthine. However, the enzyme had no 7-N-methyltransferase activity toward xanthosine and xanthosine 5'-monophosphate. The Km values of CS for paraxanthine, theobromine, 7-methylxanthine, and S-adenosylmethionine were 24, 186, 344, and 21 microM, respectively. The possible role and regulation of CS in purine alkaloid biosynthesis in tea leaves are discussed. The 20-amino acid N-terminal sequence for CS showed little homology with other methyltransferases.

  3. Gene expression in the pulp of ripening bananas. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of in vitro translation products and cDNA cloning of 25 different ripening-related mRNAs.

    PubMed Central

    Medina-Suárez, R; Manning, K; Fletcher, J; Aked, J; Bird, C R; Seymour, G B

    1997-01-01

    mRNA was extracted from the pulp and peel of preclimacteric (d 0) bananas (Musa AAA group, cv Grand Nain) and those exposed to ethylene gas for 24 h and stored in air alone for a further 1 (d 2) and 4 d (d 5). Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of in vitro translation products from the pulp and peel of these fruits revealed significant up-regulation of numerous transcripts during ripening. The majority of the changes were initiated by d 2, with the level of these messages increasing during the remainder of the ripening period. Pulp tissue from d 2 was used for the construction of a cDNA library. This library was differentially screened for ripening-related clones using cDNA from d-0 and d-2 pulp by a novel microtiter plate method. In the primary screen 250 up- and down-regulated clones were isolated. Of these, 59 differentially expressed clones were obtained from the secondary screen. All of these cDNAs were partially sequenced and grouped into families after database searches. Twenty-five nonredundant groups of pulp clones were identified. These encoded enzymes were involved in ethylene biosynthesis, respiration, starch metabolism, cell wall degradation, and several other key metabolic events. We describe the analysis of these clones and their possible involvement in ripening. PMID:9342865

  4. Radiation-induced refraction artifacts in the optical CT readout of polymer gel dosimeters.

    PubMed

    Campbell, Warren G; Wells, Derek M; Jirasek, Andrew

    2014-11-01

    The objective of this work is to demonstrate imaging artifacts that can occur during the optical computed tomography (CT) scanning of polymer gel dosimeters due to radiation-induced refractive index (RI) changes in polyacrylamide gels. A 1 L cylindrical polyacrylamide gel dosimeter was irradiated with 3 × 3 cm(2) square beams of 6 MV photons. A prototype fan-beam optical CT scanner was used to image the dosimeter. Investigative optical CT scans were performed to examine two types of rayline bending: (i) bending within the plane of the fan-beam and (ii) bending out the plane of the fan-beam. To address structured errors, an iterative Savitzky-Golay (ISG) filtering routine was designed to filter 2D projections in sinogram space. For comparison, 2D projections were alternatively filtered using an adaptive-mean (AM) filter. In-plane rayline bending was most notably observed in optical CT projections where rays of the fan-beam confronted a sustained dose gradient that was perpendicular to their trajectory but within the fan-beam plane. These errors caused distinct streaking artifacts in image reconstructions due to the refraction of higher intensity rays toward more opaque regions of the dosimeter. Out-of-plane rayline bending was observed in slices of the dosimeter that featured dose gradients perpendicular to the plane of the fan-beam. These errors caused widespread, severe overestimations of dose in image reconstructions due to the higher-than-actual opacity that is perceived by the scanner when light is bent off of the detector array. The ISG filtering routine outperformed AM filtering for both in-plane and out-of-plane rayline errors caused by radiation-induced RI changes. For in-plane rayline errors, streaks in an irradiated region (>7 Gy) were as high as 49% for unfiltered data, 14% for AM, and 6% for ISG. For out-of-plane rayline errors, overestimations of dose in a low-dose region (∼50 cGy) were as high as 13 Gy for unfiltered data, 10 Gy for AM, and 3.1 Gy

  5. Highly sensitive and quantitative detection of rare pathogens through agarose droplet microfluidic emulsion PCR at the single-cell level.

    PubMed

    Zhu, Zhi; Zhang, Wenhua; Leng, Xuefei; Zhang, Mingxia; Guan, Zhichao; Lu, Jiangquan; Yang, Chaoyong James

    2012-10-21

    Genetic alternations can serve as highly specific biomarkers to distinguish fatal bacteria or cancer cells from their normal counterparts. However, these mutations normally exist in very rare amount in the presence of a large excess of non-mutated analogs. Taking the notorious pathogen E. coli O157:H7 as the target analyte, we have developed an agarose droplet-based microfluidic ePCR method for highly sensitive, specific and quantitative detection of rare pathogens in the high background of normal bacteria. Massively parallel singleplex and multiplex PCR at the single-cell level in agarose droplets have been successfully established. Moreover, we challenged the system with rare pathogen detection and realized the sensitive and quantitative analysis of a single E. coli O157:H7 cell in the high background of 100,000 excess normal K12 cells. For the first time, we demonstrated rare pathogen detection through agarose droplet microfluidic ePCR. Such a multiplex single-cell agarose droplet amplification method enables ultra-high throughput and multi-parameter genetic analysis of large population of cells at the single-cell level to uncover the stochastic variations in biological systems.

  6. Study of the influence of the agarose hydrogel layer thickness on sensitivity of the coated silica microsphere resonator to humidity.

    PubMed

    Mallik, Arun Kumar; Farrell, Gerald; Wu, Qiang; Semenova, Yuliya

    2017-05-10

    In this paper, we investigate both theoretically and experimentally the influence of the agarose hydrogel layer thickness on the sensitivity of a proposed relative humidity (RH) sensor based on a silica microsphere resonator coated with agarose hydrogel. The operating principle of the sensor relies on excitation of whispering gallery modes (WGMs) in the coated silica microsphere using the evanescent field of a tapered fiber. A change in the ambient relative humidity is detected by measuring the wavelength shift of the WGMs in the transmission spectrum of the tapered fiber. Using perturbation theory, we analyze the influence of the agarose coating thickness on the sensitivity of the proposed sensor and compare the results of this analysis with experimental findings for different coating layer thicknesses. We demonstrate that an increase in the coating layer thickness initially leads to an increase in the sensitivity to RH and reaches saturation at higher values of the agarose layer thickness. The results of the study are useful for the design and optimization of microsphere sensor parameters to meet a performance specification.

  7. Comparison of gel properties and biochemical characteristics of myofibrillar protein from bighead carp (Aristichthys nobilis) affected by frozen storage and a hydroxyl radical-generation oxidizing system.

    PubMed

    Lu, Han; Zhang, Longteng; Li, Qingzheng; Luo, Yongkang

    2017-05-15

    We wanted to clarify whether gel properties can be affected by in vivo or in vitro myofibrillar protein oxidation and, thus, to provide relevant information and a scientific foundation for the processing of gel products. To accomplish this, we measured the changes in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), total disulfide (SS) content, surface hydrophobicity (So-ANS), carbonyl content, and gel texture and water-holding capacity (WHC) of isolated myofibrillar protein from bighead carp fillets during frozen storage and under different H 2 O 2 concentrations, which were used to represent in vivo and in vitro conditions, respectively. The results indicated that a certain range in content of disulfide crosslinks (0.91mol/10 5 g protein) would promote gel hardness. Mild protein oxidation caused by a certain degree of frozen storage and hydroxyl radicals can promote gel texture and WHC. Based on those results, freezing bighead carp for a certain period can be used to produce gel products. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Decreased poststenotic flow disturbance during drag reduction by polyacrylamide infusion without increased aortic blood flow.

    PubMed

    Hutchison, K J; Campbell, J D; Karpinski, E

    1989-07-01

    The infusion of polyacrylamide in open chest rats has been reported to increase aortic blood flow and the effect has been ascribed to the "drag reduction" properties of these compounds. In six anesthetized dogs the infusion of polyacrylamide to a total dose of 2 mg/kg caused a reduction in midline and separation zone Doppler spectral broadening in the common carotid artery poststenotic velocity field. This apparent reduction in poststenotic turbulence was interpreted as indicating the presence of a drag reducing effect. Despite this demonstration that polyacrylamide was present in the blood in drag reducing concentrations no increase in aortic blood flow was produced.

  9. Amended final report on the safety assessment of polyacrylamide and acrylamide residues in cosmetics.

    PubMed

    2005-01-01

    Polyacrylamide is a polymer of controllable molecular weight formed by the polymerization of acrylamide monomers available in one of three forms: solid (powder or micro beads), aqueous solution, or inverse emulsions (in water droplets coated with surfactant and suspended in mineral oil). Residual acrylamide monomer is likely an impurity in most Polyacrylamide preparations, ranging from <1 ppm to 600 ppm. Higher levels of acrylamide monomers are present in the solid form compared to the other two forms. Polyacrylamide is reportedly used in 110 cosmetic formulations, at concentrations ranging from 0.05% to 2.8%. Residual levels of acrylamide in Polyacrylamide can range from <.01% to 0.1%, although representative levels were reported at 0.02% to 0.03%. Because of the large sizes of Polyacrylamide polymers, they do not penetrate the skin. Polyacrylamide itself is not significantly toxic. For example, an acute oral toxicity study of Polyacrylamide in rats reported that a single maximum oral dose of 4.0 g/kg body weight was tolerated. In subchronic oral toxicity studies, rats and dogs treated with Polyacrylamide at doses up to 464 mg/kg body weight showed no signs of toxicity. Several 2-year chronic oral toxicity studies in rats and dogs fed diets containing up to 5% Polyacrylamide had no significant adverse effects. Polyacrylamide was not an ocular irritant in animal tests. No compound-related lesions were noted in a three-generation reproductive study in which rats were fed 500 or 2000 ppm Polyacrylamide in their diet. Polyacrylamide was not carcinogenic in several chronic animal studies. Human cutaneous tolerance tests performed to evaluate the irritation of 5% (w/w) Polyacrylamide indicated that the compound was well tolerated. Acrylamide monomer residues do penetrate the skin. Acrylamide tested in a two-generation reproductive study at concentrations up to 5 mg/kg day(- 1) in drinking water, was associated with prenatal lethality at the highest dose, with evidence

  10. Benchmarking the ERG valve tip and MRI Interventions Smart Flow neurocatheter convection-enhanced delivery system's performance in a gel model of the brain: employing infusion protocols proposed for gene therapy for Parkinson's disease

    NASA Astrophysics Data System (ADS)

    Sillay, Karl; Schomberg, Dominic; Hinchman, Angelica; Kumbier, Lauren; Ross, Chris; Kubota, Ken; Brodsky, Ethan; Miranpuri, Gurwattan

    2012-04-01

    Convection-enhanced delivery (CED) is an advanced infusion technique used to deliver therapeutic agents into the brain. CED has shown promise in recent clinical trials. Independent verification of published parameters is warranted with benchmark testing of published parameters in applicable models such as gel phantoms, ex vivo tissue and in vivo non-human animal models to effectively inform planned and future clinical therapies. In the current study, specific performance characteristics of two CED infusion catheter systems, such as backflow, infusion cloud morphology, volume of distribution (mm3) versus the infused volume (mm3) (Vd/Vi) ratios, rate of infusion (µl min-1) and pressure (mmHg), were examined to ensure published performance standards for the ERG valve-tip (VT) catheter. We tested the hypothesis that the ERG VT catheter with an infusion protocol of a steady 1 µl min-1 functionality is comparable to the newly FDA approved MRI Interventions Smart Flow (SF) catheter with the UCSF infusion protocol in an agarose gel model. In the gel phantom models, no significant difference was found in performance parameters between the VT and SF catheter. We report, for the first time, such benchmark characteristics in CED between these two otherwise similar single-end port VT with stylet and end-port non-stylet infusion systems. Results of the current study in agarose gel models suggest that the performance of the VT catheter is comparable to the SF catheter and warrants further investigation as a tool in the armamentarium of CED techniques for eventual clinical use and application.

  11. Coupling the Alkaline-Surfactant-Polymer Technology and The Gelation Technology to Maximize Oil Production

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malcolm Pitts; Jie Qi; Dan Wilson

    2005-10-01

    Gelation technologies have been developed to provide more efficient vertical sweep efficiencies for flooding naturally fractured oil reservoirs or more efficient areal sweep efficiency for those with high permeability contrast ''thief zones''. The field proven alkaline-surfactant-polymer technology economically recovers 15% to 25% OOIP more oil than waterflooding from swept pore space of an oil reservoir. However, alkaline-surfactant-polymer technology is not amenable to naturally fractured reservoirs or those with thief zones because much of injected solution bypasses target pore space containing oil. This work investigates whether combining these two technologies could broaden applicability of alkaline-surfactant-polymer flooding into these reservoirs. A priormore » fluid-fluid report discussed interaction of different gel chemical compositions and alkaline-surfactant-polymer solutions. Gel solutions under dynamic conditions of linear corefloods showed similar stability to alkaline-surfactant-polymer solutions as in the fluid-fluid analyses. Aluminum-polyacrylamide, flowing gels are not stable to alkaline-surfactant-polymer solutions of either pH 10.5 or 12.9. Chromium acetate-polyacrylamide flowing and rigid flowing gels are stable to subsequent alkaline-surfactant-polymer solution injection. Rigid flowing chromium acetate-polyacrylamide gels maintained permeability reduction better than flowing chromium acetate-polyacrylamide gels. Silicate-polyacrylamide gels are not stable with subsequent injection of either a pH 10.5 or a 12.9 alkaline-surfactant-polymer solution. Chromium acetate-xanthan gum rigid gels are not stable to subsequent alkaline-surfactant-polymer solution injection. Resorcinol-formaldehyde gels were stable to subsequent alkaline-surfactant-polymer solution injection. When evaluated in a dual core configuration, injected fluid flows into the core with the greatest effective permeability to the injected fluid. The same gel stability trends to

  12. Effects of Agar Gel Strength and Fat on Oral Breakdown, Volatile Release, and Sensory Perception Using in Vivo and in Vitro Systems.

    PubMed

    Frank, Damian; Eyres, Graham T; Piyasiri, Udayasika; Cochet-Broch, Maeva; Delahunty, Conor M; Lundin, Leif; Appelqvist, Ingrid M

    2015-10-21

    The density and composition of a food matrix affect the rates of oral breakdown and in-mouth flavor release as well as the overall sensory experience. Agar gels of increasing concentration (1.0, 1.7, 2.9, and 5% agarose) with and without added fat (0, 2, 5, and 10%) were spiked with seven aroma volatiles. Differences in oral processing and sensory perception were systematically measured by a trained panel using a discrete interval time intensity method. Volatile release was measured in vivo and in vitro by proton transfer reaction mass spectrometry. Greater oral processing was required as agar gel strength increased, and the intensity of flavor-related sensory attributes decreased. Volatile release was inversely related to gel strength, showing that physicochemical phenomena were the main mechanisms underlying the perceived sensory changes. Fat addition reduced the amount of oral processing and had differential effects on release, depending on the fat solubility or lipophilicity of the volatiles.

  13. Emulsifying Properties of Oxidatively Stressed Myofibrillar Protein Emulsion Gels Prepared with (-)-Epigallocatechin-3-gallate and NaCl.

    PubMed

    Feng, Xianchao; Chen, Lin; Lei, Na; Wang, Shuangxi; Xu, Xinglian; Zhou, Guanghong; Li, Zhixi

    2017-04-05

    The dose-dependent effects of (-)-epigallocatechin-3-gallate (EGCG; 0, 100, or 1000 ppm) on the textural properties and stability of a myofibrillar protein (MP) emulsion gel were investigated. Addition of EGCG significantly inhibited formation of carbonyl but promoted the loss of both thiol and free amine groups. Addition of EGCG, particularly at 1000 ppm, initiated irreversible protein modifications, as evidenced by surface hydrophobicity changes, patterns in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and differential scanning calorimetry. These results indicated that MP was modified by additive reactions between the quinone of EGCG and thiols and free amines of proteins. These adducts increased cooking loss and destabilized the texture, especially with a large EGCG dose. Confocal laser scanning microscopy and scanning electron microscopy images clearly indicated the damage to the emulsifying properties and the collapse of the internal structure when the MP emulsion gel was treated with a large EGCG dose. A high concentration of NaCl (0.6 M) improved modification of MP and increased the rate of deterioration of the internal structure, especially with the large EGCG dose (1000 ppm), resulting in an MP emulsion gel with extremely unstable emulsifying properties.

  14. Identification and In Silico Analysis of Major Redox Modulated Proteins from Brassica juncea Seedlings Using 2D Redox SDS PAGE (2-Dimensional Diagonal Redox Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis).

    PubMed

    Chaurasia, Satya Prakash; Deswal, Renu

    2017-02-01

    The thiol-disulphide exchange regulates the activity of proteins by redox modulation. Many studies to analyze reactive oxygen species (ROS), particularly, hydrogen peroxide (H 2 O 2 ) induced changes in the gene expression have been reported, but efforts to detect H 2 O 2 modified proteins are comparatively few. Two-dimensional diagonal redox sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) was used to detect polypeptides which undergo thiol-disulphide exchange in Brassica juncea seedlings following H 2 O 2 (10 mM) treatment for 30 min. Eleven redox responsive polypeptides were identified which included cruciferin, NLI [Nuclear LIM (Lin11, Isl-1 & Mec-3 domains)] interacting protein phosphatase, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) large subunit, and myrosinase. Redox modulation of RuBisCO large subunit was further confirmed by western blotting. However, the small subunit of RuBisCO was not affected by these redox changes. All redox modulated targets except NLI interacting protein (although it contains two cysteines) showed oxidation sensitive cysteines by in silico analysis. Interestingly, interactome of cruciferin and myrosinase indicated that they may have additional function(s) beside their well-known roles in the seedling development and abiotic stress respectively. Cruciferin showed interactions with stress associated proteins like defensing-like protein 192 and 2-cys peroxiredoxin. Similarly, myrosinase showed interactions with nitrilase and cytochrome p450 which are involved in nitrogen metabolism and/or hormone biosynthesis. This simple procedure can be used to detect major stress mediated redox changes in other plants.

  15. Inactivation of Vibrio parahaemolyticus by antimicrobial photodynamic technology using methylene blue.

    PubMed

    Deng, Xi; Tang, Shuze; Wu, Qian; Tian, Juan; Riley, William W; Chen, Zhenqiang

    2016-03-30

    Vibrio parahaemolyticus is the leading causative pathogen of gastroenteritis often related to contaminated seafood. Photodynamic inactivation has been recently proposed as a strategy for killing cells and viruses. The objective of this study was to verify the bactericidal effects caused by photodynamic inactivation using methylene blue (MB) over V. parahaemolyticus via flow cytometry, agarose gel electrophoresis and sodium dodecyl sulfate polyacrylamide gel electrophoresis. Vibrio parahaemolyticus counts were determined using the most probable number method. A scanning electron microscope and a transmission electron microscope were employed to intuitively analyze internal and external cell structure. Combination of MB and laser treatment significantly inhibited the growth of V. parahaemolyticus. The inactivation rate of V. parahaemolyticus was >99.99% and its counts were reduced by 5 log10 in the presence of 0.05 mg mL(-1) MB when illuminated with visible light (power density 200 mW cm(-2)) for 25 min. All inactivated cells showed morphological changes, leakage of cytoplasm and degradation of protein and DNA. Results from this study indicated that photodynamic technology using MB produced significant inactivation of V. parahaemolyticus mainly brought about by the degradation of protein and DNA. © 2015 Society of Chemical Industry.

  16. Influence of graphene-oxide nanosheets impregnation on properties of sterculia gum-polyacrylamide hydrogel formed by radiation induced polymerization.

    PubMed

    Singh, Baljit; Singh, Baldev

    2017-06-01

    Present work is an attempt, to explore the potential of graphene oxide nanoplates impregnation, on the mechanical and drug delivery properties of sterculia gum-polyacrylamide composite hydrogel formed by radiation induced polymerization. These polymers were characterized by SEM, cryo-SEM, AFM, FTIR's, 13 C NMR and swelling studies. Release profile of an anticancer drug 'gemcitabine' was studied to determine the drug release mechanism and best fit kinetic model. Furthermore, some important biomedical properties of the polymers such as blood compatibility, mucoadhesion, antioxidant properties and gel strength were also studied. Impregnation of GO into sterculia gum-poly(AAm) hydrogels decreased the swelling of hydrogels but improved the mechanical, drug loading and drug release properties of the hydrogels. Release of gemcitabine from drug loaded hydrogels occurred through non-Fickian diffusion mechanism and release profile was best fitted in first order kinetic model. These hydrogels have been found as haemocompatible, mucoadhesive, and antioxidant in nature. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Radiation-induced refraction artifacts in the optical CT readout of polymer gel dosimeters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Campbell, Warren G.; Jirasek, Andrew, E-mail: jirasek@uvic.ca; Wells, Derek M.

    2014-11-01

    Purpose: The objective of this work is to demonstrate imaging artifacts that can occur during the optical computed tomography (CT) scanning of polymer gel dosimeters due to radiation-induced refractive index (RI) changes in polyacrylamide gels. Methods: A 1 L cylindrical polyacrylamide gel dosimeter was irradiated with 3 × 3 cm{sup 2} square beams of 6 MV photons. A prototype fan-beam optical CT scanner was used to image the dosimeter. Investigative optical CT scans were performed to examine two types of rayline bending: (i) bending within the plane of the fan-beam and (ii) bending out the plane of the fan-beam. Tomore » address structured errors, an iterative Savitzky–Golay (ISG) filtering routine was designed to filter 2D projections in sinogram space. For comparison, 2D projections were alternatively filtered using an adaptive-mean (AM) filter. Results: In-plane rayline bending was most notably observed in optical CT projections where rays of the fan-beam confronted a sustained dose gradient that was perpendicular to their trajectory but within the fan-beam plane. These errors caused distinct streaking artifacts in image reconstructions due to the refraction of higher intensity rays toward more opaque regions of the dosimeter. Out-of-plane rayline bending was observed in slices of the dosimeter that featured dose gradients perpendicular to the plane of the fan-beam. These errors caused widespread, severe overestimations of dose in image reconstructions due to the higher-than-actual opacity that is perceived by the scanner when light is bent off of the detector array. The ISG filtering routine outperformed AM filtering for both in-plane and out-of-plane rayline errors caused by radiation-induced RI changes. For in-plane rayline errors, streaks in an irradiated region (>7 Gy) were as high as 49% for unfiltered data, 14% for AM, and 6% for ISG. For out-of-plane rayline errors, overestimations of dose in a low-dose region (∼50 cGy) were as high as 13 Gy for

  18. Highly effective removal of basic fuchsin from aqueous solutions by anionic polyacrylamide/graphene oxide aerogels.

    PubMed

    Yang, Xiaoxia; Li, Yanhui; Du, Qiuju; Sun, Jiankun; Chen, Long; Hu, Song; Wang, Zonghua; Xia, Yanzhi; Xia, Linhua

    2015-09-01

    Novel anionic polyacrylamide/graphene oxide aerogels were prepared by a freeze drying method and used to remove basic fuchsin from aqueous solutions. These aerogels were sponge-like solid with lightweight, fluffy and porous structure. The batch adsorption experiments were carried out to study the effect of various parameters, such as the solution pH, adsorbent dose, contact time and temperature on adsorption properties of basic fuchsin onto anionic polyacrylamide/graphene oxide aerogels. The kinetics of adsorption corresponded to the pseudo-second-order kinetic model. The Langmuir adsorption isotherm was suitable to describe the equilibrium adsorption process. The maximum adsorption capacity was up to 1034.3 mg/g, which indicated that anionic polyacrylamide/graphene oxide aerogels were promising adsorbents for removing dyes pollutants from aqueous solution. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Enhanced removal of methylene blue and methyl violet dyes from aqueous solution using a nanocomposite of hydrolyzed polyacrylamide grafted xanthan gum and incorporated nanosilica.

    PubMed

    Ghorai, Soumitra; Sarkar, Asish; Raoufi, Mohammad; Panda, Asit Baran; Schönherr, Holger; Pal, Sagar

    2014-04-09

    The synthesis and characterization of a novel nanocomposite is reported that was developed as an efficient adsorbent for the removal of toxic methylene blue (MB) and methyl violet (MV) from aqueous solution. The nanocomposite comprises hydrolyzed polyacrylamide grafted onto xanthan gum as well as incorporated nanosilica. The synthesis exploits the saponification of the grafted polyacrylamide and the in situ formation of nanoscale SiO2 by a sol-gel reaction, in which the biopolymer matrix promotes the silica polymerization and therefore acts as a novel template for nanosilica formation. The detailed investigation of the kinetics and the adsorption isotherms of MB and MV from aqueous solution showed that the dyes adsorb rapidly, in accordance with a pseudo-second-order kinetics and a Langmuir adsorption isotherm. The entropy driven process was furthermore found to strongly depend on the point of zero charge (pzc) of the adsorbent. The remarkably high adsorption capacity of dyes on the nanocomposites (efficiency of MB removal, 99.4%; maximum specific removal Qmax, 497.5 mg g(-1); and efficiency of MV removal, 99.1%; Qmax, 378.8 mg g(-1)) is rationalized on the basis of H-bonding interactions as well as dipole-dipole and electrostatic interactions between anionic adsorbent and cationic dye molecules. Because of the excellent regeneration capacity the nanocomposites are considered interesting materials for the uptake of, for instance, toxic dyes from wastewater.

  20. Hollow agarose microneedle with silver coating for intradermal surface-enhanced Raman measurements: a skin-mimicking phantom study

    NASA Astrophysics Data System (ADS)

    Yuen, Clement; Liu, Quan

    2015-06-01

    Human intradermal components contain important clinical information beneficial to the field of immunology and disease diagnosis. Although microneedles have shown great potential to act as probes to break the human skin barrier for the minimally invasive measurement of intradermal components, metal microneedles that include stainless steel could cause the following problems: (1) sharp waste production, and (2) contamination due to reuse of microneedles especially in developing regions. In this study, we fabricate agarose microneedles coated with a layer of silver (Ag) and demonstrate their use as a probe for the realization of intradermal surface-enhanced Raman scattering measurements in a set of skin-mimicking phantoms. The Ag-coated agarose microneedle quantifies a range of glucose concentrations from 5 to 150 mM inside the skin phantoms with a root-mean-square error of 5.1 mM within 10 s. The needle is found enlarged by 53.9% after another 6 min inside the phantom. The shape-changing capability of this agarose microneedle ensures that the reuse of these microneedles is impossible, thus avoiding sharp waste production and preventing needle contamination, which shows the great potential for safe and effective needle-based measurements.

  1. New GlcNAc/GalNAc-specific lectin from the ascidian Didemnum ternatanum.

    PubMed

    Molchanova, Valentina; Chikalovets, Irina; Li, Wei; Kobelev, Stanislav; Kozyrevskaya, Svetlana; Bogdanovich, Raisa; Howard, Eric; Belogortseva, Natalia

    2005-05-25

    Previously we isolated GlcNAc-specific lectin (DTL) from the ascidian Didemnum ternatanum by affinity chromatography on cross-linked ovalbumin. Here we report the purification and characterization of new D-GlcNAc/D-GalNAc-specific lectin DTL-A from the same ascidian. This lectin was isolated from non-bound cross-linked ovalbumin fraction and further was purified by gel filtration on Sepharose CL-4B, affinity chromatography on GlcNAc-agarose and gel filtration on Superdex 200. SDS-polyacrylamide gel electrophoresis and gel filtration of purified lectin on Sepharose CL-4B indicates that it exists as large aggregates in the native state. Investigations of the carbohydrate specificity of DTL-A by enzyme-linked lectin assay suggest the multi-specificity of this lectin. DTL-A binds BSM, asialo-BSM as well as heparin and dextran sulfate. The binding of DTL-A to BSM was inhibited by monosaccharides D-GlcNAc and D-GalNAc, their alpha- but not beta-anomers. Among polysaccharides and glycoconjugates, DTL-A binding to BSM was effectively inhibited by BSM, asialo-BSM, pronase-treated BSM and synthetic alpha-D-GalNAc-PAA. Fetuin and asialofetuin showed a much lower inhibitory potency, heparin and dextran sulfate were noninhibitory. On the other hand, DTL-A binding to heparin was effectively inhibited by dextran sulfate, fucoidan, whereas BSM showed insignificantly inhibitory effect. DTL-A binding to heparin was not inhibited by D-GlcNAc and D-GalNAc.

  2. Electronic speckle pattern interferometry: a tool for determining diffusion and partition coefficients for proteins in gels.

    PubMed

    Karlsson, David; Zacchi, Guido; Axelsson, Anders

    2002-01-01

    The aim of this study was to demonstrate electronic speckle pattern interferometry (ESPI) as a powerful tool in determining diffusion coefficients and partition coefficients for proteins in gels. ESPI employs a CCD camera instead of a holographic plate as in conventional holographic interferometry. This gives the advantage of being able to choose the reference state freely. If a hologram at the reference state is taken and compared to a hologram during the diffusion process, an interferometric picture can be generated that describes the refraction index gradients and thus the concentration gradients in the gel as well as in the liquid. MATLAB is then used to fit Fick's law to the experimental data to obtain the diffusion coefficients in gel and liquid. The partition coefficient is obtained from the same experiment from the flux condition at the interface between gel and liquid. This makes the comparison between the different diffusants more reliable than when the measurements are performed in separate experiments. The diffusion and partitioning coefficients of lysozyme, BSA, and IgG in 4% agarose gel at pH 5.6 and in 0.1 M NaCl have been determined. In the gel the diffusion coefficients were 11.2 +/- 1.6, 4.8 +/- 0.6, and 3.0 +/- 0.3 m(2)/s for lysozyme, BSA, and IgG, respectively. The partition coefficients were determined to be 0.65 +/- 0.04, 0.44 +/- 0.06, and 0.51 +/- 0.04 for lysozyme, BSA, and IgG, respectively. The current study shows that ESPI is easy to use and gives diffusion coefficients and partition coefficients for proteins with sufficient accuracy from the same experiment.

  3. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

    PubMed Central

    Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; Roessler, Christian G.; Teplitsky, Ella; Joshi, Karan; Campos, Olven; Agarwal, Rakhi; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

    2015-01-01

    Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s−1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening. PMID:25615864

  4. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

    DOE PAGES

    Cuttitta, Christina M.; Ericson, Daniel L.; Scalia, Alexander; ...

    2014-06-01

    Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s -1) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away frommore » the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.« less

  5. A thermodynamically-consistent large deformation theory coupling photochemical reaction and electrochemistry for light-responsive gels

    NASA Astrophysics Data System (ADS)

    Dehghany, Mohammad; Zhang, Haohui; Naghdabadi, Reza; Hu, Yuhang

    2018-07-01

    effect of salt concentration and pH value of the external solution on the photo-induced swelling of the polyacrylamide gels incorporated with triphenylmethane leucohydroxide groups. Finally, for the optically thick gels, we develop a finite element code to study their inhomogeneous deformations due to the light attenuation. This work will be of great importance for precise control and optimal design of photo-ionizable gels in future applications.

  6. Can You Solve the Crime? Using Agarose Electrophoresis To Identify an Unknown Colored Protein.

    ERIC Educational Resources Information Center

    Wiltfong, Cynthia L.; Chester, Emily; Albertin, Faith; Smith, Julia; Hall, Judith C.; Arth, Emily C.; Martin, Stephanie

    2003-01-01

    Describes a lab that introduces agarose electrophoresis techniques and basic information on proteins to middle school and high school students. Insists that, built around a scenario in which students must solve a crime, the lab has real-world applications that should spark student interest. (KHR)

  7. Highly parallel single-molecule amplification approach based on agarose droplet polymerase chain reaction for efficient and cost-effective aptamer selection.

    PubMed

    Zhang, Wei Yun; Zhang, Wenhua; Liu, Zhiyuan; Li, Cong; Zhu, Zhi; Yang, Chaoyong James

    2012-01-03

    We have developed a novel method for efficiently screening affinity ligands (aptamers) from a complex single-stranded DNA (ssDNA) library by employing single-molecule emulsion polymerase chain reaction (PCR) based on the agarose droplet microfluidic technology. In a typical systematic evolution of ligands by exponential enrichment (SELEX) process, the enriched library is sequenced first, and tens to hundreds of aptamer candidates are analyzed via a bioinformatic approach. Possible candidates are then chemically synthesized, and their binding affinities are measured individually. Such a process is time-consuming, labor-intensive, inefficient, and expensive. To address these problems, we have developed a highly efficient single-molecule approach for aptamer screening using our agarose droplet microfluidic technology. Statistically diluted ssDNA of the pre-enriched library evolved through conventional SELEX against cancer biomarker Shp2 protein was encapsulated into individual uniform agarose droplets for droplet PCR to generate clonal agarose beads. The binding capacity of amplified ssDNA from each clonal bead was then screened via high-throughput fluorescence cytometry. DNA clones with high binding capacity and low K(d) were chosen as the aptamer and can be directly used for downstream biomedical applications. We have identified an ssDNA aptamer that selectively recognizes Shp2 with a K(d) of 24.9 nM. Compared to a conventional sequencing-chemical synthesis-screening work flow, our approach avoids large-scale DNA sequencing and expensive, time-consuming DNA synthesis of large populations of DNA candidates. The agarose droplet microfluidic approach is thus highly efficient and cost-effective for molecular evolution approaches and will find wide application in molecular evolution technologies, including mRNA display, phage display, and so on. © 2011 American Chemical Society

  8. Refractive-index-matched hydrogel materials for measuring flow-structure interactions

    NASA Astrophysics Data System (ADS)

    Byron, Margaret L.; Variano, Evan A.

    2013-02-01

    In imaging-based studies of flow around solid objects, it is useful to have materials that are refractive-index-matched to the surrounding fluid. However, materials currently in use are usually rigid and matched to liquids that are either expensive or highly viscous. This does not allow for measurements at high Reynolds number, nor accurate modeling of flexible structures. This work explores the use of two hydrogels (agarose and polyacrylamide) as refractive-index-matched models in water. These hydrogels are inexpensive, can be cast into desired shapes, and have flexibility that can be tuned to match biological materials. The use of water as the fluid phase allows this method to be implemented immediately in many experimental facilities and permits investigation of high-Reynolds-number phenomena. We explain fabrication methods and present a summary of the physical and optical properties of both gels, and then show measurements demonstrating the use of hydrogel models in quantitative imaging.

  9. Agarose drug delivery systems upgraded by surfactants inclusion: critical role of the pore architecture.

    PubMed

    Marras-Marquez, T; Peña, J; Veiga-Ochoa, M D

    2014-03-15

    Anionic or non-ionic surfactants have been introduced in agarose-based hydrogels aiming to tailor the release of drugs with different solubility. The release of a hydrophilic model drug, Theophylline, shows the predictable release enhancement that varies depending on the surfactant. However, when the hydrophobic Tolbutamide is considered, an unexpected retarded release is observed. This effect can be explained not only considering the interactions established between the drug loaded micelles and agarose but also to the alteration of the freeze-dried hydrogels microstructure. It has been observed that the modification of the porosity percentage as well as the pore size distribution during the lyophilization plays a critical role in the different phenomena that take place as soon as desiccated hydrogel is rehydrated. The possibility of tailoring the pore architecture as a function of the surfactant nature and percentage can be applied from drug control release to the widespread and growing applications of materials based on hydrogel matrices. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Visualization of yeast chromosomal DNA

    NASA Technical Reports Server (NTRS)

    Lubega, Seth

    1990-01-01

    The DNA molecule is the most significant life molecule since it codes the blue print for other structural and functional molecules of all living organisms. Agarose gel electrophoresis is now being widely used to separate DNA of virus, bacteria, and lower eukaryotes. The task was undertaken of reviewing the existing methods of DNA fractionation and microscopic visualization of individual chromosonal DNA molecules by gel electrophoresis as a basis for a proposed study to investigate the feasibility of separating DNA molecules in free fluids as an alternative to gel electrophoresis. Various techniques were studied. On the molecular level, agarose gel electrophoresis is being widely used to separate chromosomal DNA according to molecular weight. Carl and Olson separate and characterized the entire karyotype of a lab strain of Saccharomyces cerevisiae. Smith et al. and Schwartz and Koval independently reported the visualization of individual DNA molecules migrating through agarose gel matrix during electrophoresis. The techniques used by these researchers are being reviewed in the lab as a basis for the proposed studies.

  11. Gel stretch method: a new method to measure constitutive properties of cardiac muscle cells

    NASA Technical Reports Server (NTRS)

    Zile, M. R.; Cowles, M. K.; Buckley, J. M.; Richardson, K.; Cowles, B. A.; Baicu, C. F.; Cooper G, I. V.; Gharpuray, V.

    1998-01-01

    Diastolic dysfunction is an important cause of congestive heart failure; however, the basic mechanisms causing diastolic congestive heart failure are not fully understood, especially the role of the cardiac muscle cell, or cardiocyte, in this process. Before the role of the cardiocyte in this pathophysiology can be defined, methods for measuring cardiocyte constitutive properties must be developed and validated. Thus this study was designed to evaluate a new method to characterize cardiocyte constitutive properties, the gel stretch method. Cardiocytes were isolated enzymatically from normal feline hearts and embedded in a 2% agarose gel containing HEPES-Krebs buffer and laminin. This gel was cast in a shape that allowed it to be placed in a stretching device. The ends of the gel were held between a movable roller and fixed plates that acted as mandibles. Distance between the right and left mandibles was increased using a stepper motor system. The force applied to the gel was measured by a force transducer. The resultant cardiocyte strain was determined by imaging the cells with a microscope, capturing the images with a CCD camera, and measuring cardiocyte and sarcomere length changes. Cardiocyte stress was characterized with a finite-element method. These measurements of cardiocyte stress and strain were used to determine cardiocyte stiffness. Two variables affecting cardiocyte stiffness were measured, the passive elastic spring and viscous damping. The passive spring was assessed by increasing the force on the gel at 1 g/min, modeling the resultant stress vs. strain relationship as an exponential [sigma = A/k(ekepsilon - 1)]. In normal cardiocytes, A = 23.0 kN/m2 and k = 16. Viscous damping was assessed by examining the loop area between the stress vs. strain relationship during 1 g/min increases and decreases in force. Normal cardiocytes had a finite loop area = 1.39 kN/m2, indicating the presence of viscous damping. Thus the gel stretch method provided accurate

  12. Determination of glycated albumin using boronic acid-derived agarose beads on paper-based devices.

    PubMed

    Ko, Euna; Tran, Van-Khue; Geng, Yanfang; Kim, Min Ki; Jin, Ga Hyun; Son, Seong Eun; Hur, Won; Seong, Gi Hun

    2018-01-01

    Self-monitoring of glycated albumin (GA), a useful glycemic marker, is an established method for preventing diabetes complications. Here, the paper-based lateral flow assay devices were developed for the sensitive detection of GA and the total human serum albumin (tHSA) in self-monitoring diabetes patients. Boronic acid-derived agarose beads were packed into a hole on a lateral flow channel. These well-coordinated agarose beads were used to capture GA through specific cis-diol interactions and to enhance the colorimetric signals by concentrating the target molecules. The devices exhibited large dynamic ranges (from 10  μ g/ml to 10 mg/ml for GA and from 10 mg/ml to 50 mg/ml for tHSA) and low detection limits (7.1  μ g/ml for GA and 4.7 mg/ml for tHSA), which cover the range of GA concentration in healthy plasma, which is 0.21-1.65 mg/ml (0.6%-3%). In determining the unknown GA concentrations in two commercial human plasma samples, the relative percentage difference between the values found by a standard ELISA kit and those found by our developed devices was 2.62% and 8.80%, which are within an acceptable range. The measurements of GA and tHSA were completed within 20 min for the total sample-to-answer diagnosis, fulfilling the demand for rapid analysis. Furthermore, the recovery values ranged from 99.4% to 110% in device accuracy tests. These results indicate that the developed paper-based device with boronic acid-derived agarose beads is a promising platform for GA and tHSA detection as applied to self-monitoring systems.

  13. New cellular automaton designed to simulate geometration in gel electrophoresis

    NASA Astrophysics Data System (ADS)

    Krawczyk, M. J.; Kułakowski, K.; Maksymowicz, A. Z.

    2002-08-01

    We propose a new kind of cellular automaton to simulate transportation of molecules of DNA through agarose gel. Two processes are taken into account: reptation at strong electric field E, described in the particle model, and geometration, i.e. subsequent hookings and releases of long molecules at and from gel fibres. The automaton rules are deterministic and they are designed to describe both processes within one unified approach. Thermal fluctuations are not taken into account. The number of simultaneous hookings is limited by the molecule length. The features of the automaton are: (i) the size of the cell neighbourhood for the automaton rule varies dynamically, from nearest neighbors to the entire molecule; (ii) the length of the time step is determined at each step according to dynamic rules. Calculations are made up to N=244 reptons in a molecule. Two subsequent stages of the motion are found. Firstly, an initial set of random configurations of molecules is transformed into a more ordered phase, where most molecules are elongated along the applied field direction. After some transient time, the mobility μ reaches a constant value. Then, it varies with N as 1/ N for long molecules. The band dispersion varies with time t approximately as Nt1/2. Our results indicate that the well-known plateau of the mobility μ vs. N does not hold at large electric fields.

  14. A tailored three-dimensionally printable agarose-collagen blend allows encapsulation, spreading, and attachment of human umbilical artery smooth muscle cells.

    PubMed

    Köpf, Marius; Campos, Daniela F Duarte; Blaeser, Andreas; Sen, Kshama S; Fischer, Horst

    2016-05-20

    In recent years, novel biofabrication technologies have enabled the rapid manufacture of hydrogel-cell suspensions into tissue-imitating constructs. The development of novel materials for biofabrication still remains a challenge due to a gap between contradicting requirements such as three-dimensional printability and optimal cytocompatibility. We hypothesise that blending of different hydrogels could lead to a novel material with favourable biological and printing properties. In our work, we combined agarose and type I collagen in order to develop a hydrogel blend capable of long-term cell encapsulation of human umbilical artery smooth muscle cells (HUASMCs) and 3D drop-on-demand printing. Different blends were prepared with 0.25%, 0.5%, 0.75%, and 1.5% agarose and 0.2% type I collagen. The cell morphology of HUASMCs and the printing accuracy were assessed for each agarose-collagen combination, keeping the content of collagen constant. The hydrogel blend which displayed sufficient cell spreading and printing accuracy (0.5% agarose, 0.2% type I collagen, AGR0.5COLL0.2) was then characterised based on swelling and degradation over 21 days and mechanical stiffness. The cellular response regarding cell attachment of HUASMCs embedded in the hydrogel blend was further studied using SEM, TEM, and TPLSM. Printing trials were fabricated in a drop-on-demand printing process. The swelling and degradation evaluation showed an average of 20% mass loss and less than 10% swelling. AGR0.5COLL0.2 exhibited significant increase in stiffness compared to pure agarose and type I collagen. In addition, columns of AGR0.5COLL0.2 three centimeters in height were successfully printed submerged in cooled perfluorocarbon, proving the intrinsic printability of the hydrogel blend. Ultimately, a promising novel hydrogel blend showing cell spreading and attachment as well as suitability for bioprinting was identified and could, for example, serve in the manufacture of in vitro 3D models to

  15. Design of a mechanical larynx with agarose as a soft tissue substitute for vocal fold applications.

    PubMed

    Choo, J Q; Lau, D P C; Chui, C K; Yang, T; Chng, C B; Teoh, S H

    2010-06-01

    Mechanical and computational models consisting of flow channels with convergent and oscillating constrictions have been applied to study the dynamics of human vocal fold vibration. To the best of our knowledge, no mechanical model has been studied using a material substitute with similar physical properties to the human vocal fold for surgical experimentation. In this study, we design and develop a mechanical larynx with agarose as a vocal fold substitute, and assess its suitability for surgical experimentation. Agarose is selected as a substitute for the vocal fold as it exhibits similar nonlinear hyperelastic characteristics to biological soft tissue. Through uniaxial compression and extension tests, we determined that agarose of 0.375% concentration most closely resembles the vocal fold mucosa and ligament of a 20-year old male for small tensile strain with an R(2) value of 0.9634 and root mean square error of 344.05±39.84 Pa. Incisions of 10 mm lengthwise and 3 mm in depth were created parallel to the medial edge on the superior surface of agar phantom. These were subjected to vibrations of 80, 130, and 180 Hz, at constant amplitude of 0.9 mm over a period of 10 min each in the mechanical larynx model. Lateral expansion of the incision was observed to be most significant for the lower frequency of 80 Hz. This model serves as a basis for future assessments of wound closure techniques during microsurgery to the vocal fold.

  16. One-step synthesis of highly efficient nanocatalysts on the supports with hierarchical pores using porous ionic liquid-water gel.

    PubMed

    Kang, Xinchen; Zhang, Jianling; Shang, Wenting; Wu, Tianbin; Zhang, Peng; Han, Buxing; Wu, Zhonghua; Mo, Guang; Xing, Xueqing

    2014-03-12

    Stable porous ionic liquid-water gel induced by inorganic salts was created for the first time. The porous gel was used to develop a one-step method to synthesize supported metal nanocatalysts. Au/SiO2, Ru/SiO2, Pd/Cu(2-pymo)2 metal-organic framework (Cu-MOF), and Au/polyacrylamide (PAM) were synthesized, in which the supports had hierarchical meso- and macropores, the size of the metal nanocatalysts could be very small (<1 nm), and the size distribution was very narrow even when the metal loading amount was as high as 8 wt %. The catalysts were extremely active, selective, and stable for oxidative esterification of benzyl alcohol to methyl benzoate, benzene hydrogenation to cyclohexane, and oxidation of benzyl alcohol to benzaldehyde because they combined the advantages of the nanocatalysts of small size and hierarchical porosity of the supports. In addition, this method is very simple.

  17. Fabrication of agarose concave petridish for 3D-culture microarray method for spheroids formation of hepatic cells.

    PubMed

    Zhang, Binbin; Li, Yang; Wang, Gaoshang; Jia, Zhidong; Li, Haiyan; Peng, Qing; Gao, Yi

    2018-04-19

    Liver is one of the most important organ in the body. But there are many limitations about liver transplantation for liver failure. It is quite important to develop the xenogeneic biological liver for providing an alternation to transplantation or liver regeneration. In this paper, we proposed a method to construct a novel kind of agarose 3D-culture concave microwell array for spheroids formation of hepatic cells. Using the 3D printing method, the microwell array was fabricated with an overall size of 6.4 mm × 6.4 mm, containing 121 microwells with 400 μm width/400 μm thickness. By exploiting the Polydimethylsiloxane (PDMS) membranes as a bridge, we finally fabricated the agarose one. We co-cultured three types of liver cells with bionics design in the microwell arrays. Using the methods described above, the resulting co-formed hepatocyte spheroids maintained the high viability and stable liver-specific functions. This engineered agarose concave microwell array could be a potentially useful tool for forming the elements for biological liver support. After developing the complete system, we also would consider to scale up the application of this system. It will be not only applied to the therapy of human organ damage, but also to the development of disease models and drug screening models.

  18. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

    PubMed Central

    McElfresh, Cameron; Wong, Lily R.

    2015-01-01

    Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. PMID:26070672

  19. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.

    PubMed

    Jaeger, Philipp A; McElfresh, Cameron; Wong, Lily R; Ideker, Trey

    2015-08-15

    Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  20. Spleen-specific suppression of TNF-alpha by cationic hydrogel-delivered antisense nucleotides for the prevention of arthritis in animal models.

    PubMed

    Dong, Lei; Xia, Suhua; Chen, Huan; Chen, Jiangning; Zhang, Junfeng

    2009-09-01

    This study developed a transplantable platform based on cationic hydrogels to deliver antisense oligodeoxynucleotides (ASOs) targeting the mRNA of TNF-alpha. Cationic agarose (c-agarose) was obtained by conjugating ethylenediamine to agarose via an N,N'-carbonyldiimidazole (CDI)-activation method. ASO-c-agarose system was constructed by mixing ASO in cationic agarose gel of proper concentration and gelation temperature. In vivo assessment of ASO distribution suggested that the system specifically target to spleen, wherein the c-agarose-delivered ASO had a concentration remarkably 50-fold higher than that of the naked ASO. The distribution of c-agarose-delivered ASO was scarcely detectable in liver and kidney. Next, three types of animal models were setup to evaluate the therapeutic efficacies of ASO-Gel, including the adjuvant-induced arthritis (AA), carrageen/lipopolysaccharide (LPS)-induced arthritis (CLA) and collagen-induced arthritis (CIA) models. The effects of ASO-c-agarose in alleviating inflammation and tissue destruction were evidenced in more than 90% of the testing animals, with decrease of main inflammatory cytokines, lightening of joint swelling and tissue damage, as well as increase in their body weights. All these findings suggest that this highly operable devise for the conveyance of antisense nucleotides together with its spleen-targeting property, could become a useful means of antisense-based therapeutics against rheumatoid arthritis and other diseases.

  1. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes

    PubMed Central

    Greenough, Lucia; Schermerhorn, Kelly M.; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Slatko, Barton E.; Gardner, Andrew F.

    2016-01-01

    Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner. PMID:26365239

  2. [Study of androgen receptor and phosphoglycerate kinase gene polymorphism in major cellular components of the so-called pulmonary sclerosing hemangioma].

    PubMed

    Qi, Feng-jie; Zhang, Xiu-wei; Zhang, Yong-xing; Dai, Shun-dong; Wang, En-hua

    2006-05-01

    To study the clonality of polygonal cells and surface cuboidal cells in the so-called pulmonary sclerosing hemangioma (PSH). 17 female surgically resected PSH were found. The polygonal cells and surface cuboidal cells of the 17 PSH cases were microdissected from routine hematoxylin and eosin-stained sections. Genomic DNA was extracted, pretreated through incubation with methylation-sensitive restrictive endonuclease HhaI or HpaII, and amplified by nested polymerase chain reaction for X chromosome-linked androgen receptor (AR) and phosphoglycerate kinase (PGK) genes. The length polymorphism of AR gene was demonstrated by denaturing polyacrylamide gel electrophoresis and silver staining. The PGK gene products were treated with Bst XI and resolved on agarose gel. Amongst the 17 female cases of PSH, 15 samples were successfully amplified for AR and PGK genes. The rates of polymorphism were 53% (8/15) and 27% (4/15) for AR and PGK genes respectively. Polygonal cells and surface cuboidal cells of 10 cases which were suitable for clonality study, showed the same loss of alleles (clonality ratio = 0) or unbalanced methylation pattern (clonality ratio < 0.25). The polygonal cells and surface cuboidal cells in PSH demonstrate patterns of monoclonal proliferation, indicating that both represent true neoplastic cells.

  3. No effect of femtosecond laser pulses on M13, E. coli, DNA, or protein.

    PubMed

    Wigle, Jeffrey C; Holwitt, Eric A; Estlack, Larry E; Noojin, Gary D; Saunders, Katharine E; Yakovlev, Valdislav V; Rockwell, Benjamin A

    2014-01-01

    Data showing what appears to be nonthermal inactivation of M13 bacteriophage (M13), Tobacco mosaic virus, Escherichia coli (E. coli), and Jurkatt T-cells following exposure to 80-fs pulses of laser radiation have been published. Interest in the mechanism led to attempts to reproduce the results for M13 and E. coli. Bacteriophage plaque-forming and bacteria colony-forming assays showed no inactivation of the microorganisms; therefore, model systems were used to see what, if any, damage might be occurring to biologically important molecules. Purified plasmid DNA (pUC19) and bovine serum albumin were exposed to and analyzed by agarose gel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively, and no effect was found. DNA and coat proteins extracted from laser-exposed M13 and analyzed by AGE or PAGE found no effect. Raman scattering by M13 in phosphate buffered saline was measured to determine if there was any physical interaction between M13 and femtosecond laser pulses, and none was found. Positive controls for the endpoints measured produced the expected results with the relevant assays. Using the published methods, we were unable to reproduce the inactivation results or to show any interaction between ultrashort laser pulses and buffer/water, DNA, protein, M13 bacteriophage, or E. coli.

  4. No effect of femtosecond laser pulses on M13, E. coli, DNA, or protein

    NASA Astrophysics Data System (ADS)

    Wigle, Jeffrey C.; Holwitt, Eric A.; Estlack, Larry E.; Noojin, Gary D.; Saunders, Katharine E.; Yakovlev, Valdislav V.; Rockwell, Benjamin A.

    2014-01-01

    Data showing what appears to be nonthermal inactivation of M13 bacteriophage (M13), Tobacco mosaic virus, Escherichia coli (E. coli), and Jurkatt T-cells following exposure to 80-fs pulses of laser radiation have been published. Interest in the mechanism led to attempts to reproduce the results for M13 and E. coli. Bacteriophage plaque-forming and bacteria colony-forming assays showed no inactivation of the microorganisms; therefore, model systems were used to see what, if any, damage might be occurring to biologically important molecules. Purified plasmid DNA (pUC19) and bovine serum albumin were exposed to and analyzed by agarose gel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively, and no effect was found. DNA and coat proteins extracted from laser-exposed M13 and analyzed by AGE or PAGE found no effect. Raman scattering by M13 in phosphate buffered saline was measured to determine if there was any physical interaction between M13 and femtosecond laser pulses, and none was found. Positive controls for the endpoints measured produced the expected results with the relevant assays. Using the published methods, we were unable to reproduce the inactivation results or to show any interaction between ultrashort laser pulses and buffer/water, DNA, protein, M13 bacteriophage, or E. coli.

  5. Rheological characterization of human fibrin and fibrin-agarose oral mucosa substitutes generated by tissue engineering.

    PubMed

    Rodríguez, I A; López-López, M T; Oliveira, A C X; Sánchez-Quevedo, M C; Campos, A; Alaminos, M; Durán, J D G

    2012-08-01

    In regenerative medicine, the generation of biocompatible substitutes of tissues by in vitro tissue engineering must fulfil certain requirements. In the case of human oral mucosa, the rheological properties of tissues deserve special attention because of their influence in the acoustics and biomechanics of voice production. This work is devoted to the rheological characterization of substitutes of the connective tissue of the human oral mucosa. Two substitutes, composed of fibrin and fibrin-agarose, were prepared in cell culture for periods in the range 1-21 days. The time evolution of the rheological properties of both substitutes was studied by two different experimental procedures: steady-state and oscillatory measurements. The former allows the plastic behaviour of the substitutes to be characterized by estimating their yield stress; the latter is employed to quantify their viscoelastic responses by obtaining the elastic (G') and viscous (G'') moduli. The results demonstrate that both substitutes are characterized by a predominant elastic response, in which G' (order 100 Pa) is roughly one order of magnitude larger than G'' (order 10 Pa). But the most relevant insight is the stability, throughout the 21 days of culture time, of the rheological quantities in the case of fibrin-agarose, whereas the fibrin substitute shows a significant hardening. This result provides evidence that the addition to fibrin of a small amount of agarose allows the rheological stability of the oral mucosa substitute to be maintained. This feature, together with its viscoelastic similitude with native tissues, makes this biomaterial appropriate for potential use as a scaffold in regenerative therapies of human oral mucosa. Copyright © 2011 John Wiley & Sons, Ltd.

  6. Bio-catalytic performance and dye-based industrial pollutants degradation potential of agarose-immobilized MnP using a Packed Bed Reactor System.

    PubMed

    Bilal, Muhammad; Asgher, Muhammad; Iqbal, Hafiz M N; Hu, Hongbo; Wang, Wei; Zhang, Xuehong

    2017-09-01

    In this study, the matrix-entrapment technique was adopted to immobilize a novel manganese peroxidase (MnP). Agarose beads developed from 3.0% agarose concentration furnished the preeminent immobilization yield (92.76%). The immobilized MnP exhibited better resistance to changes in the pH and temperature as compared to the free counterpart, with optimal conditions being pH 6.0 and 45°C. Thermal and storage stability characteristics were significantly improved after immobilization, and the immobilized-MnP displayed higher tolerance against different temperatures than free MnP state. After 72h, the insolubilized MnP retained its activity up to 41.2±1.7% and 33.6±1.4% at 55°C and 60°C, respectively, and 34.3±1.9% and 22.0±1.1% activities at 65°C and 70°C, respectively, after 48h of the incubation period. A considerable reusability profile was recorded with ten consecutive cycles. Moreover, to explore the industrial applicability, the agarose-immobilized-MnP was tested for bioremediation of textile industry effluent purposes. After six consecutive cycles, the tested effluents were decolorized to different extents (with a maximum of 98.4% decolorization). In conclusion, the remarkable bioremediation potential along with catalytic, thermo-stability, reusability, as well as storage stability features of the agarose-immobilized-MnP reflect its prospects as a biocatalyst for bioremediation and other industrial applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Characterization of Proteinuria in Dogue de Bordeaux Dogs, a Breed Predisposed to a Familial Glomerulonephropathy: A Retrospective Study.

    PubMed

    Lavoué, Rachel; Trumel, Catherine; Smets, Pascale M Y; Braun, Jean-Pierre; Aresu, Luca; Daminet, Sylvie; Concordet, Didier; Palanché, Florence; Peeters, Dominique

    2015-01-01

    Dogue de Bordeaux dog has been reported to be predisposed to a familial glomerulonephropathy that displays some morphological modifications reported in focal and segmental glomerulosclerosis. Prevalence of quantitatively abnormal renal proteinuria was recently reported to be 33% in this breed. The nature of the proteinuria was assessed by sodium dodecyl sulfate-agarose gel electrophoresis and determinations of urinary markers (urinary retinol-binding protein, urinary N-acetyl-β-glucosaminidase, urinary albumin and urinary immunoglobulin G) on stored specimens. Diagnostic performances of sodium dodecyl sulfate-agarose gel electrophoresis to identify dogs with elevated urinary biomarkers were assessed. Samples from 102 adult Dogue de Bordeaux dogs (47 non-proteinuric [urine protein-to-creatinine ratio ≤ 0.2], 20 borderline-proteinuric [0.2< urine protein-to-creatinine ratio ≤ 0.5] and 35 proteinuric dogs [urine protein-to-creatinine ratio >0.5]) were used, of which 2 were suffering from familial glomerulonephropathy. The electrophoretic protein patterns, for all but one proteinuric dog, were indicative of a glomerular origin and, in all dogs, the urinary albumin concentration related to creatinine concentration and the urinary immunoglobulin G concentration related to creatinine concentration were above the upper limit of the reference interval established for the breed. Sensitivity and specificity of sodium dodecyl sulfate-agarose gel electrophoresis identifying dogs with elevated urinary albumin concentration were 94% and 92%, respectively, while diagnostic performance of sodium dodecyl sulfate-agarose gel electrophoresis in detecting dogs with elevated urinary immunoglobulin G concentration yielded sensitivity and specificity of 90% and 74%, respectively. These results suggest that all proteinuric and some borderline-proteinuric Dogue de Bordeaux dogs likely have underlying glomerular lesions and that sodium dodecyl sulfate-agarose gel electrophoresis and

  8. A novel bio electro active alginate-aniline tetramer/ agarose scaffold for tissue engineering: synthesis, characterization, drug release and cell culture study.

    PubMed

    Atoufi, Zhale; Zarrintaj, Payam; Motlagh, Ghodratollah Hashemi; Amiri, Anahita; Bagher, Zohreh; Kamrava, Seyed Kamran

    2017-10-01

    In this study, synthesis of a novel biocompatible stimuli-responsive conducting hydrogel based on agarose/alginate-aniline tetramer with the capability of a tailored electrically controlled drug-release for neuroregeneration is investigated. First, aniline tetramer is synthesized and grafted onto sodium alginate. Then, this material is added to agarose as an electrical conductivity modifier to obtain Agarose/alginate-aniline tetramer hydrogel. The synthesized materials are characterized by H NMR and FTIR. The hydrogels are prepared with varying content of aniline tetramer and their swelling-deswelling and shape memory behavior is evaluated. The electroactivity and ionic conductivity of hydrogels against temperature is measured. The sample with 10% aniline tetramer (AT10) reveals the highest ionic conductivity. In MTT and SEM assays, AT10 shows the best cell viability and cell proliferation due to its highest ionic conductivity highlighting the fact that electrical stimuli cell signaling. Hydrogels also represent great potentials for passive and electro-stimulated dexamethasone release. These results demonstrate that the newly developed conducting hydrogels are promising materials for neuroregenerative medicine.

  9. Identification of adequate vehicles to carry nerve regeneration inducers using tubulisation.

    PubMed

    do Nascimento-Elias, Adriana Helena; Fresnesdas, Bruno César; Schiavoni, Maria Cristina Lopes; de Almeida, Natália Fernanda Gaspar; Santos, Ana Paula; de Oliveira Ramos, Jean; Junior, Wilson Marques; Barreira, Amilton Antunes

    2012-08-14

    Axonal regeneration depends on many factors, such as the type of injury and repair, age, distance from the cell body and distance of the denervated muscle, loss of surrounding tissue and the type of injured nerve. Experimental models use tubulisation with a silicone tube to research regenerative factors and substances to induce regeneration. Agarose, collagen and DMEM (Dulbecco's modified Eagle's medium) can be used as vehicles. In this study, we compared the ability of these vehicles to induce rat sciatic nerve regeneration with the intent of finding the least active or inert substance. The experiment used 47 female Wistar rats, which were divided into four experimental groups (agarose 4%, agarose 0.4%, collagen, DMEM) and one normal control group. The right sciatic nerve was exposed, and an incision was made that created a 10 mm gap between the distal and proximal stumps. A silicone tube was grafted onto each stump, and the tubes were filled with the respective media. After 70 days, the sciatic nerve was removed. We evaluated the formation of a regeneration cable, nerve fibre growth, and the functional viability of the regenerated fibres. Comparison among the three vehicles showed that 0.4% agarose gels had almost no effect on provoking the regeneration of peripheral nerves and that 4% agarose gels completely prevented fibre growth. The others substances were associated with profuse nerve fibre growth. In the appropriate concentration, agarose gel may be an important vehicle for testing factors that induce regeneration without interfering with nerve growth.

  10. Interaction of Electromagnetic Fields with Chondrocytes in Gel Culture

    DTIC Science & Technology

    1990-02-01

    biosynthesis due to applied electromagnetic fields. The results suggest that both normal chondrocytes and swarm rat chondrosarcoma cells in agarose Culture...and Swarm rat chondrosarcoma cells in agarose iii culture can, under proper culture conditions, continue to synthesize ma- trix macromolecules at a...cartilagc, and in rat chondrosarcoma cells (a continuous cell line). The overt gene expression of chondrocytes results in the synthesis and deposition of a

  11. Erythrocyte membrane protein analysis by sodium dodecyl sulphate-capillary gel electrophoresis in the diagnosis of hereditary spherocytosis.

    PubMed

    Debaugnies, France; Cotton, Frédéric; Boutique, Charles; Gulbis, Béatrice

    2011-03-01

    Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) is currently the reference method for detecting protein deficiencies related to hereditary spherocytosis. The aim of the study was to evaluate an automated capillary gel electrophoresis system, the Experion instrument from BioRad, for its ability to separate and quantify the erythrocyte membrane proteins. The major erythrocyte membrane proteins (actin, protein 4.2, protein 4.1, band 3, ankyrin, α- and β-spectrin) were extracted and purified from membrane ghosts by centrifugation, immunoprecipitation and electroelution. Analyses were performed using SDS-PAGE and sodium dodecyl sulphate capillary gel electrophoresis (SDS-CGE) to establish a separation profile of the total ghosts. Then, the samples from patients received for investigations of erythrocyte membrane defects were analysed. Five of the seven expected erythrocyte membrane proteins were finally separated and identified. In the 20 studied cases, taking into account the screening test results and the clinical and family histories, the SDS-CGE method allowed us to achieve the same conclusion as with SDS-PAGE, except for the patient with elliptocytosis. The new SDS-CGE method presents interesting features that could make this instrument a powerful diagnostic tool for detection of erythrocyte membrane protein abnormalities, and can be proposed as an automated alternative method to the labour intensive SDS-PAGE analysis.

  12. Further development of an electroosmotic medium pump system for preparative disk gel electrophoresis.

    PubMed

    Hayakawa, Mitsuo; Hosogi, Yumiko; Takiguchi, Hisashi; Shiroza, Teruaki; Shibata, Yasuko; Hiratsuka, Koichi; Kiyama-Kishikawa, Michiko; Hamajima, Susumu; Abiko, Yoshimitsu

    2003-02-01

    A simple and practical 6.8-cm-diameter (36.30-cm(2) cross-sectional-area) preparative disk gel electrophoresis device, based on the design of M. Hayakawa et al. (Anal. Biochem. 288 (2001) 168), in which the elution buffer is driven by an electroosmotic buffer flow through the membrane into the elution chamber from the anode chamber was constructed. We have found that the dialysis membranes employed provide suitable flow rates for the elution buffer, similar to those of an earlier 3.6-cm-diameter device, resulting in the prevention of excess eluate dilution. The efficiency of this device was demonstrated by the fractionation of a bovine serum albumin (BSA) Cohn V fraction into monomer, dimer, and oligomer components using nondenaturing polyacrylamide gel electrophoresis (native-PAGE). The maximum protein concentration of the eluate achieved was 133 mg/ml of BSA monomer, which required a dilution of the eluate for subsequent analytical PAGE performance. As a practical example, the two-dimensional fractionation of soluble dipeptidyl peptidase IV (sDPP IV) from 50 ml fetal bovine serum (3.20 g protein) per gel is presented. The sDPP IV enzyme protein was recovered in a relatively short time, utilizing a 6.5% T native-PAGE and subsequential sodium dodecyl sulfate-PAGE system. This device enhances the possibility of continuous electrophoretic fractionation of complex protein mixtures on a preparative scale. Copyright 2003 Elsevier Science (USA)

  13. Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

    PubMed

    Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

    2015-01-01

    DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA

  14. Ultrarapid electrophoretic transfer of high and low molecular weight proteins using heat.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2009-01-01

    An ultrarapid method for the electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate (SDS) polyacrylamide gel is described here. The transfer was performed with heated (70-75 degrees C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight antigens (molecular weight protein standards, a purified protein, and proteins from a human tissue extract) could be carried out in 10 min for a 7% (0.75 mm) SDS polyacrylamide gel. For 10 and 12.5% gels (0.75 mm) the corresponding time was 15 min. A complete transfer could be carried out in 20 min for 7, 10, and 12.5% gels (1.5 mm gels). The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. The heat mediated transfer method was compared with a conventional transfer protocol, under similar conditions. The conventional method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is particularly useful for the transfer of high molecular weight proteins, very rapid, and avoids the use of methanol.

  15. Western blotting of high and low molecular weight proteins using heat.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2015-01-01

    A method for the electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate (SDS) polyacrylamide gel is described here. The transfer was performed with heated (70-75 °C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight antigens (molecular weight protein standards, a purified protein, and proteins from a human tissue extract) could be carried out in 10 min for a 7 % (0.75 mm) SDS polyacrylamide gel. For 10 and 12.5 % gels (0.75 mm) the corresponding time was 15 min. A complete transfer could be carried out in 20 min for 7, 10, and 12.5 % gels (1.5 mm gels). The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. The heat mediated transfer method was compared with a conventional transfer protocol, under similar conditions. The conventional method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is particularly useful for the transfer of high molecular weight proteins, very rapid, and avoids the use of methanol.

  16. Improved Mobility Control for Carbon Dioxide (CO{sub 2}) Enhanced Oil Recovery Using Silica-Polymer-Initiator (SPI) Gels

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oglesby, Kenneth

    2014-01-31

    SPI gels are multi-component silicate based gels for improving (areal and vertical) conformance in oilfield enhanced recovery operations, including water-floods and carbon dioxide (CO{sub 2}) floods, as well as other applications. SPI mixtures are like-water when pumped, but form light up to very thick, paste-like gels in contact with CO{sub 2}. When formed they are 3 to 10 times stronger than any gelled polyacrylamide gel now available, however, they are not as strong as cement or epoxy, allowing them to be washed / jetted out of the wellbore without drilling. This DOE funded project allowed 8 SPI field treatments tomore » be performed in 6 wells (5 injection wells and 1 production well) in 2 different fields with different operators, in 2 different basins (Gulf Coast and Permian) and in 2 different rock types (sandstone and dolomite). Field A was in a central Mississippi sandstone that injected CO{sub 2} as an immiscible process. Field B was in the west Texas San Andres dolomite formation with a mature water-alternating-gas miscible CO{sub 2} flood. Field A treatments are now over 1 year old while Field B treatments have only 4 months data available under variable WAG conditions. Both fields had other operational events and well work occurring before/ during / after the treatments making definitive evaluation difficult. Laboratory static beaker and dynamic sand pack tests were performed with Ottawa sand and both fields’ core material, brines and crude oils to improve SPI chemistry, optimize SPI formulations, ensure SPI mix compatibility with field rocks and fluids, optimize SPI treatment field treatment volumes and methods, and ensure that strong gels set in the reservoir. Field quality control procedures were designed and utilized. Pre-treatment well (surface) injectivities ranged from 0.39 to 7.9 MMCF/psi. The SPI treatment volumes ranged from 20.7 cubic meters (m{sup 3}, 5460 gallons/ 130 bbls) to 691 m{sup 3} (182,658 gallons/ 4349 bbls). Various size and

  17. Estimation of sonodynamic treatment region with sonochemiluminescence in gel phantom

    NASA Astrophysics Data System (ADS)

    Mashiko, Daisaku; Nishitaka, Shinya; Iwasaki, Ryosuke; Lafond, Maxime; Yoshizawa, Shin; Umemura, Shin-ichiro

    2018-07-01

    Sonodynamic treatment is a non-invasive cancer treatment using ultrasound through the generation of reactive oxygen species (ROS) by acoustic cavitation. High-intensity focused ultrasound (HIFU) can generate cavitation bubbles using highly negative pressure in its focal region. When cavitation bubbles are forced to collapse, they generate ROS, which can attack cancer cells, typically assisted by a sonodynamically active antitumor agent. For sonodynamic treatment, both localization and efficiency of generating ROS are important. To improve them, the region of ROS generation was quantitatively estimated in this study using a polyacrylamide gel containing luminol as the target exposed to “Trigger HIFU”, consisting of a highly intense short “trigger pulse” to generate a cavitation cloud followed by a moderate-intensity long “sustaining burst” to keep the cavitation bubbles oscillating. It was found to be important for efficient ROS generation that the focal region of the trigger pulse should be immediately exposed to the sustaining burst.

  18. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes.

    PubMed

    Greenough, Lucia; Schermerhorn, Kelly M; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Slatko, Barton E; Gardner, Andrew F

    2016-01-29

    Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3'-5' exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Laboratory and Field Evaluations of Polyacrylamide Hydrogel Baits Against Argentine Ants (Hymenoptera: Formicidae).

    PubMed

    Rust, Michael K; Soeprono, Andrew; Wright, Sarajean; Greenberg, Les; Choe, Dong-Hwan; Boser, Christina L; Cory, Coleen; Hanna, Cause

    2015-06-01

    The development of effective baits to control the Argentine ant, Linepithema humile (Mayr), has been problematic because foragers prefer sweet liquids, while many toxicants are insoluble in water and liquid baits are generally difficult to deliver. The incorporation of thiamethoxam and sucrose solutions into a water-absorbing polyacrylamide hydrogel provides a unique and novel carrier and method of application for liquid baits. Formulations of thiamethoxam affected the size of the hydrogels, and sucrose solutions containing 0.0003% technical thiamethoxam provided hydrogels as large as those made with 25% sucrose solution or deionized water. Concentrations of thiamethoxam as low as 0.000075% in the hydrogels provided 50% kill of workers within 3 d in a laboratory setting. In small colony studies, baiting with 0.00015 and 0.000075% thiamethoxam hydrogels provided 100% mortality of workers and queens within 8 d. An enzyme-linked immunosorbent assay indicated that thiamethoxam was absorbed into the interior of the polyacrylamide matrix. The water loss rates of the hydrogels were dependent upon the relative humidity. Polyacrylamide hydrogels with >50% water loss were less attractive to ants. Field studies in highly infested areas indicated that concentrations of 0.0006 or 0.0018% thiamethoxam were more effective than 0.00015%. Hydrogels may provide a cost-effective alternative to providing aqueous baits to control Argentine ants. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

    PubMed

    Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

    2018-01-01

    Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

  1. Visualization of DNA molecules in time during electrophoresis

    NASA Technical Reports Server (NTRS)

    Lubega, Seth

    1991-01-01

    For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.

  2. A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs.

    PubMed

    Manage, Dammika P; Lauzon, Jana; Atrazhev, Alexey; Morrissey, Yuen C; Edwards, Ann L; Stickel, Alexander J; Crabtree, H John; Pabbaraju, Kanti; Zahariadis, George; Yanow, Stephanie K; Pilarski, Linda M

    2012-05-07

    Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 2-14 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be performed within 1-2 h. We here describe a multiparameter PCR assay to simultaneously detect HSV-1 and HSV-2 DNA templates, together with integrated positive and negative controls, with product detection by melting curve analysis (MCA), in an array of semi-solid polyacrylamide gel posts. Each gel post is 0.67 μL in volume, and polymerized with all the components required for PCR. Both PCR and MCA can currently be performed in one hour and 20 min. Unprocessed genital swabs collected in universal transport medium were directly added to the reagents before or after polymerization, diffusing from atop the gel posts. The gel post platform detects HSV templates in as little as 2.5 nL of raw sample. In this study, 45 genital swab specimens were tested blindly as a preliminary validation of this platform. The concordance of PCR on gel posts with conventional PCR was 91%. The primer sequestration method introduced here (wherein different primers are placed in different sets of posts) enables the simultaneous detection of multiple pathogens for the same sample, together with positive and negative controls, on a single chip. This platform accepts unprocessed samples and is readily adaptable to detection of multiple different pathogens or biomarkers for point-of-care diagnostics.

  3. Location of Biomarkers and Reagents within Agarose Beads of a Programmable Bio-nano-chip

    PubMed Central

    Jokerst, Jesse V.; Chou, Jie; Camp, James P.; Wong, Jorge; Lennart, Alexis; Pollard, Amanda A.; Floriano, Pierre N.; Christodoulides, Nicolaos; Simmons, Glennon W.; Zhou, Yanjie; Ali, Mehnaaz F.

    2012-01-01

    The slow development of cost-effective medical microdevices with strong analytical performance characteristics is due to a lack of selective and efficient analyte capture and signaling. The recently developed programmable bio-nano-chip (PBNC) is a flexible detection device with analytical behavior rivaling established macroscopic methods. The PBNC system employs ≈300 μm-diameter bead sensors composed of agarose “nanonets” that populate a microelectromechanical support structure with integrated microfluidic elements. The beads are an efficient and selective protein-capture medium suitable for the analysis of complex fluid samples. Microscopy and computational studies probe the 3D interior of the beads. The relative contributions that the capture and detection of moieties, analyte size, and bead porosity make to signal distribution and intensity are reported. Agarose pore sizes ranging from 45 to 620 nm are examined and those near 140 nm provide optimal transport characteristics for rapid (<15 min) tests. The system exhibits efficient (99.5%) detection of bead-bound analyte along with low (≈2%) nonspecific immobilization of the detection probe for carcinoembryonic antigen assay. Furthermore, the role analyte dimensions play in signal distribution is explored, and enhanced methods for assay building that consider the unique features of biomarker size are offered. PMID:21290601

  4. Preparation of a novel pH optical sensor using orange (II) based on agarose membrane as support.

    PubMed

    Heydari, Rouhollah; Hosseini, Mohammad; Amraei, Ahmadreza; Mohammadzadeh, Ali

    2016-04-01

    A novel and cost effective optical pH sensor was prepared using covalent immobilization of orange (II) indicator on the agarose membrane as solid support. The fabricated optical sensor was fixed into a sample holder of a spectrophotometer instrument for pH monitoring. Variables affecting sensor performance including pH of dye bonding to agarose membrane and dye concentration were optimized. The sensor responds to the pH changes in the range of 3.0-10.0 with a response time of 2.0 min and appropriate reproducibility (RSD ≤ 0.9%). No significant variation was observed on sensor response after increasing the ionic strength in the range of 0.0-0.5M of sodium chloride. Determination of pH using the proposed optical sensor is quick, simple, inexpensive, selective and sensitive in the pH range of 3.0-10.0. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Enhancement of Dose Response and Nuclear Magnetic Resonance Image of PAGAT Polymer Gel Dosimeter by Adding Silver Nanoparticles

    PubMed Central

    Sabbaghizadeh, Rahim; Shamsudin, Roslinda; Deyhimihaghighi, Najmeh; Sedghi, Arman

    2017-01-01

    In the present study, the normoxic polyacrylamide gelatin and tetrakis hydroxy methyl phosphoniun chloride (PAGAT) polymer gel dosimeters were synthesized with and without the presence of silver (Ag) nanoparticles. The amount of Ag nanoparticles varied from 1 to 3 ml with concentration 3.14 g/l, thus forming two types of PAGAT polymer gel dosimeters before irradiating them with 6 to 25 Gy produced by 1.25-MeV 60Co gamma rays. In this range, the predominant gamma ray interaction with matter is by Compton scattering effect, as the photoelectric absorption effect diminishes. MRI was employed when evaluating the polymerization of the dosimeters and the gray scale of the MRI film was determined via an optical densitometer. Subsequent analyses of optical densities revealed that the extent of polymerization increased with the increase in the absorbed dose, while the increase of penetration depth within the dosimeters has a reverse effect. Moreover, a significant increase in the optical density-dose response (11.82%) was noted for dosimeters containing 2 ml Ag nanoparticles. PMID:28060829

  6. Distributed vasculogenesis from modular agarose-hydroxyapatite-fibrinogen microbeads.

    PubMed

    Rioja, Ana Y; Daley, Ethan L H; Habif, Julia C; Putnam, Andrew J; Stegemann, Jan P

    2017-06-01

    Critical limb ischemia impairs circulation to the extremities, causing pain, disrupted wound healing, and potential tissue necrosis. Therapeutic angiogenesis seeks to repair the damaged microvasculature directly to restore blood flow. In this study, we developed modular, micro-scale constructs designed to possess robust handling qualities, allow in vitro pre-culture, and promote microvasculature formation. The microbead matrix consisted of an agarose (AG) base to prevent aggregation, combined with cell-adhesive components of fibrinogen (FGN) and/or hydroxyapatite (HA). Microbeads encapsulating a co-culture of human umbilical vein endothelial cells (HUVEC) and fibroblasts were prepared and characterized. Microbeads were generally 80-100µm in diameter, and the size increased with the addition of FGN and HA. Addition of HA increased the yield of microbeads, as well as the homogeneity of distribution of FGN within the matrix. Cell viability was high in all microbead types. When cell-seeded microbeads were embedded in fibrin hydrogels, HUVEC sprouting and inosculation between neighboring microbeads were observed over seven days. Pre-culture of microbeads for an additional seven days prior to embedding in fibrin resulted in significantly greater HUVEC network length in AG+HA+FGN microbeads, as compared to AG, AG+HA or AG+FGN microbeads. Importantly, composite microbeads resulted in more even and widespread endothelial network formation, relative to control microbeads consisting of pure fibrin. These results demonstrate that AG+HA+FGN microbeads support HUVEC sprouting both within and between adjacent microbeads, and can promote distributed vascularization of an external matrix. Such modular microtissues may have utility in treating ischemic tissue by rapidly re-establishing a microvascular network. Critical limb ischemia (CLI) is a chronic disease that can lead to tissue necrosis, amputation, and death. Cell-based therapies are being explored to restore blood flow and

  7. Macrophages influence a competition of contact guidance and chemotaxis for fibroblast alignment in a fibrin gel coculture assay.

    PubMed

    Bromberek, B A; Enever, P A J; Shreiber, D I; Caldwell, M D; Tranquillo, R T

    2002-05-01

    Rat dermal fibroblasts were dispersed initially in the outer shell of a fibrin gel sphere, while the inner core either was devoid of cells or contained peritoneal exudate cells (primarily macrophages), thereby mimicking the inflammatory phase of wound healing. The fibroblasts compacted floating fibrin microspheres over time. In the absence of macrophages, the initial distribution of fibroblasts (only in the shell) induced circumferential alignment of fibrin fibrils via compaction of the shell relative to the core. The aligned fibrils created a contact guidance field, which was manifested by strong circumferential alignment of the fibroblasts. However, in the presence of macrophages, the fibroblasts exhibited more radial alignment despite the simultaneous contact guidance field in the circumferential direction associated with compaction. This was attributed to a chemotactic gradient emanating from the core due to a putative factor(s) released by the macrophages. The presence of a radial chemotactic stimulus was supported by the finding of even greater radial alignment when fibrin microspheres were embedded in an agarose-fibrin gel that abolished compaction and consequently the contact guidance field. Our assay permits the simulation of tissue morphogenetic processes that involve cell guidance phenomena and tractional restructuring of the extracellular matrix.

  8. A lightweight scalable agarose-gel-synthesized thermoelectric composite

    NASA Astrophysics Data System (ADS)

    Kim, Jin Ho; Fernandes, Gustavo E.; Lee, Do-Joong; Hirst, Elizabeth S.; Osgood, Richard M., III; Xu, Jimmy

    2018-03-01

    Electronic devices are now advancing beyond classical, rigid systems and moving into lighweight flexible regimes, enabling new applications such as body-wearables and ‘e-textiles’. To support this new electronic platform, composite materials that are highly conductive yet scalable, flexible, and wearable are needed. Materials with high electrical conductivity often have poor thermoelectric properties because their thermal transport is made greater by the same factors as their electronic conductivity. We demonstrate, in proof-of-principle experiments, that a novel binary composite can disrupt thermal (phononic) transport, while maintaining high electrical conductivity, thus yielding promising thermoelectric properties. Highly conductive Multi-Wall Carbon Nanotube (MWCNT) composites are combined with a low-band gap semiconductor, PbS. The work functions of the two materials are closely matched, minimizing the electrical contact resistance within the composite. Disparities in the speed of sound in MWCNTs and PbS help to inhibit phonon propagation, and boundary layer scattering at interfaces between these two materials lead to large Seebeck coefficient (> 150 μV/K) (Mott N F and Davis E A 1971 Electronic Processes in Non-crystalline Materials (Oxford: Clarendon), p 47) and a power factor as high as 10 μW/(K2 m). The overall fabrication process is not only scalable but also conformal and compatible with large-area flexible hosts including metal sheets, films, coatings, possibly arrays of fibers, textiles and fabrics. We explain the behavior of this novel thermoelectric material platform in terms of differing length scales for electrical conductivity and phononic heat transfer, and explore new material configurations for potentially lightweight and flexible thermoelectric devices that could be networked in a textile.

  9. Controlling tailwater sediment and phosphorus concentrations with polyacrylamide in the Imperial Valley, California.

    PubMed

    Goodson, Christopher C; Schwartz, Gregory; Amrhein, Christopher

    2006-01-01

    External loading of phosphorus (P) from agricultural surface discharge (tailwater) is the main cause of excessive algae growth and the eutrophication of the Salton Sea, California. Continuous polyacrylamide (PAM) applications to agricultural irrigation water inflows were evaluated as a means of reducing sediment and P in tailwater. Zero (control) and 1 mg L(-1) PAM (PAM1) treatments were compared at 17 Imperial Valley field sites. Five and 10 mg L(-1) PAM treatments (PAM5, PAM10) were conducted at one site. The particulate phosphorus (Pp) fraction was determined as the difference between total phosphorus (Pt) and the soluble phosphorus (Ps) fraction. We observed 73, 82, and 98% turbidity reduction with PAM1, PAM5, and PAM10 treatments. Although eight field sites had control tailwater sediment concentrations above the New River total maximum daily loads (TMDL), all but one were made compliant during their paired PAM1 treatments. While PAM1 and PAM10 reduced tail water Pp by 31 and 78%, none of the treatments tested reduced Ps. This may have been caused by high irrigation water Na concentrations which would reduce Ca adsorption and Ca-phosphate bridging on the PAM. The PAM1 treatments resulted in <0.5 mg L(-1) drain water polyacrylamide concentrations 1.6 km downstream of PAM addition, while PAM5 and PAM10 treatments produced > 2 mg L(-1) drain water polyacrylamide concentrations. We concluded that, although PAM practically eliminates Imperial Valley tailwater sediment loads, it does not effectively reduce tailwater Ps, the P fraction most responsible for the eutrophication of the Salton Sea.

  10. Isolation of Lysophosphatidic Acid Phosphatase from Developing Peanut Cotyledons1

    PubMed Central

    Shekar, Sunil; Tumaney, Ajay W.; Rao, T.J.V. Sreenivasa; Rajasekharan, Ram

    2002-01-01

    The soluble fraction of immature peanut (Arachis hypogaea) was capable of dephosphorylating [3H]lysophosphatidic acid (LPA) to generate monoacylglycerol (MAG). The enzyme responsible for the generation of MAG, LPA phosphatase, has been identified in plants and purified by successive chromatography separations on octyl-Sepharose, Blue Sepharose, Superdex-75, and heparin-agarose to apparent homogeneity from developing peanuts. This enzyme was purified 5,048-fold to a final specific activity of 858 nmol min−1 mg−1. The enzyme has a native molecular mass of approximately 39 kD determined by gel filtration and migrates as a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a subunit molecular mass of 39 ± 1.5 kD. The Km values for oleoyl-, stearoyl-, and palmitoyl-sn-glycerol-3-phosphate were determined to be 28.6, 39.3, and 47.9 μm, respectively. The LPA phosphatase was specific to LPA and did not utilize any other substrate such as glycerol-3-phosphate, phosphatidic acid, or p-nitrophenylphosphate. The enzyme activity was stimulated by the low concentrations of detergents such as Triton X-100 and octylglucoside. Cations had no effect on the enzyme activity. Fatty acids, sphingosine, and sphingomyelin at low concentrations stimulated the enzyme activity. The identification of LPA phosphatase in plants demonstrates the existence of MAG biosynthetic machinery in plants. PMID:11891254

  11. A comparison of the binding of secretory component to immunoglobulin A (IgA) in human colostral S-IgA1 and S-IgA2

    PubMed Central

    Almogren, Adel; Senior, Bernard W; Kerr, Michael A

    2007-01-01

    A detailed investigation of the binding of secretory component to immunoglobulin A (IgA) in human secretory IgA2 (S-IgA2) was made possible by the development of a new method of purifying S-IgA1, S-IgA2 and free secretory component from human colostrum using thiophilic gel chromatography and chromatography on Jacalin-agarose. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis of unreduced pure S-IgA2 revealed that, unlike in S-IgA1, a significant proportion of the secretory component was bound non-covalently in S-IgA2. When S-IgA1 was incubated with a protease purified from Proteus mirabilis the secretory component, but not the α-chain, was cleaved. This is in contrast to serum IgA1, in which the α-chain was cleaved under the same conditions – direct evidence that secretory component does protect the α-chain from proteolytic cleavage in S-IgA. Comparisons between the products of cleavage with P. mirabilis protease of free secretory component and bound secretory component in S-IgA1 and S-IgA2 also indicated that, contrary to the general assumption, the binding of secretory component to IgA is different in S-IgA2 from that in S-IgA1. PMID:17156102

  12. Use of X-Chromosome Inactivation Pattern to Analyze the Clonality of 14 Female Cases of Kaposi Sarcoma.

    PubMed

    Yuan, Ding; XiuJuan, Wu; Yan, Zhang; JunQin, Liang; Fang, Xiang; Shirong, Yu; Xiaojing, Kang; Yanyan, Feng; Weidong, Wu; Dong, Luo; Qingli, Lu; DeZhi, Zhang; XiongMing, Pu

    2015-06-16

    Kaposi sarcoma (KS) has features of both neoplastic growth and hyperplastic proliferation. It is the most common tumor seen in patients with HIV infection. Whether KS is a real tumor or a benign hyperplastic disease is not known. Tissues from KS and cutaneous hemangioma lesion DNA were extracted, and then digested with methylation-sensitive restriction endonuclease HpaII. Human androgen receptor gene (HUMARA) was amplified with PCR method and the product was separated on 10% denaturing polyacrylamide gels and stained with ethylene dibromide (EB) to show the polymorphism of HUMARA. Phosphoglycerate kinase (PGK) was amplified and the product was digested by BStXI, agarose gel and EB stained to show the polymorphism of PGK. Finally, we analyzed the clonality of KS. In the 14 patients with KS, heterozygosity of the HUMARA gene was observed in 12 (85.7%) cases. Loss of heterozygosity of HUMARA gene on X-chromosome (without HpaII digestion there were 2 bands, after HpaII digestion there were just 1 of the bands), representing monoclonal origin, was present in 11 cases of Kaposi sarcoma. Heterozygosity of the PGK gene was observed in 5 (35.7%) cases, which all represent monoclonal origin. There was no significant difference according to country, stage, or HIV and HHV-8 (P>0.05). The current findings suggest that Kaposi sarcoma is a clonal neoplasm, not a reactive proliferation.

  13. New primer for specific amplification of the CAG repeat in Huntington disease alleles

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bond, C.E.; Hodes, M.E.

    1994-09-01

    Huntington disease is an autosomal dominant neurodegenerative disorder caused by an expansion of a CAG trinucleotide repeat near the 5{prime} end of the gene for Huntington disease (IT15). The CAG repeat is flanked by a variable-length CCG repeat that is included in the amplification product obtained with most currently used primer sets and PCR protocols. Inclusion of this adjacent CCG repeat complicates the accurate assessment of CAG repeat length and interferes with the genotype determination of those individuals carrying alleles in the intermediate range between normal and expanded sized. Due to the GC-rich nature of this region, attempts at designingmore » a protocol for amplification of only the CAG repeat have proved unreliable and difficult to execute. We report here the development of a compatible primer set and PCR protocol that yields consistent amplification of the CAG-repeat region. PCR products can be visualized in ethidium bromide-stained agarose gels for rapid screening or in 6% polyacrylamide gels for determination of exact repeat length. This assay produces bands that can be sized accurately, while eliminating most nonspecific products. Fifty-five specimens examined showed consistency with another well-known method, but one that amplifies the CCG repeats as well. The results we obtained also matched the known carrier status of the donors.« less

  14. Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

    PubMed

    Duarte, José M; Barbier, Içvara; Schaerli, Yolanda

    2017-11-17

    Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g., being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges. First, we encapsulate single bacteria into microfluidic agarose gel beads. After incubation, they harbor monoclonal bacterial microcolonies (e.g., expressing a synthetic construct) and can be sorted according their fluorescence by fluorescence activated cell sorting (FACS). We determine enrichment rates and demonstrate that we can measure the average fluorescent signals of microcolonies containing phenotypically heterogeneous cells, obviating the problem of cell-to-cell variability. Finally, we apply this method to sort a pBAD promoter library at ON and OFF states.

  15. Adhesion of and to soil in runoff as influenced by polyacrylamide.

    PubMed

    Bech, Tina B; Sbodio, Adrian; Jacobsen, Carsten S; Suslow, Trevor

    2014-11-01

    Polyacrylamide (PAM) is used in agriculture to reduce soil erosion and has been reported to reduce turbidity, nutrients, and pollutants in surface runoff water. The objective of this work was to determine the effect of PAM on the concentration of enteric bacteria in surface runoff by comparing four enteric bacteria representing phenotypically different motility and hydrophobicity from three soils. Results demonstrated that bacterial surface runoff was differentially influenced by the PAM treatment. Polyacrylamide treatment increased surface runoff for adhered and planktonic cells from a clay soil; significantly decreased surface runoff of adhered bacteria, while no difference was observed for planktonic bacteria from the sandy loam; and significantly decreased the surface runoff of planktonic cells, while no difference was observed for adhered bacteria from the clay loam. Comparing strains from a final water sample collected after 48 h showed a greater loss of while serovar Poona was almost not detected. Thus, (i) the PAM efficiency in reducing the concentration of enteric bacteria in surface runoff was influenced by soil type and (ii) variation in the loss of enteric bacteria highlights the importance of strain-specific properties that may not be captured with general fecal indicator bacteria. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  16. Role of Electrostatic Interactions on the Transport of Druglike Molecules in Hydrogel-Based Articular Cartilage Mimics: Implications for Drug Delivery.

    PubMed

    Ye, Fengbin; Baldursdottir, Stefania; Hvidt, Søren; Jensen, Henrik; Larsen, Susan W; Yaghmur, Anan; Larsen, Claus; Østergaard, Jesper

    2016-03-07

    In the field of drug delivery to the articular cartilage, it is advantageous to apply artificial tissue models as surrogates of cartilage for investigating drug transport and release properties. In this study, artificial cartilage models consisting of 0.5% (w/v) agarose gel containing 0.5% (w/v) chondroitin sulfate or 0.5% (w/v) hyaluronic acid were developed, and their rheological and morphological properties were characterized. UV imaging was utilized to quantify the transport properties of the following four model compounds in the agarose gel and in the developed artificial cartilage models: H-Ala-β-naphthylamide, H-Lys-Lys-β-naphthylamide, lysozyme, and α-lactalbumin. The obtained results showed that the incorporation of the polyelectrolytes chondroitin sulfate or hyaluronic acid into agarose gel induced a significant reduction in the apparent diffusivities of the cationic model compounds as compared to the pure agarose gel. The decrease in apparent diffusivity of the cationic compounds was not caused by a change in the gel structure since a similar reduction in apparent diffusivity was not observed for the net negatively charged protein α-lactalbumin. The apparent diffusivity of the cationic compounds in the negatively charged hydrogels was highly dependent on the ionic strength, pointing out the importance of electrostatic interactions between the diffusant and the polyelectrolytes. Solution based affinity studies between the model compounds and the two investigated polyelectrolytes further confirmed the electrostatic nature of their interactions. The results obtained from the UV imaging diffusion studies are important for understanding the effect of drug physicochemical properties on the transport in articular cartilage. The extracted information may be useful in the development of hydrogels for in vitro release testing having features resembling the articular cartilage.

  17. Effect of DEXTRAN-graft-POLYACRYLAMIDE Internal Structure on Flocculation Process Parameters

    NASA Astrophysics Data System (ADS)

    Bezugla, T.; Kutsevol, N.; Shyichuk, A.; Ziolkowska, D.

    2008-08-01

    Dextran-graft-Polyacrylamide copolymers (D-g-PAA) of brush-like architecture were tested as flocculation aids in the model kaolin suspensions. Due to expanded conformation the D-g-PAA copolymers are more effective flocculants than individual PAA with close molecular mass. The internal structure of D-g-PAA copolymers which is determined by number and length of grafted PAA chains, the distance between grafts, etc., has the significant influence on flocculation behavior of such polymers.

  18. Polyacrylamide Molecular Weight and Phosphogypsum Effects on Infiltration and Erosion in Semi-Arid Soils

    USDA-ARS?s Scientific Manuscript database

    Seal formation at the surface of semi-arid soils during rainstorms reduces soil infiltration rate (IR) and causes runoff and erosion. Surface application of dry anionic polyacrylamide (PAM) with high molecular weight (MW) has been found to be effective in stabilizing soil aggregates, and decreasing ...

  19. Polyacrylamide molecular weight and phosphogypsum effects on infiltration and erosion in semi-arid soils

    USDA-ARS?s Scientific Manuscript database

    Seal formation at the surface of semi-arid soils during rainstorms reduces soil infiltration rate (IR) and causes runoff and erosion. Surface application of dry anionic polyacrylamide (PAM) with high molecular weight (MW) has been found to be effective in stabilizing soil aggregates, and decreasing ...

  20. Homogeneity of gels and gel-derived glasses

    NASA Technical Reports Server (NTRS)

    Mukherjee, S. P.

    1984-01-01

    The significance and implications of gel preparation procedures in controlling the homogeneity of multicomponent oxide gels are discussed. The role of physicochemical factors such as the structure and chemical reactivities of alkoxides, the formation of double-metal alkoxides, and the nature of solvent(s) are critically analyzed in the context of homogeneity of gels during gelation. Three procedures for preparing gels in the SiO2-B2O3-Na2O system are examined in the context of cation distribution. Light scattering results for glasses in the SiO2-B2O3-Na2O system prepared by both the gel technique and the conventional technique are examined.

  1. Influence of solvent and salt concentration on the alignment properties of acrylamide copolymer gels for the measurement of RDC.

    PubMed

    Trigo-Mouriño, Pablo; Navarro-Vázquez, Armando; Sánchez-Pedregal, Víctor M

    2012-12-01

    The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration. Copyright © 2012 John Wiley & Sons, Ltd.

  2. Transdermal delivery of paeonol using cubic gel and microemulsion gel

    PubMed Central

    Luo, Maofu; Shen, Qi; Chen, Jinjin

    2011-01-01

    Background The aim of this study was to develop new systems for transdermal delivery of paeonol, in particular microemulsion gel and cubic gel formulations. Methods Various microemulsion vehicles were prepared using isopropyl myristate as an oil phase, polyoxyethylated castor oil (Cremophor® EL) as a surfactant, and polyethylene glycol 400 as a cosurfactant. In the optimum microemulsion gel formulation, carbomer 940 was selected as the gel matrix, and consisted of 1% paeonol, 4% isopropyl myristate, 28% Cremophor EL/polyethylene glycol 400 (1:1), and 67% water. The cubic gel was prepared containing 3% paeonol, 30% water, and 67% glyceryl monooleate. Results A skin permeability test using excised rat skins indicated that both the cubic gel and microemulsion gel formulations had higher permeability than did the paeonol solution. An in vivo pharmacokinetic study done in rats showed that the relative bioavailability of the cubic gel and microemulsion gel was enhanced by about 1.51-fold and 1.28-fold, respectively, compared with orally administered paeonol suspension. Conclusion Both the cubic gel and microemulsion gel formulations are promising delivery systems to enhance the skin permeability of paeonol, in particular the cubic gel. PMID:21904450

  3. Simple agarose micro-confinement array and machine-learning-based classification for analyzing the patterned differentiation of mesenchymal stem cells

    PubMed Central

    Sato, Asako; Vogel, Viola; Tanaka, Yo

    2017-01-01

    The geometrical confinement of small cell colonies gives differential cues to cells sitting at the periphery versus the core. To utilize this effect, for example to create spatially graded differentiation patterns of human mesenchymal stem cells (hMSCs) in vitro or to investigate underpinning mechanisms, the confinement needs to be robust for extended time periods. To create highly repeatable micro-fabricated structures for cellular patterning and high-throughput data mining, we employed here a simple casting method to fabricate more than 800 adhesive patches confined by agarose micro-walls. In addition, a machine learning based image processing software was developed (open code) to detect the differentiation patterns of the population of hMSCs automatically. Utilizing the agarose walls, the circular patterns of hMSCs were successfully maintained throughout 15 days of cell culture. After staining lipid droplets and alkaline phosphatase as the markers of adipogenic and osteogenic differentiation, respectively, the mega-pixels of RGB color images of hMSCs were processed by the software on a laptop PC within several minutes. The image analysis successfully showed that hMSCs sitting on the more central versus peripheral sections of the adhesive circles showed adipogenic versus osteogenic differentiation as reported previously, indicating the compatibility of patterned agarose walls to conventional microcontact printing. In addition, we found a considerable fraction of undifferentiated cells which are preferentially located at the peripheral part of the adhesive circles, even in differentiation-inducing culture media. In this study, we thus successfully demonstrated a simple framework for analyzing the patterned differentiation of hMSCs in confined microenvironments, which has a range of applications in biology, including stem cell biology. PMID:28380036

  4. The effect of milk processing on the microstructure of the milk fat globule and rennet induced gel observed using confocal laser scanning microscopy.

    PubMed

    Ong, L; Dagastine, R R; Kentish, S E; Gras, S L

    2010-04-01

    Confocal laser scanning microscopy (CLSM) was successfully used to observe the effect of milk processing on the size and the morphology of the milk fat globule in raw milk, raw ultrafiltered milk, and standardized and pasteurized milk prepared for cheese manufacture (cheese-milk) and commercial pasteurized and homogenized milk. Fat globule size distributions for the milk preparations were analyzed using both image analysis and light scattering and both measurements produced similar data trends. Changes to the native milk fat globule membrane (MFGM) were tracked using a MFGM specific fluorescent stain that allowed MFGM proteins and adsorbed proteins to be differentiated on the fat globule surface. Sodium dodecyl sulfate polyacrylamide gel electrophoresis confirmed the identity of native MFGM proteins isolated from the surface of fat globules within raw, UF retentate, and cheese-milk preparations, whereas only casein was detected on the surface of fat globules in homogenized milk. The microstructure, porosity, and gel strength of the rennet induced gel made from raw milk and cheese-milk was also found to be comparable and significantly different to that made from homogenized milk. Our results highlight the potential use of CLSM as a tool to observe the structural details of the fat globule and associated membrane close to its native environment.

  5. Cumulative irritation potential among metronidazole gel 1%, metronidazole gel 0.75%, and azelaic acid gel 15%.

    PubMed

    Colón, Luz E; Johnson, Lori A; Gottschalk, Ronald W

    2007-04-01

    Topical therapy for rosacea aims to reduce inflammatory lesions and decrease erythema but can carry side effects such as stinging, pruritus, and burning. Metronidazole and azelaic acid gel 15% are U.S. Food and Drug Administration-approved for the treatment of rosacea. The current study was conducted to assess the cumulative irritation potential of 2 formulations of metronidazole 0.75% gel and 1% gel--and azelaic acid gel 15% over 21 days (N=36). Results of this study demonstrated a significantly greater poten tial for irritation from azelaic acid compared with metronidazole gel 0.75% (P < .0001), which had significantly greater potential for irritation compared with metronidazole gel 1% (P = .0054). Metronidazole gel 1% had a similar profile to white petrolatum.

  6. The significance of gtf genes in caries expression: a rapid identification of Streptococcus mutans from dental plaque of child patients.

    PubMed

    Mishra, Apurva; Pandey, Ramesh K; Manickam, Natesan

    2015-01-01

    Rapid phylogenetic and functional gene (gtfB) identification of S. mutans from the dental plaque derived from children. Dental plaque collected from fifteen patients of age group 7-12 underwent centrifugation followed by genomic DNA extraction for S. mutans. Genomic DNA was processed with S. mutans specific primers in suitable PCR condtions for phylogenetic and functional gene (gtfB) identification. The yield and results were confirmed by agarose gel electrophoresis. 1% agarose gel electrophoresis depicts the positive PCR amplification at 1,485 bp when compared with standard 1 kbp indicating the presence of S. mutans in the test sample. Another PCR reaction was set using gtfB primers specific for S. mutans for functional gene identification. 1.2% agarose gel electrophoresis was done and a positive amplication was observed at 192 bp when compared to 100 bp standards. With the advancement in molecular biology techniques, PCR based identification and quantification of the bacterial load can be done within hours using species-specific primers and DNA probes. Thus, this technique may reduce the laboratory time spend in conventional culture methods, reduces the possibility of colony identification errors and is more sensitive to culture techniques.

  7. Polyacrylamide and biopolymer effects on flocculation, aggregate stability, and water seepage in a silt loam

    USDA-ARS?s Scientific Manuscript database

    Researcher’s seek a more renewable and natural alternative for water soluble anionic polyacrylamide (PAM), a highly-effective, petroleum-derived polymer used in agriculture to control erosion and reduce water seepage from unlined irrigation structures. This study evaluated two anionic polymers: a ba...

  8. Micro- and Nanomechanical Analysis of Articular Cartilage by Indentation-Type Atomic Force Microscopy: Validation with a Gel-Microfiber Composite

    PubMed Central

    Loparic, Marko; Wirz, Dieter; Daniels, A.U.; Raiteri, Roberto; VanLandingham, Mark R.; Guex, Geraldine; Martin, Ivan; Aebi, Ueli; Stolz, Martin

    2010-01-01

    Abstract As documented previously, articular cartilage exhibits a scale-dependent dynamic stiffness when probed by indentation-type atomic force microscopy (IT-AFM). In this study, a micrometer-size spherical tip revealed an unimodal stiffness distribution (which we refer to as microstiffness), whereas probing articular cartilage with a nanometer-size pyramidal tip resulted in a bimodal nanostiffness distribution. We concluded that indentation of the cartilage's soft proteoglycan (PG) gel gave rise to the lower nanostiffness peak, whereas deformation of its collagen fibrils yielded the higher nanostiffness peak. To test our hypothesis, we produced a gel-microfiber composite consisting of a chondroitin sulfate-containing agarose gel and a fibrillar poly(ethylene glycol)-terephthalate/poly(butylene)-terephthalate block copolymer. In striking analogy to articular cartilage, the microstiffness distribution of the synthetic composite was unimodal, whereas its nanostiffness exhibited a bimodal distribution. Also, similar to the case with cartilage, addition of the negatively charged chondroitin sulfate rendered the gel-microfiber composite's water content responsive to salt. When the ionic strength of the surrounding buffer solution increased from 0.15 to 2 M NaCl, the cartilage's microstiffness increased by 21%, whereas that of the synthetic biomaterial went up by 31%. When the nanostiffness was measured after the ionic strength was raised by the same amount, the cartilage's lower peak increased by 28%, whereas that of the synthetic biomaterial went up by 34%. Of interest, the higher peak values remained unchanged for both materials. Taken together, these results demonstrate that the nanoscale lower peak is a measure of the soft PG gel, and the nanoscale higher peak measures collagen fibril stiffness. In contrast, the micrometer-scale measurements fail to resolve separate stiffness values for the PG and collagen fibril moieties. Therefore, we propose to use

  9. Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

    PubMed

    Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

    2013-12-19

    To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

  10. Comparative assessment of intrinsic mechanical stimuli on knee cartilage and compressed agarose constructs.

    PubMed

    Completo, A; Bandeiras, C; Fonseca, F

    2017-06-01

    A well-established cue for improving the properties of tissue-engineered cartilage is mechanical stimulation. However, the explicit ranges of mechanical stimuli that correspond to favorable metabolic outcomes are elusive. Usually, these outcomes have only been associated with the applied strain and frequency, an oversimplification that can hide the fundamental relationship between the intrinsic mechanical stimuli and the metabolic outcomes. This highlights two important key issues: the firstly is related to the evaluation of the intrinsic mechanical stimuli of native cartilage; the second, assuming that the intrinsic mechanical stimuli will be important, deals with the ability to replicate them on the tissue-engineered constructs. This study quantifies and compares the volume of cartilage and agarose subjected to a given magnitude range of each intrinsic mechanical stimulus, through a numerical simulation of a patient-specific knee model coupled with experimental data of contact during the stance phase of gait, and agarose constructs under direct-dynamic compression. The results suggest that direct compression loading needs to be parameterized with time-dependence during the initial culture period in order to better reproduce each one of the intrinsic mechanical stimuli developed in the patient-specific cartilage. A loading regime which combines time periods of low compressive strain (5%) and frequency (0.5Hz), in order to approach the maximal principal strain and fluid velocity stimulus of the patient-specific cartilage, with time periods of high compressive strain (20%) and frequency (3Hz), in order to approach the pore pressure values, may be advantageous relatively to a single loading regime throughout the full culture period. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

  11. Silk sericin/polyacrylamide in situ forming hydrogels for dermal reconstruction.

    PubMed

    Kundu, Banani; Kundu, Subhas C

    2012-10-01

    In situ forming tissue sealants are advantageous due to ease in application, complete coverage of defect site and assured comfort levels to patients. The interconnected three-dimensional hydrophilic networks perfectly manage typical dermal wounds by suitably scaffolding skin fibroblast, diffusing the nutrients, therapeutics and exudates while still maintaining an adequately moist environment. We evaluate the cell homing ability of semi-interpenetrating non-mulberry tropical tasar silk sericin/polyacrylamide hydrophilic network with a keen understanding of its network characteristics and correlation of protein concentration with the performance as cell scaffold. Interconnectivity of porous networks observed through scanning electron micrograph revealed pore sizes ranging from 23 to 52 μm. The enhanced β-sheet content with the increasing sericin concentration in far red spectroscopy study supported their corresponding improved compressive strength. These semi-interpenetrating networks were found to possess a maximum fluid uptake of 112% of its weight, hence preventing the accumulation of exudates at the wound area. The present systems appear to possess characteristics like rapid gelation (~5min) at 37 °C, 98% porosity enabling the migration of fibroblasts during healing (observed through confocal and scanning electron micrographs), cell adhesion together with the absence of any cyto-toxic effect suggesting its potential as in situ tissue sealants. The compressive strength up to 61 kPa ensured ease in handling even when wet. The results prove the suitability to use non-mulberry tasar cocoon silk sericin/polyacrylamide semi-interpenetrating network as a reconstructive dermal sealant. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. A gel probe equilibrium sampler for measuring arsenic porewater profiles and sorption gradients in sediments: II. Field application to Haiwee reservoir sediment

    USGS Publications Warehouse

    Campbell, K.M.; Root, R.; O'Day, P. A.; Hering, J.G.

    2008-01-01

    Arsenic (As) geochemistry and sorption behavior were measured in As- and iron (Fe)-rich sediments of Haiwee Reservoir by deploying undoped (clear) polyacrylamide gels and hydrous ferric oxide (HFO)-doped gels in a gel probe equilibrium sampler, which is a novel technique for directly measuring the effects of porewater composition on As adsorption to Fe oxides phases in situ. Arsenic is deposited at the sediment surface as As(V) and is reduced to As(III) in the upper layers of the sediment (0-8 cm), but the reduction of As(V) does not cause mobilization into the porewater. Dissolved As and Fe concentrations increased at depth in the sediment column driven by the reductive dissolution of amorphous Fe(III) oxyhydroxides and conversion to a mixed Fe(II, III) green rust-type phase. Adsorption of As and phosphorous (P) onto HFO-doped gels was inhibited at intermediate depths (10-20 cm), possibly due to dissolved organic or inorganic carbon, indicating that dissolved As concentrations were at least partially controlled by porewater composition rather than surface site availability. In sediments that had been recently exposed to air, the region of sorption inhibition was not observed, suggesting that prior exposure to air affected the extent of reductive dissolution, porewater chemistry, and As adsorption behavior. Arsenic adsorption onto the HFO-doped gels increased at depths >20 cm, and the extent of adsorption was most likely controlled by the competitive effects of dissolved phosphate. Sediment As adsorption capacity appeared to be controlled by changes in porewater composition and competitive effects at shallower depths, and by reductive dissolution and availability of sorption sites at greater burial depths. ?? 2008 American Chemical Society.

  13. Probing the Effects of Templating on the UV and Visible Light Photocatalytic Activity of Porous Nitrogen-Modified Titania Monoliths for Dye Removal.

    PubMed

    Nursam, Natalita M; Wang, Xingdong; Tan, Jeannie Z Y; Caruso, Rachel A

    2016-07-13

    Porous nitrogen-modified titania (N-titania) monoliths with tailored morphologies were prepared using phase separation and agarose gel templating techniques. The doping and templating process were simultaneously carried out in a one-pot step using alcohol amine-assisted sol-gel chemistry. The amount of polymer used in the monoliths that were prepared using phase separation was shown to affect both the physical and optical properties: higher poly(ethylene glycol) content increased the specific surface area, porosity, and visible light absorption of the final materials. For the agarose-templated monoliths, the infiltration conditions affected the monolith morphology. A porous monolith with high surface area and the least shrinkage was obtained when the N containing alkoxide precursor was infiltrated into the agarose scaffolds at 60 °C. The effect of the diverse porous morphologies on the photocatalytic activity of N-titania was studied for the decomposition of methylene blue (MB) under visible and UV light irradiation. The highest visible light activity was achieved by the agarose-templated N-titania monolith, in part due to higher N incorporation. This sample also showed better UV activity, partly because of the higher specific surface area (up to 112 m(2) g(-1)) compared to the phase separation-induced monoliths (up to 103 m(2) g(-1)). Overall, agarose-templated, porous N-titania monoliths provided better features for effectively removing the MB contaminant.

  14. Protein Stains to Detect Antigen on Membranes.

    PubMed

    Dsouza, Anil; Scofield, R Hal

    2015-01-01

    Western blotting (protein blotting/electroblotting) is the gold standard in the analysis of complex protein mixtures. Electroblotting drives protein molecules from a polyacrylamide (or less commonly, of an agarose) gel to the surface of a binding membrane, thereby facilitating an increased availability of the sites with affinity for both general and specific protein reagents. The analysis of these complex protein mixtures is achieved by the detection of specific protein bands on a membrane, which in turn is made possible by the visualization of protein bands either by chemical staining or by reaction with an antibody of a conjugated ligand. Chemical methods employ staining with organic dyes, metal chelates, autoradiography, fluorescent dyes, complexing with silver, or prelabeling with fluorophores. All of these methods have differing sensitivities and quantitative determinations vary significantly. This review will describe the various protein staining methods applied to membranes after western blotting. "Detection" precedes and is a prerequisite to obtaining qualitative and quantitative data on the proteins in a sample, as much as to comparing the protein composition of different samples. "Detection" is often synonymous to staining, i.e., the reversible or irreversible binding by the proteins of a colored organic or inorganic chemical.

  15. PCR synthesis of double stranded DNA labeled with 5-bromouridine. A step towards finding a bromonucleoside for clinical trials.

    PubMed

    Michalska, Barbara; Sobolewski, Ireneusz; Polska, Katarzyna; Zielonka, Justyna; Zylicz-Stachula, Agnieszka; Skowron, Piotr; Rak, Janusz

    2011-12-05

    Incorporation of 5-bromouridine (5BrdU) into DNA makes it sensitive to UV and ionizing radiation, which opens up a prospective route for the clinical usage of 5-bromouridine and other halonucleosides. In the present work the polymerase chain reaction (PCR) protocol, which enables a long DNA fragment (resembling DNA synthesized in the cell in the presence of halonucleosides) to be completely substituted with 5BrdU, was optimized. Using HPLC coupled to enzymatic digestion, it was demonstrated that the actual amounts of native nucleosides and 5BrdU correspond very well to those calculated from the sequence of PCR products. The synthesized DNA is photosensitive to photons of 300nm. HPLC analysis demonstrated that the photolysis of labeled PCR products leads to a significant decrease in the 5BrdU signal and the simultaneous occurrence of a uridine peak. Agarose and polyacrylamide gel electrophoresis suggest that single strand breaks and cross-links are formed as a result of UV irradiation. The PCR protocol described in the current paper may be employed for labeling DNA not only with BrdU but also with other halonucleosides. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Protein stains to detect antigen on membranes.

    PubMed

    D'souza, Anil; Scofield, R Hal

    2009-01-01

    Western blotting (protein blotting/electroblotting) is the gold standard in the analysis of complex protein mixtures. Electroblotting drives protein molecules from a polyacrylamide (or less commonly, of an agarose) gel to the surface of a binding membrane, thereby facilitating an increased availability of the sites with affinity for both general and specific protein reagents. The analysis of these complex protein mixtures is achieved by the detection of specific protein bands on a membrane, which in turn is made possible by the visualization of protein bands either by chemical staining or by reaction with an antibody of a conjugated ligand. Chemical methods employ staining with organic dyes, metal chelates, autoradiography, fluorescent dyes, complexing with silver, or prelabeling with fluorophores. All of these methods have differing sensitivities and quantitative determinations vary significantly. This review will describe the various protein staining methods applied to membranes after electrophoresis. "Detection" precedes and is a prerequisite to obtaining qualitative and quantitative data on the proteins in a sample, as much as to comparing the protein composition of different samples. Detection is often synonymous to staining, i.e., the reversible or irreversible binding by the proteins of a colored organic or inorganic chemical.

  17. [Effects of polyacrylamide on settling and separation of oil droplets in polymer flooding produced water].

    PubMed

    Deng, Shubo; Zhou, Fusheng; Chen, Zhongxi; Xia, Fujun; Yu, Gang; Jiang, Zhanpeng

    2002-03-01

    The research found anion polyacrylamide (HPAM) had positive and negative effects on oil-water separation. Polymer made oily wastewater's viscosity increase and reduce rising velocity, and polymer can also increase intensity of water films between oil droplets and lengthen coalescence time of oil droplets. Those were not in favor of settling and separation for oil droplets. The positive effects on separation were that polyacrylamide had flocculating activity and made small droplets contact each other and combine into big droplets. When polymer's molecular weight was 2.72 x 10(6), and concentration was less than 800 mg/L, polymer was in favor of oil droplets settling and separation. The prime reason for oily wastewater of polymer flooding difficult to dispose was that initial median diameters of oil droplets were small. The transverse flow oil separator can intensify oil droplets combination and shorten rising time. The locale experiments showed the separator was suitable for dealing with oily wastewater of polymer flooding.

  18. Lipoprotein Agarose Gel Electrophoresis. Application in HDL-Cholesterol Methodology.

    DTIC Science & Technology

    1985-06-01

    on determination of high-density lipo- protein cholesterol by precipitation with sodium phosphotungstate- magnesium. Clin Chem 25(4):560 (1979). 6...determinations of cholesterol levels in supernates obtained after addition of various amounts of precipitants , lipo- protein electrophoresis can help to...plotted against the corresponding volumes of sodium phosphotungstate-MgCl2 (NAPT) precipitant added. 10 ’ ’’ ’i - n

  19. Monte-Carlo based assessment of MAGIC, MAGICAUG, PAGATUG and PAGATAUG polymer gel dosimeters for ovaries and uterus organ dosimetry in brachytherapy, nuclear medicine and Tele-therapy.

    PubMed

    Adinehvand, Karim; Rahatabad, Fereidoun Nowshiravan

    2018-06-01

    Calculation of 3D dose distribution during radiotherapy and nuclear medicine helps us for better treatment of sensitive organs such as ovaries and uterus. In this research, we investigate two groups of normoxic dosimeters based on meta-acrylic acid (MAGIC and MAGICAUG) and polyacrylamide (PAGATUG and PAGATAUG) for brachytherapy, nuclear medicine and Tele-therapy in their sensitive and critical role as organ dosimeters. These polymer gel dosimeters are compared with soft tissue while irradiated by different energy photons in therapeutic applications. This comparison has been simulated by Monte-Carlo based MCNPX code. ORNL phantom-Female has been used to model the critical organs of kidneys, ovaries and uterus. Right kidney is proposed to be the source of irradiation and another two organs are exposed to this irradiation. Effective atomic numbers of soft tissue, MAGIC, MAGICAUG, PAGATUG and PAGATAUG are 6.86, 7.07, 6.95, 7.28, and 7.07 respectively. Results show the polymer gel dosimeters are comparable to soft tissue for using in nuclear medicine and Tele-therapy. Differences between gel dosimeters and soft tissue are defined as the dose responses. This difference is less than 4.1%, 22.6% and 71.9% for Tele-therapy, nuclear medicine and brachytherapy respectively. The results approved that gel dosimeters are the best choice for ovaries and uterus in nuclear medicine and Tele-therapy respectively. Due to the slight difference between the effective atomic numbers of these polymer gel dosimeters and soft tissue, these polymer gels are not suitable for brachytherapy since the dependence of photon interaction to atomic number, for low energy brachytherapy, had been so effective. Also this dependence to atomic number, decrease for photoelectric and increase for Compton. Therefore polymer gel dosimeters are not a good alternative to soft tissue replacement in brachytherapy. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Ribosomal RNA maturation in Schizosaccharomyces pombe is dependent on a large ribonucleoprotein complex of the internal transcribed spacer 1.

    PubMed

    Lalev, A I; Abeyrathne, P D; Nazar, R N

    2000-09-08

    The interdependency of steps in the processing of pre-rRNA in Schizosaccharomyces pombe suggests that RNA processing, at least in part, acts as a quality control mechanism which helps assure that only functional RNA is incorporated into mature ribosomes. To determine further the role of the transcribed spacer regions in rRNA processing and to detect interactions which underlie the interdependencies, the ITS1 sequence was examined for its ability to form ribonucleoprotein complexes with cellular proteins. When incubated with protein extract, the spacer formed a specific large RNP. This complex was stable to fractionation by agarose or polyacrylamide gel electrophoresis. Modification exclusion analyses indicated that the proteins interact with a helical domain which is conserved in the internal transcribed spacers. Mutagenic analyses confirmed an interaction with this sequence and indicated that this domain is critical to the efficient maturation of the precursor RNA. The protein constituents, purified by affinity chromatography using the ITS1 sequence, retained an ability to form stable RNP. Protein analyses of gel purified complex, prepared with affinity-purified proteins, indicated at least 20 protein components ranging in size from 20-200 kDa. Peptide mapping by Maldi-Toff mass spectroscopy identified eight hypothetical RNA binding proteins which included four different RNA-binding motifs. Another protein was putatively identified as a pseudouridylate synthase. Additional RNA constituents were not detected. The significance of this complex with respect to rRNA maturation and interdependence in rRNA processing is discussed. Copyright 2000 Academic Press.

  1. Removal of Polyacrylamide Gel (Aquamid®) from the Lip as a Solution for Late-Onset Complications: Our 8-Year Experience.

    PubMed

    Kästner, Sonja; Gonser, Phillipp; Paprottka, Felix; Kaye, Kai O

    2018-06-01

    The polyacrylamide hydrogel Aquamid ® has been used as a permanent filler to enhance facial soft tissue volume and correct wrinkles since 2001. Various long-term studies have proved the safety of the product. Nonetheless, if complications such as migration occur, they can be difficult to treat. Eleven patients suffering from late-onset complications after taking Aquamid ® injections in the lips underwent product removal and subsequent labial reconstruction between 2009 and 2017. The reconstruction was performed using a modified bikini reduction technique combined, in eight cases, with immediate autologous fat grafting. In all the patients, general fibrosis and a diffused distribution of the product within all three layers of the lips resulted in the need for labial reconstruction. Migration, as far as in the mucosa and perioral skin, accounted for macroscopically visible yellowish accumulations. In ten out of eleven cases, an individually modified bikini reduction technique, with or without any combination of autologous fat grafting, led to an esthetically satisfying result. One patient developed a severe upper lip necrosis. Contradictory to several previous studies attesting to the lack of migration after Aquamid ® application to the lips, capsule formation around the product is impaired, allowing for migration even years after the injection. Product aspiration is not possible in these cases, thus necessitating complex lip reconstruction. Bikini reduction and fat grafting are valuable tools for labial reconstruction. Product residuals within the mucosa have to be accepted. Special care has to be taken while treating smokers. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  2. Salivary proteins and early childhood caries: A gel electrophoretic analysis

    PubMed Central

    Bhalla, Sumati; Tandon, Shobha; Satyamoorthy, K.

    2010-01-01

    Background: Early childhood caries (ECC) is a common disease process that afflicts a large proportion of the child population worldwide. Extensive research in past indicates that it is the result of bacterial infection, also influenced by host and dietary factors. Current caries research seeks to identify risk factors as well as natural oral defenses that may protect against or prevent caries development. Saliva, in spite of being the strongest defense system, still has a wide array of properties and proteins whose role is yet not clearly known. Aim: To compare the resting human whole salivary characteristics in children with ECC and those who are caries free. Settings and Design: The study was conducted over a period of 9 months in 4- to 6-year-old 100 children comprising two groups – 50 with ECC and 50 caries free. Materials and Methods: The whole salivary flow rate, pH, mean protein concentration, and the electrophoretic profile of salivary proteins by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) were compared among both groups. Statistical Analysis: The SPSS (version 11.0) software package was used to conduct the chi-square, Fisher's exact and Pearson's chi-square tests to compare the data. Results: On gel electrophoresis, there was a significant difference among both groups with caries-free subjects having a higher number of proline-rich protein bands, substantiating the protective role of this protein. A significantly higher number of glycoprotein bands were observed in the whole saliva of subjects with ECC. A significant inverse correlation between the mean protein concentration and the whole salivary flow rate was observed in both groups. PMID:22114372

  3. A comparison of fibrin, agarose and gellan gum hydrogels as carriers of stem cells and growth factor delivery microspheres for cartilage regeneration.

    PubMed

    Ahearne, Mark; Kelly, Daniel J

    2013-06-01

    The limited intrinsic repair capacity of articular cartilage has led to the investigation of different treatment options to promote its regeneration. The delivery of hydrogels containing stem or progenitor cells and growth factor releasing microspheres represents an attractive approach to cartilage repair. In this study, the influence of the encapsulating hydrogel on the ability of progenitor cells coupled with TGF-β3 releasing microspheres to form cartilaginous tissue was investigated. Fibrin, agarose and gellan gum hydrogels containing TGF-β3 loaded gelatin microspheres and progenitor cells derived from the infrapatellar fat-pad of the knee were cultured for 21 days in a chemically defined media. In the presence of TGF-β3 releasing microspheres, gellan gum hydrogels were observed to facilitate greater cell proliferation than fibrin or agarose hydrogels. Histological and biochemical analysis of the hydrogels indicated that fibrin was the least chondro-inductive of the three hydrogels, while agarose and gellan gum appeared to support more robust cartilage formation as demonstrated by greater sGAG accumulation within these constructs. Gellan gum hydrogels also stained more intensely for collagen type II and collagen type I, suggesting that although total collagen synthesis was higher in these constructs, that the phenotype may be more fibrocartilaginous in nature than normal hyaline cartilage. This study demonstrates how the encapsulating hydrogel can have a significant impact on the ability of stem cells to form cartilage when incorporated into a growth factor delivery system.

  4. Sol-Gel Glasses

    NASA Technical Reports Server (NTRS)

    Mukherjee, S. P.

    1985-01-01

    Multicomponent homogeneous, ultrapure noncrystalline gels/gel derived glasses are promising batch materials for the containerless glass melting experiments in microgravity. Hence, ultrapure, homogeneous gel precursors could be used to: (1) investigate the effect of the container induced nucleation on the glass forming ability of marginally glass forming compositions; and (2) investigate the influence of gravity on the phase separation and coarsening behavior of gel derived glasses in the liquid-liquid immiscibility zone of the nonsilicate systems having a high density phase. The structure and crystallization behavior of gels in the SiO2-GeO2 as a function of gel chemistry and thermal treatment were investigated. As are the chemical principles involved in the distribution of a second network former in silica gel matrix being investigated. The procedures for synthesizing noncrystalline gels/gel-monoliths in the SiO2-GeO2, GeO2-PbO systems were developed. Preliminary investigations on the levitation and thermal treatment of germania silicate gel-monoliths in the Pressure Facility Acoustic Levitator were done.

  5. From the Macro to the Micro: Gel Mapping to Differentiate between Sporozoites of Two Immunologically Distinct Strains of Eimeria maxima (Strains M6 and Guelph)

    PubMed Central

    Liu, Hongbin; Al Nasr, Ibrahim; Liu, Xianyong; Suo, Xun; Barta, John

    2015-01-01

    Two immunologically distinct strains of E. maxima were examined in this study: the M6 strain and the Guelph strain. The differential expression between the sporozoites of the two strains of E. maxima was determined by image analysis of 100 μg of protein from each strain separated by standard one- and conventional two-dimensional polyacrylamide gel electrophoresis. In addition to differences in both molecular weight and the electrophoretic mobility, differences in the intensity of polypeptide bands for example, GS 136.4 and M6 169 were explored. Pooled gels were prepared from each strain. A representative 2D-PAGE gel spanning a non-linear pH range of 3–10 of E. maxima strain M6 consisted of approximately 694 polypeptide spots with about 67 (9.6%) of the polypeptide spots being unique relative to the other strain. E. maxima strain GS had about 696 discernable polypeptide spots with 69 spots (9.9%) that differed from those of the M6 strain. In-depth characterization of the variable polypeptide spots; unique polypeptide spots (absence or presence) and shared polypeptide spots with modifications may lead to novel vaccine target in the form of multi-component, multi-stage, multi-immunovariant strains, multi-species subunit vaccine, and diagnostic probe for E. maxima. PMID:26641262

  6. From the Macro to the Micro: Gel Mapping to Differentiate between Sporozoites of Two Immunologically Distinct Strains of Eimeria maxima (Strains M6 and Guelph).

    PubMed

    El-Ashram, Saeed; Yin, Qing; Liu, Hongbin; Al Nasr, Ibrahim; Liu, Xianyong; Suo, Xun; Barta, John

    2015-01-01

    Two immunologically distinct strains of E. maxima were examined in this study: the M6 strain and the Guelph strain. The differential expression between the sporozoites of the two strains of E. maxima was determined by image analysis of 100 μg of protein from each strain separated by standard one- and conventional two-dimensional polyacrylamide gel electrophoresis. In addition to differences in both molecular weight and the electrophoretic mobility, differences in the intensity of polypeptide bands for example, GS 136.4 and M6 169 were explored. Pooled gels were prepared from each strain. A representative 2D-PAGE gel spanning a non-linear pH range of 3-10 of E. maxima strain M6 consisted of approximately 694 polypeptide spots with about 67 (9.6%) of the polypeptide spots being unique relative to the other strain. E. maxima strain GS had about 696 discernable polypeptide spots with 69 spots (9.9%) that differed from those of the M6 strain. In-depth characterization of the variable polypeptide spots; unique polypeptide spots (absence or presence) and shared polypeptide spots with modifications may lead to novel vaccine target in the form of multi-component, multi-stage, multi-immunovariant strains, multi-species subunit vaccine, and diagnostic probe for E. maxima.

  7. Microplate array diagonal gel electrophoresis (MADGE), CpG-PCR and temporal thermal ramp-MADGE (Melt-MADGE) for single nucleotide analyses in populations.

    PubMed

    Day, I N; O'Dell, S D; Spanakis, E; Weavind, G P

    1999-02-01

    Important requirements for molecular genetic epidemiological studies are economy, sample parallelism, convenience of setup and accessibility, goals inadequately met by existent approaches. We invented microplate array diagonal gel electrophoresis (MADGE) to gain simultaneously the advantages of simple setup, 96-well microplate compatibility, horizontal electrophoresis, and the resolution of polyacrylamide. At essentially no equipment cost (one simple plastic gel former), 10-100-fold savings on time for sample coding, liquid transfers, and data documentation, in addition to volume reductions and gel re-use, can be achieved. MADGE is compatible with ARMS, restriction analysis and other pattern analyses. CpG-PCR is a general PCR approach to CpG sites (10-20% of all human single base variation): both primers have 3' T, and are abutted to the CpG, forcing a TaqI restriction site if the CpG is intact. Typically, a 52 bp PCR product is then cut in half. CpG-PCR also illustrates that PAGE-MADGE readily permits analysis of 'ultrashort' PCRs. Melt-MADGE employs real-time-variable-temperature electrophoresis to examine duplex mobility during melting, achieving DGGE-like de novo, mutation scanning, but with the conveniences of arbitrary programmability, MADGE compatibility and short run time. This suite of methods enhances our capability to type or scan thousands of samples simultaneously, by 10-100-fold.

  8. Hindered diffusion of high molecular weight compounds in brain extracellular microenvironment measured with integrative optical imaging.

    PubMed

    Nicholson, C; Tao, L

    1993-12-01

    This paper describes the theory of an integrative optical imaging system and its application to the analysis of the diffusion of 3-, 10-, 40-, and 70-kDa fluorescent dextran molecules in agarose gel and brain extracellular microenvironment. The method uses a precisely defined source of fluorescent molecules pressure ejected from a micropipette, and a detailed theory of the intensity contributions from out-of-focus molecules in a three-dimensional medium to a two-dimensional image. Dextrans tagged with either tetramethylrhodamine or Texas Red were ejected into 0.3% agarose gel or rat cortical slices maintained in a perfused chamber at 34 degrees C and imaged using a compound epifluorescent microscope with a 10 x water-immersion objective. About 20 images were taken at 2-10-s intervals, recorded with a cooled CCD camera, then transferred to a 486 PC for quantitative analysis. The diffusion coefficient in agarose gel, D, and the apparent diffusion coefficient, D*, in brain tissue were determined by fitting an integral expression relating the measured two-dimensional image intensity to the theoretical three-dimensional dextran concentration. The measurements in dilute agarose gel provided a reference value of D and validated the method. Values of the tortuosity, lambda = (D/D*)1/2, for the 3- and 10-kDa dextrans were 1.70 and 1.63, respectively, which were consistent with previous values derived from tetramethylammonium measurements in cortex. Tortuosities for the 40- and 70-kDa dextrans had significantly larger values of 2.16 and 2.25, respectively. This suggests that the extracellular space may have local constrictions that hinder the diffusion of molecules above a critical size that lies in the range of many neurotrophic compounds.

  9. Tolerability of clindamycin/tretinoin gel vs. tretinoin microsphere gel and adapalene gel.

    PubMed

    Leyden, James; Wortzman, Mitchell; Baldwin, Edward K

    2009-04-01

    Newer agents and formulations seek to improve the tolerability of topical retinoid therapy. Recently, a gel containing crystalline clindamycin 1.2% and tretinoin 0.025% (CLIN/RA) was approved by the U.S. Food and Drug Administration (FDA) for the treatment of treating mild-to-moderate acne. This single-center, randomized, evaluator-blind phase 1 study compared the tolerability of CLIN/RA to 0.1% tretinoin gel or 0.1% adapalene gel. Forty-five patients applied CLIN/RA once daily to one side of their face every day for 21 days. Patients were randomized to either tretinoin 0.1% (n = 23) or adapalene 0.1% (n = 22) on the contralateral side. A clinical evaluator assessed degree of erythema and scaling; patients provided subjective evaluations of burning, stinging, and itching. CLIN/RA was significantly better tolerated than was 0.1% tretinoin gel, as evidenced by significantly reduced erythema (P < 0.04), scaling (P < 0.03), itching (P < 0.02), burning (P < 0.03) and stinging (P < 0.04). A trend for greater erythema, scaling, and subjective discomfort for 0.1% adapalene gel compared to CLIN/RA was also evident.

  10. Spectrophotometric determination of substrate-borne polyacrylamide.

    PubMed

    Lu, Jianhang; Wu, Laosheng

    2002-08-28

    Polyacrylamides (PAMs) have wide application in many industries and in agriculture. Scientific research and industrial applications manifested a need for a method that can quantify substrate-borne PAM. The N-bromination method (a PAM analytical technique based on N-bromination of amide groups and spectrophotometric determination of the formed starch-triiodide complex), which was originally developed for determining PAM in aqueous solutions, was modified to quantify substrate-borne PAM. In the modified method, the quantity of substrate-borne PAM was converted to a concentration of starch-triiodide complex in aqueous solution that was then measured by spectrophotometry. The method sensitivity varied with substrates due to sorption of reagents and reaction intermediates on the substrates. Therefore, separate calibration for each substrate was required. Results from PAM samples in sand, cellulose, organic matter burnt soils, and clay minerals showed that this method had good accuracy and reproducibility. The PAM recoveries ranged from 95.8% to 103.7%, and the relative standard deviations (n = 4) were <7.5% in all cases. The optimum range of PAM in each sample is 10-80 microg. The technique can serve as an effective tool in improving PAM application and facilitating PAM-related research.

  11. Molecular Epidemiology of Mycobacterium tuberculosis Isolates in 100 Patients With Tuberculosis Using Pulsed Field Gel Electrophoresis

    PubMed Central

    Pooideh, Mohammad; Jabbarzadeh, Ismail; Ranjbar, Reza; Saifi, Mahnaz

    2015-01-01

    Background: Tuberculosis (TB) is a widespread infectious disease. Today, TB has created a public health crisis in the world. Genotyping of Mycobacterium tuberculosis isolates is useful for surveying the dynamics of TB infection, identifying new outbreaks, and preventing the disease. Different molecular methods for clustering of M. tuberculosis isolates have been used. Objectives: During a one year study of genotyping, 100 M. tuberculosis isolates from patients referred to Pasteur Institute of Iran were collected and their genotyping was accomplished using pulsed field gel electrophoresis (PFGE) method. Materials and Methods: Identification of all M. tuberculosis isolates was accomplished using standard biochemical and species-specific polymerase chain reaction (PCR) methods. Antibiotic susceptibility tests were performed using proportional method. After preparing PFGE plaques for each isolate of M. tuberculosis, XbaI restriction enzyme was applied for genome digestion. Finally, the digested DNA fragments were separated on 1% agarose gel and analyzed with GelCompar II software. Results: Genotyping of the studied isolates in comparison with the molecular weight marker revealed two common types; pulsotype A with 71 isolates and one multidrug resistant mycobacterium (MDR) case, and pulsotype B including 29 isolates and three MDR cases. No correlation between the antibiotypes and pulsotypes was observed. Conclusions: Molecular epidemiology studies of infectious diseases have been useful when bacterial isolates have been clustered in a period of time and in different geographical regions with variable antibiotic resistance patterns. In spite of high geographical differences and different antibiotic resistant patterns, low genetic diversity among the studied TB isolates may refer to the low rate of mutations in XbaI restriction sites in the mycobacterial genome. We also identified three MDR isolates in low-incidence pulsotype B, which could be disseminated and is highly

  12. The detection and differentiation of canine respiratory pathogens using oligonucleotide microarrays.

    PubMed

    Wang, Lih-Chiann; Kuo, Ya-Ting; Chueh, Ling-Ling; Huang, Dean; Lin, Jiunn-Horng

    2017-05-01

    Canine respiratory diseases are commonly seen in dogs along with co-infections with multiple respiratory pathogens, including viruses and bacteria. Virus infections in even vaccinated dogs were also reported. The clinical signs caused by different respiratory etiological agents are similar, which makes differential diagnosis imperative. An oligonucleotide microarray system was developed in this study. The wild type and vaccine strains of canine distemper virus (CDV), influenza virus, canine herpesvirus (CHV), Bordetella bronchiseptica and Mycoplasma cynos were detected and differentiated simultaneously on a microarray chip. The detection limit is 10, 10, 100, 50 and 50 copy numbers for CDV, influenza virus, CHV, B. bronchiseptica and M. cynos, respectively. The clinical test results of nasal swab samples showed that the microarray had remarkably better efficacy than the multiplex PCR-agarose gel method. The positive detection rate of microarray and agarose gel was 59.0% (n=33) and 41.1% (n=23) among the 56 samples, respectively. CDV vaccine strain and pathogen co-infections were further demonstrated by the microarray but not by the multiplex PCR-agarose gel. The oligonucleotide microarray provides a highly efficient diagnosis alternative that could be applied to clinical usage, greatly assisting in disease therapy and control. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Towards more realistic in vitro release measurement techniques for biodegradable microparticles.

    PubMed

    Klose, D; Azaroual, N; Siepmann, F; Vermeersch, G; Siepmann, J

    2009-03-01

    To better understand the importance of the environmental conditions for drug release from biodegradable microparticles allowing for the development of more appropriate in vitro release measurement techniques. Propranolol HCl diffusion in various agarose gels was characterized by NMR and UV analysis. Fick's law was used to theoretically predict the mass transport kinetics. Drug release from PLGA-based microparticles in such agarose gels was compared to that measured in agitated bulk fluids ("standard" method). NMR analysis revealed that the drug diffusivity was almost independent of the hydrogel concentration, despite of the significant differences in the systems' mechanical properties. This is due to the small size of the drug molecules/ions with respect to the hydrogel mesh size. Interestingly, the theoretically predicted drug concentration-distance-profiles could be confirmed by independent experiments. Most important from a practical point of view, significant differences in the release rates from the same batch of PLGA-based microparticles into a well agitated bulk fluid versus a semi-solid agarose gel were observed. Great care must be taken when defining the in vitro conditions for drug release measurements from biodegradable microparticles. The obtained new insight can help facilitating the development of more appropriate in vitro release testing procedures.

  14. Anaerobic biodegradation of partially hydrolyzed polyacrylamide in long-term methanogenic enrichment cultures from production water of oil reservoirs.

    PubMed

    Hu, Hao; Liu, Jin-Feng; Li, Cai-Yun; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2018-06-01

    The increasing usage of partially hydrolyzed polyacrylamide (HPAM) in oilfields as a flooding agent to enhance oil recovery at so large quantities is an ecological hazard to the subsurface ecosystem due to persistence and inertness. Biodegradation of HPAM is a potentially promising strategy for dealing with this problem among many other methods available. To understand the responsible microorganisms and mechanism of HPAM biodegradation under anaerobic conditions, an enrichment culture from production waters of oil reservoirs were established with HPAM as the sole source of carbon and nitrogen incubated for over 328 days, and analyzed using both molecular microbiology and chemical characterization methods. Gel permeation chromatography, High-pressure liquid chromatography and Fourier-transformed infrared spectroscopy results indicated that, after 328 days of anaerobic incubation, some of the amide groups on HPAM were removed and released as ammonia/ammonium and carboxylic groups, while the carbon backbone of HPAM was converted to smaller polymeric fragments, including oligomers and various fatty acids. Based on these results, the biochemical process of anaerobic biodegradation of HPAM was proposed. The phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichments showed that Proteobacteria and Planctomycetes were the dominant bacteria in the culture with HPAM as the source of carbon and nitrogen, respectively. For archaea, Methanofollis was more abundant in the anaerobic enrichment. These results are helpful for understanding the process of HPAM biodegradation and provide significant insights to the fate of HPAM in subsurface environment and for possible bioremediation.

  15. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

    PubMed

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2010-09-01

    The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

  16. Equivalent of a cartilage tissue for simulations of laser-induced temperature fields

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kondyurin, A V; Sviridov, A P

    2008-07-31

    The thermal and optical properties of polyacrylamide hydrogels and cartilages are studied by the method of IR laser radiometry. The thermal diffusivity, heat capacity, and the effective absorption coefficient at a wavelength of 1.56 {mu}m measured for polyacrylamide gel with 70% water content and the degree of cross-linking 1:9 and for the nasal septum cartilage proved to be close. This allows the use of polyacrylamide hydrogels as equivalents of cartilages in simulations of laser-induced temperature fields. (biophotonics)

  17. Effects of polyacrylamide on soil erosion and nutrient losses from substrate material in steep rocky slope stabilization projects.

    PubMed

    Chen, Zhang; Chen, Wenlu; Li, Chengjun; Pu, Yanpin; Sun, Haifeng

    2016-06-01

    Erosion of denuded steep rocky slopes causes increasing losses of nitrogen and phosphorus, which is a severe problem in rocky slope protection. Thus, it is important to determine the appropriate materials that can reduce the erodibility and losses of nitrogen and phosphorus of the soil. In this paper, twenty-seven simulated rainfall events were carried out in a greenhouse, in which the substrate material was artificial soil; nine types of anionic polyacrylamide (PAM) were studied, which consisted of three molecular weight (6, 12, and 18 Mg mol(-1)) and three charge density (10, 20, and 30%) formulations in a 3 by 3 factorial design. The results showed that: (1) Polyacrylamide application reduced total nitrogen losses by 35.3% to 50.0% and total phosphorus losses by 34.9% to 48.0% relative to the control group. (2) The losses of total nitrogen and total phosphorus had significant correlation with the molecular weight. Besides, the losses of total phosphorus, particulate-bound phosphorus and inorganic nitrogen (NH4-N) were significantly correlated with their molecular weight and charge density. However, the losses of dissolved organic nitrogen, inorganic nitrogen (NO3-N), dissolved organic phosphorus, inorganic phosphorus (PO4-P) were non-significantly correlated with molecular weight and charge density. (3) Particulate-bound nitrogen and phosphorus were responsible for the losses of nitrogen and phosphorus during runoff events, where particulate-bound nitrogen made up 71.7% to 73.2% of total nitrogen losses, and particulate-bound phosphorus made up 82.3% to 85.2% of total phosphorus losses. (4) Polyacrylamide treatments increased water-stable aggregates content by 32.3% to 59.1%, total porosity by 11.3% to 49.0%, final infiltrative rate by 41.3% to 72.5%, and reduced soil erosion by 18.9% to 39.8% compared with the control group. Overall, the results of this study indicated that polyacrylamide application in the steep rocky slope stabilization projects could

  18. The isolation and characterisation of jacalin [Artocarpus heterophyllus (jackfruit) lectin] based on its charge properties.

    PubMed

    Kabir, S

    1995-02-01

    Jackfruit extracts contain a protein termed jacalin which possesses diverse biological properties. A detailed analysis of its charge properties has been lacking. The present investigation was initiated to study isoelectric properties of jacalin in detail and to isolate a single isoform of jacalin. Jacalin was isolated from jackfruit extracts by affinity chromatography on immunoglobulin-A immobilised to Sepharose 4B. Various techniques such as ion-exchange chromatography, isoelectric focusing (IEF) on polyacrylamide gels and preparative liquid IEF with the Rotofor cell were used. When analysed by IEF on thin layer polyacrylamide gels, jacalin was resolved into 35 bands over a pH range of 5.0-8.5. Upon SDS-PAGE in the second dimension all these charge species gave rise to only two-bands at 12 and 15.4 kDa. The lectin was mostly eluted with 50 and 100 mM sodium chloride when jackfruit extracts were fractionated on an anion-exchange column of DEAE-cellulose. In a single 6 hour run by preparative IEF with the Rotofor cell in the pH range of 3-9.5, it has been possible to isolate pure jacalin fractions containing fewer number of charged isomers. A single jacalin isoform was isolated by subjecting a Rotofor fraction containing fewer charged species to preparative IEF on thin layer polyacrylamide gel and eluting the band of interest from the gel. The isolated jacalin isoform was biologically active as it agglutinated erythrocytes. The study reveals the complexity of jacalin as it exists as multiple charge isomers over a broad pH range. By performing preparative IEF in solution as well as in thin layer polyacrylamide gels, it was possible to isolate a single jacalin isoform with the retention of biological activity.

  19. Pattern transition between periodic Liesegang pattern and crystal growth regime in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Lagzi, István; Ueyama, Daishin

    2009-01-01

    The pattern transition between periodic precipitation pattern formation (Liesegang phenomenon) and pure crystal growth regimes is investigated in silver nitrate and potassium dichromate system in mixed agarose-gelatin gel. Morphologically different patterns were found depending on the quality of the gel, and transition between these typical patterns can be controlled by the concentration of gelatin in mixed gel. Effect of temperature and hydrodynamic force on precipitation pattern structure was also investigated.

  20. Delivery of DNA vaccines by agarose hydrogel implants facilitates genetic immunization in cattle.

    PubMed

    Toussaint, J F; Dubois, A; Dispas, M; Paquet, D; Letellier, C; Kerkhofs, P

    2007-01-26

    The present study demonstrates the interest of two slow-release systems as vaccination tools in cattle. Two experiments show that a first intradermal administration of one DNA vaccine dose combined with the slow-release of a second dose conduct to a priming of the bovine herpesvirus 1-specific immune response similar to the one generated by two discrete administrations 4 weeks apart. The first experiment demonstrates the efficacy of the slow-release system with well-characterized Alzet osmotic pumps, whereas the second experiment extends the same concept with innovative agarose hydrogel implants. These latter implants are cheaper and more convenient than the osmotic pumps or repeated intradermal administrations since they contribute to an efficient priming of the immune response in a single manipulation of the animals.

  1. Initial Characterization of a Gel Patch Dosimeter for In Vivo Dosimetry

    PubMed Central

    Matrosic, C; Culberson, W; Rosen, B; Madsen, E; Frank, G; Bednarz, B

    2016-01-01

    In vivo dosimetry is a greatly underutilized tool for patient safety in clinical external beam radiotherapy treatments, despite being recommended by several national and international organizations (AAPM, ICRU, IAEA, NACP). The reasons for this underutilization mostly relate to the feasibility and cost of in vivo dosimetry methods. Due to the increase in the number of beam angles and dose per fraction in modern treatments, there is a compelling need for a novel dosimeter that is robust and affordable while able to operate properly in these complex conditions. This work presents a gel patch dosimeter as a novel method of in vivo dosimetry. DEFGEL, a 6%T normoxic polyacrylamide gel, was injected into 1-cm thick acrylic molds to create 1-cm thick small cylindrical patch dosimeters. To evaluate the change in optical density due to radiation induced polymerization, dosimeters were scanned before and after irradiation using an in-house developed laser densitometer. The dose-responses of three separate batches of gel were evaluated and compared to check for linearity and repeatability. The response development time was evaluated to ensure that the patch dosimeter could be high throughput. Additionally, the potential of this system to be used as an in vivo dosimeter was tested with a clinically relevant end-to-end in vivo phantom test. All irradiations were performed with a Varian Clinac 21EX at the University of Wisconsin Medical Radiation Research Center (UWMRRC). The dose response of all three batches of gel was found to be linear within the range of 2–20 Gy. At doses below 0.5 Gy the statistical uncertainties were prohibitively large to make quantitative assessments of the results. The three batches demonstrated good repeatability in the range of 2 Gy to up to 10 Gy, with only slight variations in response at higher doses. For low doses the dosimeter fully developed within an hour while at higher doses they fully developed within four hours. During the in vivo

  2. Initial characterization of a gel patch dosimeter for in vivo dosimetry

    NASA Astrophysics Data System (ADS)

    Matrosic, C.; Culberson, W.; Rosen, B.; Madsen, E.; Frank, G.; Bednarz, B.

    2016-05-01

    In vivo dosimetry is a greatly underutilized tool for patient safety in clinical external beam radiotherapy treatments, despite being recommended by several national and international organizations (AAPM, ICRU, IAEA, NACP). The reasons for this underutilization mostly relate to the feasibility and cost of in vivo dosimetry methods. Due to the increase in the number of beam angles and dose per fraction in modern treatments, there is a compelling need for a novel dosimeter that is robust and affordable while able to operate properly in these complex conditions. This work presents a gel patch dosimeter as a novel method of in vivo dosimetry. DEFGEL, a 6% T normoxic polyacrylamide gel, was injected into 1 cm thick acrylic molds to create 1 cm thick small cylindrical patch dosimeters. To evaluate the change in optical density due to radiation induced polymerization, dosimeters were scanned before and after irradiation using an in-house developed laser densitometer. The dose-responses of three separate batches of gel were evaluated and compared to check for linearity and repeatability. The response development time was evaluated to ensure that the patch dosimeter could be high throughput. Additionally, the potential of this system to be used as an in vivo dosimeter was tested with a clinically relevant end-to-end in vivo phantom test. All irradiations were performed with a Varian Clinac 21EX at the University of Wisconsin Medical Radiation Research Center (UWMRRC). The dose-response of all three batches of gel was found to be linear within the range of 2-20 Gy. At doses below 0.5 Gy the statistical uncertainties were prohibitively large to make quantitative assessments of the results. The three batches demonstrated good repeatability in the range of 2 Gy to up to 10 Gy, with only slight variations in response at higher doses. For low doses the dosimeter fully developed within an hour while at higher doses they fully developed within four hours. During the in vivo

  3. A Chip-Capillary Hybrid Device for Automated Transfer of Sample Pre-Separated by Capillary Isoelectric Focusing to Parallel Capillary Gel Electrophoresis for Two-Dimensional Protein Separation

    PubMed Central

    Lu, Joann J.; Wang, Shili; Li, Guanbin; Wang, Wei; Pu, Qiaosheng; Liu, Shaorong

    2012-01-01

    In this report, we introduce a chip-capillary hybrid device to integrate capillary isoelectric focusing (CIEF) with parallel capillary sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS-PAGE) or capillary gel electrophoresis (CGE) toward automating two-dimensional (2D) protein separations. The hybrid device consists of three chips that are butted together. The middle chip can be moved between two positions to re-route the fluidic paths, which enables the performance of CIEF and injection of proteins partially resolved by CIEF to CGE capillaries for parallel CGE separations in a continuous and automated fashion. Capillaries are attached to the other two chips to facilitate CIEF and CGE separations and to extend the effective lengths of CGE columns. Specifically, we illustrate the working principle of the hybrid device, develop protocols for producing and preparing the hybrid device, and demonstrate the feasibility of using this hybrid device for automated injection of CIEF-separated sample to parallel CGE for 2D protein separations. Potentials and problems associated with the hybrid device are also discussed. PMID:22830584

  4. Polyacrylamide brush coatings preventing microbial adhesion to silicone rubber.

    PubMed

    Fundeanu, Irina; van der Mei, Henny C; Schouten, Arend J; Busscher, Henk J

    2008-07-15

    Silicone rubber is a frequently used biomaterial in biomedical devices and implants, yet highly prone to microbial adhesion and the development of a biomaterial-centered infection. Effective coating of silicone rubber to discourage microbial adhesion has thus far been impossible due to the hydrophobic character of its surface, surface deterioration upon treatment and instability of coatings under physiological conditions. Here we present a method to successfully grow polyacrylamide (PAAm) brushes from silicone rubber surfaces after removal of low molecular weight organic molecules (LMWOM), such as silane oligomers. PAAm brush coating did not cause any surface deterioration and discouraged microbial adhesion, even after 1-month exposure to physiological fluids. The method presented opens many new avenues for the use of silicone rubber as a biomaterial, without the risk of developing a biomaterial-centered infection.

  5. The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

    PubMed Central

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J. Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2011-01-01

    The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for mass spectrometry data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications. PMID:20677327

  6. Relative quantitative comparisons of the extracellular protein profiles of Staphylococcus aureus UAMS-1 and its sarA, agr, and sarA agr regulatory mutants using one-dimensional polyacrylamide gel electrophoresis and nanocapillary liquid chromatography coupled with tandem mass spectrometry.

    PubMed

    Jones, Richard C; Deck, Joanna; Edmondson, Ricky D; Hart, Mark E

    2008-08-01

    One-dimensional polyacrylamide gel electrophoresis followed by nanocapillary liquid chromatography coupled with mass spectrometry was used to analyze proteins isolated from Staphylococcus aureus UAMS-1 after 3, 6, 12, and 24 h of in vitro growth. Protein abundance was determined using a quantitative value termed normalized peptide number, and overall, proteins known to be associated with the cell wall were more abundant early on in growth, while proteins known to be secreted into the surrounding milieu were more abundant late in growth. In addition, proteins from spent media and cell lysates of strain UAMS-1 and its isogenic sarA, agr, and sarA agr regulatory mutant strains during exponential growth were identified, and their relative abundances were compared. Extracellular proteins known to be regulated by the global regulators sarA and agr displayed protein levels in accordance with what is known regarding the effects of these regulators. For example, cysteine protease (SspB), endopeptidase (SspA), staphopain (ScpA), and aureolysin (Aur) were higher in abundance in the sarA and sarA agr mutants than in strain UAMS-1. The immunoglobulin G (IgG)-binding protein (Sbi), immunodominant staphylococcal antigen A (IsaA), IgG-binding protein A (Spa), and the heme-iron-binding protein (IsdA) were most abundant in the agr mutant background. Proteins whose abundance was decreased in the sarA mutant included fibrinogen-binding protein (Fib [Efb]), IsaA, lipase 1 and 2, and two proteins identified as putative leukocidin F and S subunits of the two-component leukotoxin family. Collectively, this approach identified 1,263 proteins (matches of two peptides or more) and provided a convenient and reliable way of identifying proteins and comparing their relative abundances.

  7. Structural features of the nonionic surfactants stabilizing long-lived bubble nuclei

    NASA Technical Reports Server (NTRS)

    Darrigo, J. S.

    1980-01-01

    A study of the effects of various electrolytes and one organic compound on bubble production in agarose gels is presented. Several preparations of ultrapure agarose were compared for 42 electrolytes and phenol to identify trends in bubble formation. The anion and cation sequences of bubble suppression are similar to processes for salting out of nonionic surfactants. The reduction of bubble number by polyvalent ions and 1% phenol suggests that the polar portions of these nonionic surfactants represent amide groups. The evidence for amide groups is consistent with the relative positions of Mg(2+) in all cation sequences; this result makes it unlikely that either linkages contribute to the hydrophilicity of the nonionic surfactants stabilizing bubble nuclei in the different aqueous gels tested.

  8. A Small Stem Loop Structure Of The Ebola Virus Trailer Is Essential For Replication And Interacts With Heat Shock Protein A8

    DTIC Science & Technology

    2016-12-02

    agarose gel electrophoresis TR-16-205 Nucleic Acids Research, 2016 3 (Seakem GTG , Sigma-Aldrich) and purified using the QI- Aquick Gel Extraction Kit... gtg +cga 1923-1938 3′ LNA2 +caa+aaa+ga+aa+gaa+gaa 3E-5E eGFP, 3E-5E plasmid containing enhanced green fluorescent protein; aiSHAPE, antisense-interfered

  9. Assessing Mercury and Methylmercury Bioavailability in Sediment Pore Water Using Mercury-Specific Hydrogels

    DTIC Science & Technology

    2015-06-01

    gram AVS acid volatile sulfides BrCl bromium chloride cm centimeter(s) cm2 g-1 square centimeter(s) per gram CVAFS cold vapor atomic...Production The DGT devices used in our experiments consist of three principal components: a diffusive gel, a resin gel, and a membrane. Gel synthesis is...based on the laboratory procedures for the synthesis of polyacrylamide electrophoresis gels (Clarisse and Hintelmann 2006); although, instead of

  10. Comparison of potassium and sodium binding in vivo and in agarose samples using TQTPPI pulse sequence

    NASA Astrophysics Data System (ADS)

    Schepkin, Victor D.; Neubauer, Andreas; Nagel, Armin M.; Budinger, Thomas F.

    2017-04-01

    Potassium and sodium specific binding in vivo were explored at 21.1 T by triple quantum (TQ) magnetic resonance (MR) signals without filtration to achieve high sensitivities and precise quantifications. The pulse sequence used time proportional phase increments (TPPI). During simultaneous phase-time increments, it provided total single quantum (SQ) and TQ MR signals in the second dimension at single and triple quantum frequencies, respectively. The detection of both TQ and SQ signals was performed at identical experimental conditions and the resulting TQ signal equals 60 ± 3% of the SQ signal when all ions experience sufficient time for binding. In a rat head in vivo the TQ percentage relative to SQ for potassium is 41.5 ± 3% and for sodium is 16.1 ± 1%. These percentages were compared to the matching values in an agarose tissue model with MR relaxation times similar to those of mammalian brain tissue. The sodium TQ signal in agarose samples decreased in the presence of potassium, suggesting a competitive binding of potassium relative to sodium ions for the same binding sites. The TQTPPI signals correspond to almost two times more effective binding of potassium than sodium. In vivo, up to ∼69% of total potassium and ∼27% of total sodium can be regarded as bound or experiencing an association time in the range of several milliseconds. Experimental data analyses show that more than half of the in vivo total sodium TQ signal could be from extracellular space, which is an important factor for quantification of intracellular MR signals.

  11. Purification of the major endoglucanase from Aspergillus fumigatus Fresenius.

    PubMed

    Parry, J B; Stewart, J C; Heptinstall, J

    1983-08-01

    Aspergillus fumigatus (Fresenius), IMI 246651, A.T.C.C. 46324, produces two beta-glucosidase enzymes, cotton-solubilizing activity, xylanase and endoglucanase enzymes which can be separated by gel-filtration chromatography. The major endoglucanase does not bind to concanavalin A-Sepharose and does not stain with periodic acid/Schiff reagent. It is homogeneous on polyacrylamide isoelectric focusing (pI = 7.1) and has a mol.wt. of 12500 by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. The endoglucanase produces glucose and a mixture of oligosaccharides from cellulose; the purified enzyme has a small dextranase activity. It is stable at 50 degrees C and pH 6.

  12. GEM printer: 3D gel printer for free shaping of functional gel engineering materials

    NASA Astrophysics Data System (ADS)

    Furukawa, Hidemitsu; Muroi, Hisato; Yamamoto, Kouki; Serizawa, Ryo; Gong, Jin

    2013-04-01

    In the past decade, several high-strength gels have been developed. These gels are expected to use as a kind of new engineering materials in the fields of industry and medical as substitutes to polyester fibers, which are materials of artificial blood vessels. The gels have both low surface friction and well permeability due to a large amount of water absorbed in the gels, which are superiority of the gels compering to the polyester fibers. It is, however, difficult for gels to be forked structure or cavity structure by using cutting or mold. Consequently, it is necessary to develop the additive manufacturing device to synthesize and mode freely gels at the same time. Here we try to develop an optical 3D gel printer that enables gels to be shaped precisely and freely. For the free forming of high-strength gels, the 1st gels are ground to particles and mixed with 2nd pregel solution, and the mixed solution is gelled by the irradiation of UV laser beam through an optical fiber. The use of the optical fiber makes one-point UV irradiation possible. Since the optical fiber is controlled by 3D-CAD, the precise and free molding in XYZ directions is easily realized. We successfully synthesized tough gels using the gel printer.

  13. An NMR relaxometry and gravimetric study of gelatin-free aqueous polyacrylamide dosimeters.

    PubMed

    Babic, Steven; Schreiner, L John

    2006-09-07

    In conformal radiation therapy, a high dose of radiation is given to a target volume to increase the probability of cure, and care is taken to minimize the dose to surrounding healthy tissue. The techniques used to achieve this are very complicated and the precise verification of the resulting three-dimensional (3D) dose distribution is required. Polyacrylamide gelatin (PAG) dosimeters with magnetic resonance imaging and optical computed tomography scanning provide the required 3D dosimetry with high spatial resolution. Many basic studies have characterized these chemical dosimeters that polymerize under irradiation. However, the investigation of the fundamental properties of the radiation-induced polymerization in PAG dosimeters is complicated by the presence of the background gelatin matrix. In this work, a gelatin-free model system for the study of the basic radiation-induced polymerization in PAG dosimeters has been developed. Experiments were performed on gelatin-free dosimeters, named aqueous polyacrylamide (APA) dosimeters, containing equal amounts of acrylamide and N,N'-methylene-bisacrylamide. The APA dosimeters were prepared with four different total monomer concentrations (2, 4, 6 and 8% by weight). Nuclear magnetic resonance (NMR) spin-spin and spin-lattice proton relaxation measurements at 20 MHz, and gravimetric analyses performed on all four dosimeters, show a continuous degree of polymerization over the dose range of 0-25 Gy. The developed NMR model explains the relationship observed between the relaxation data and the amount of crosslinked polymer formed at each dose. This model can be extended with gelatin relaxation data to provide a fundamental understanding of radiation-induced polymerization in the conventional PAG dosimeters.

  14. An NMR relaxometry and gravimetric study of gelatin-free aqueous polyacrylamide dosimeters

    NASA Astrophysics Data System (ADS)

    Babic, Steven; Schreiner, L. John

    2006-09-01

    In conformal radiation therapy, a high dose of radiation is given to a target volume to increase the probability of cure, and care is taken to minimize the dose to surrounding healthy tissue. The techniques used to achieve this are very complicated and the precise verification of the resulting three-dimensional (3D) dose distribution is required. Polyacrylamide gelatin (PAG) dosimeters with magnetic resonance imaging and optical computed tomography scanning provide the required 3D dosimetry with high spatial resolution. Many basic studies have characterized these chemical dosimeters that polymerize under irradiation. However, the investigation of the fundamental properties of the radiation-induced polymerization in PAG dosimeters is complicated by the presence of the background gelatin matrix. In this work, a gelatin-free model system for the study of the basic radiation-induced polymerization in PAG dosimeters has been developed. Experiments were performed on gelatin-free dosimeters, named aqueous polyacrylamide (APA) dosimeters, containing equal amounts of acrylamide and N,N'-methylene-bisacrylamide. The APA dosimeters were prepared with four different total monomer concentrations (2, 4, 6 and 8% by weight). Nuclear magnetic resonance (NMR) spin-spin and spin-lattice proton relaxation measurements at 20 MHz, and gravimetric analyses performed on all four dosimeters, show a continuous degree of polymerization over the dose range of 0-25 Gy. The developed NMR model explains the relationship observed between the relaxation data and the amount of crosslinked polymer formed at each dose. This model can be extended with gelatin relaxation data to provide a fundamental understanding of radiation-induced polymerization in the conventional PAG dosimeters.

  15. DNA sequencing up to 1300 bases in two hours by capillary electrophoresis with mixed replaceable linear polyacrylamide solutions.

    PubMed

    Zhou, H; Miller, A W; Sosic, Z; Buchholz, B; Barron, A E; Kotler, L; Karger, B L

    2000-03-01

    This paper presents results on ultralong read DNA sequencing with relatively short separation times using capillary electrophoresis with replaceable polymer matrixes. In previous work, the effectiveness of mixed replaceable solutions of linear polyacrylamide (LPA) was demonstrated, and 1000 bases were routinely obtained in less than 1 h. Substantially longer read lengths have now been achieved by a combination of improved formulation of LPA mixtures, optimization of temperature and electric field, adjustment of the sequencing reaction, and refinement of the base-caller. The average molar masses of LPA used as DNA separation matrixes were measured by gel permeation chromatography and multiangle laser light scattering. Newly formulated matrixes comprising 0.5% (w/w) 270 kDa and 2% (w/w) 10 or 17 MDa LPA raised the optimum column temperature from 60 to 70 degrees C, increasing the selectivity for large DNA fragments, while maintaining high selectivity for small fragments as well. This improved resolution was further enhanced by reducing the electric field strength from 200 to 125 V/cm. In addition, because sequencing accuracy beyond 1000 bases was diminished by the low signal from G-terminated fragments when the standard reaction protocol for a commercial dye primer kit was used, the amount of these fragments was doubled. Augmenting the base-calling expert system with rules specific for low peak resolution also had a significant effect, contributing slightly less than half of the total increase in read length. With full optimization, this read length reached up to 1300 bases (average 1250) with 98.5% accuracy in 2 h for a single-stranded M13 template.

  16. Clinical application of a rapid method using agarose gel electrophoresis and Western blotting to evaluate von Willebrand factor protease activity.

    PubMed

    Kirzek, D M; Rick, M E

    2001-03-01

    A method for evaluating the activity of the von Willebrand factor (vWF) protease is described, and a clinical application is illustrated. The procedure utilizes gel electrophoresis, Western blotting, and luminographic detection methods to evaluate the distribution of vWF multimers before and after incubation of clinical samples under conditions that favor proteolysis by this enzyme. Physiologically, the high-molecular-weight multimers of vWF are cleaved by the vWF protease under conditions of high shear stress in parts of the arterial circulation; cleavage of vWF multimers is also observed after exposure of vWF to denaturing agents in vitro and thus can serve as a laboratory test for the activity of the protease. vWF protease activity is decreased or absent in patients with thrombotic thrombocytopenic purpura due to an inhibiting autoantibody, and this leads to high levels of noncleaved vWF and to life-threatening thrombosis, thrombocytopenia and anemia. The assay evaluates the activity of the protease by assessing the cleavage of vWF multimers after patient plasmas are incubated in vitro under denaturing conditions. With the use of these electrophoresis and Western blotting techniques, patient plasmas can be rapidly assessed for the activity of the vWF protease which may aid in the treatment strategy for these patients.

  17. CONFORMANCE IMPROVEMENT USING GELS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysismore » suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the flow capacity

  18. Human thyrotropin receptor subunits characterized by thyrotropin affinity purification and western blotting.

    PubMed

    Leedman, P J; Newman, J D; Harrison, L C

    1989-07-01

    We studied the subunit structure of the human TSH receptor in thyroid tissue from patients with Graves' disease and multinodular goiter by TSH affinity chromatography, immunoprecipitation with Graves' immunoglobulins (Igs), and a modified technique of Western blotting. Human TSH receptor-binding activity was purified about 1,270-fold by sequential affinity chromatography on wheat germ lectin-agarose and TSH-agarose. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of nonreduced affinity-purified receptors eluted in sodium dodecyl sulfate sample buffer revealed three noncovalently linked subunits of 70,000, 50,000, and 35,000 mol wt. When reduced, a major subunit of 25,000 mol wt was identified. When 3 mol/L NaCl was used to elute affinity-purified receptors only the 50,000 mol wt nonreduced subunit was detected. This subunit bound [125I]bovine TSH and was precipitated by Graves' Igs. Modifications to the conventional Western blotting technique enabled thyroglobulin components (approximately 220,000 mol wt), thyroid microsomal antigen (a doublet of approximately 110,000 mol wt), and putative TSH receptor subunits of 70,000 and 50,000 mol wt to be identified in thyroid particulate membranes by Graves' Igs. Blotting of affinity-purified receptors eluted in sodium dodecyl sulfate sample buffer revealed subunits of either 70,000 or 50,000 mol wt, with a minority of Graves' serum samples. We conclude that the nonreduced human TSH receptor is an oligomeric complex comprising three different subunits of 70,000, 50,000, and 35,000 mol wt. The reduced receptor exists as a single subunit of 25,000 mol wt, which may be disulfide linked to form the higher mol wt forms. The 70,000 and 50,000 mol wt subunits contain epitopes that bind Graves' Igs in modified Western blots, thus directly confirming that the human TSH receptor is a target for Graves' Igs.

  19. Waste-Activated Sludge Fermentation for Polyacrylamide Biodegradation Improved by Anaerobic Hydrolysis and Key Microorganisms Involved in Biological Polyacrylamide Removal

    PubMed Central

    Dai, Xiaohu; Luo, Fan; Zhang, Dong; Dai, Lingling; Chen, Yinguang; Dong, Bin

    2015-01-01

    During the anaerobic digestion of dewatered sludge, polyacrylamide (PAM), a chemical conditioner, can usually be consumed as a carbon and nitrogen source along with other organic matter (e.g., proteins and carbohydrates in the sludge). However, a significant accumulation of acrylamide monomers (AMs) was observed during the PAM biodegradation process. To improve the anaerobic hydrolysis of PAM, especially the amide hydrolysis process, and to avoid the generation of the intermediate product AM, a new strategy is reported herein that uses an initial pH of 9, 200 mg COD/L of PAM and a fermentation time of 17 d. First, response surface methodology (RSM) was applied to optimize PAM removal in the anaerobic digestion of the sludge. The biological hydrolysis of PAM reached 86.64% under the optimal conditions obtained from the RSM. Then, the mechanisms for the optimized parameters that significantly improved the biological hydrolysis of PAM were investigated by the synergistic effect of the main organic compounds in the sludge, the floc size distribution, and the enzymatic activities. Finally, semi-continuous-flow experiments for a microbial community study were investigated based on the determination of key microorganisms involved in the biological hydrolysis of PAM. PMID:26144551

  20. Waste-Activated Sludge Fermentation for Polyacrylamide Biodegradation Improved by Anaerobic Hydrolysis and Key Microorganisms Involved in Biological Polyacrylamide Removal.

    PubMed

    Dai, Xiaohu; Luo, Fan; Zhang, Dong; Dai, Lingling; Chen, Yinguang; Dong, Bin

    2015-07-06

    During the anaerobic digestion of dewatered sludge, polyacrylamide (PAM), a chemical conditioner, can usually be consumed as a carbon and nitrogen source along with other organic matter (e.g., proteins and carbohydrates in the sludge). However, a significant accumulation of acrylamide monomers (AMs) was observed during the PAM biodegradation process. To improve the anaerobic hydrolysis of PAM, especially the amide hydrolysis process, and to avoid the generation of the intermediate product AM, a new strategy is reported herein that uses an initial pH of 9, 200 mg COD/L of PAM and a fermentation time of 17 d. First, response surface methodology (RSM) was applied to optimize PAM removal in the anaerobic digestion of the sludge. The biological hydrolysis of PAM reached 86.64% under the optimal conditions obtained from the RSM. Then, the mechanisms for the optimized parameters that significantly improved the biological hydrolysis of PAM were investigated by the synergistic effect of the main organic compounds in the sludge, the floc size distribution, and the enzymatic activities. Finally, semi-continuous-flow experiments for a microbial community study were investigated based on the determination of key microorganisms involved in the biological hydrolysis of PAM.

  1. A semester-long project for teaching basic techniques in molecular biology such as restriction fragment length polymorphism analysis to undergraduate and graduate students.

    PubMed

    DiBartolomeis, Susan M

    2011-01-01

    Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky(73). Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers.

  2. A Semester-Long Project for Teaching Basic Techniques in Molecular Biology Such as Restriction Fragment Length Polymorphism Analysis to Undergraduate and Graduate Students

    PubMed Central

    DiBartolomeis, Susan M.

    2011-01-01

    Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky73. Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers. PMID:21364104

  3. Identification of a human erythrocyte receptor for colonization factor antigen I pili expressed by H10407 enterotoxigenic Escherichia coli.

    PubMed Central

    Pieroni, P; Worobec, E A; Paranchych, W; Armstrong, G D

    1988-01-01

    We have identified a receptor for colonization factor antigen I (CFA/I) pili in human erythrocyte membranes. Erythrocyte binding assays, using whole organisms, suggested that the CFA/I receptor was a glycoprotein containing important sialic acid moieties. Subsequently, human erythrocyte membranes were extracted with lithium diiodosalicylate to obtain a soluble glycoprotein fraction from which to isolate receptors. The extracted material caused agglutination of the CFA/I+ but not the CFA/I- organisms at a protein concentration of 0.5 mg/ml. The CFA/I receptor was identified in iodinated extract by an affinity isolation procedure, using whole bacterial cells. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography of the washed, extract-coated H10407 CFA/I+ organisms revealed a band with an apparent molecular weight of 26,000 which was present in the original extract but was not observed on extract-coated H10407 CFA/I- bacteria. The addition of purified CFA/I pili reduced binding of the 26,000-molecular-weight receptor to CFA/I+ bacteria. The CFA/I-specific receptor species also bound to wheat germ agglutinin-agarose. This observation supported the suggestion that the CFA/I receptor identified in this report is a sialoglycoprotein. Images PMID:2895745

  4. Purification of CD47-streptavidin fusion protein from bacterial lysate using biotin-agarose affinity chromatography.

    PubMed

    Salehi, Nasrin; Peng, Ching-An

    2016-07-08

    CD47 is a widely expressed transmembrane glycoprotein that modulates the activity of a plethora of immune cells via its extracellular domain. Therefore, CD47 plays important roles in the regulation of immune responses and may serve as targets for the development of immunotherapeutic agents. To make sure CD47 functionality is intact under the process of protein conjugation, CD47-streptavidin fusion protein was expressed and purified because it can easily bind to biotin-tagged materials via the unique biotin-streptavidin affinity. In this study, gene sequences of CD47 extracellular domain (CD47ECD) and core streptavidin (coreSA) with a total 834 bp were inserted into pET20b plasmid to construct recombinant plasmid encoding CD47-SA fusion gene. After bacteria transformation, the CD47-SA fusion protein was expressed by isopropyl-β-d-thiogalactopyranoside (IPTG) induction. The collected bacteria lysate was loaded on biotinylated agarose to proceed the purification of CD47-SA fusion protein. Due to the unexpected high affinity between biotin and coreSA, standard washing and elution approaches (e.g., varying pH, using biotin, and applying guanidine hydrochloride) reported for biotin-streptavidin affinity chromatography were not able to separate the target fusion protein. Instead, using low concentration of the non-ionic detergent Triton X-100 followed with alkaline buffer could efficiently weaken the binding between biotin and coreSA, thereby eluting out CD47-SA fusion protein from the biotin agarose column. The purified CD47-SA fusion protein was further characterized by molecular biology methods and its antiphagocytic functionality was confirmed by the phagocytosis assay. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:949-958, 2016. © 2016 American Institute of Chemical Engineers.

  5. Polyacrylamide Ferrogels with Magnetite or Strontium Hexaferrite: Next Step in the Development of Soft Biomimetic Matter for Biosensor Applications

    PubMed Central

    Safronov, Alexander P.; Mikhnevich, Ekaterina A.; Blyakhman, Felix A.; Sklyar, Tatyana F.; Larrañaga Varga, Aitor; Medvedev, Anatoly I.; Fernández Armas, Sergio

    2018-01-01

    Magnetic biosensors are an important part of biomedical applications of magnetic materials. As the living tissue is basically a “soft matter.” this study addresses the development of ferrogels (FG) with micron sized magnetic particles of magnetite and strontium hexaferrite mimicking the living tissue. The basic composition of the FG comprised the polymeric network of polyacrylamide, synthesized by free radical polymerization of monomeric acrylamide (AAm) in water solution at three levels of concentration (1.1 M, 0.85 M and 0.58 M) to provide the FG with varying elasticity. To improve FG biocompatibility and to prevent the precipitation of the particles, polysaccharide thickeners—guar gum or xanthan gum were used. The content of magnetic particles in FG varied up to 5.2 wt % depending on the FG composition. The mechanical properties of FG and their deformation in a uniform magnetic field were comparatively analyzed. FG filled with strontium hexaferrite particles have larger Young’s modulus value than FG filled with magnetite particles, most likely due to the specific features of the adhesion of the network’s polymeric subchains on the surface of the particles. FG networks with xanthan are stronger and have higher modulus than the FG with guar. FG based on magnetite, contract in a magnetic field 0.42 T, whereas some FG based on strontium hexaferrite swell. Weak FG with the lowest concentration of AAm shows a much stronger response to a field, as the concentration of AAm governs the Young’s modulus of ferrogel. A small magnetic field magnetoimpedance sensor prototype with Co68.6Fe3.9Mo3.0Si12.0B12.5 rapidly quenched amorphous ribbon based element was designed aiming to develop a sensor working with a disposable stripe sensitive element. The proposed protocol allowed measurements of the concentration dependence of magnetic particles in gels using magnetoimpedance responses in the presence of magnetite and strontium hexaferrite ferrogels with xanthan. We

  6. Kinetics of Adsorption of Diethylene-triaminomethylated Polyacrylamide on Dispersed Kaolin Accompanied by Flocculation.

    PubMed

    Kislenko; Verlinskaya

    1999-08-01

    The kinetics of the adsorption of diethylene-triaminomethylated polyacrylamide on kaolin dispersed in water has been investigated. An influence of the flocculation of kaolin dispersion on polymer adsorption has been found. The kinetics of particle aggregation under the influence of dissolved polymer has been studied. Polymer adsorption and particle aggregation proceed simultaneously, accompanied by a steady decrease in the amount of adsorbed polymer per unit mass of kaolin. A mathematical model of the adsorption process, consistent with the experimental data, is described. The rate constants and their ratios have been determined. Copyright 1999 Academic Press.

  7. Real-Time UV-Visible Spectroscopy Analysis of Purple Membrane-Polyacrylamide Film Formation Taking into Account Fano Line Shapes and Scattering

    PubMed Central

    Gomariz, María; Blaya, Salvador; Acebal, Pablo; Carretero, Luis

    2014-01-01

    We theoretically and experimentally analyze the formation of thick Purple Membrane (PM) polyacrylamide (PA) films by means of optical spectroscopy by considering the absorption of bacteriorhodopsin and scattering. We have applied semiclassical quantum mechanical techniques for the calculation of absorption spectra by taking into account the Fano effects on the ground state of bacteriorhodopsin. A model of the formation of PM-polyacrylamide films has been proposed based on the growth of polymeric chains around purple membrane. Experimentally, the temporal evolution of the polymerization process of acrylamide has been studied as function of the pH solution, obtaining a good correspondence to the proposed model. Thus, due to the formation of intermediate bacteriorhodopsin-doped nanogel, by controlling the polymerization process, an alternative methodology for the synthesis of bacteriorhodopsin-doped nanogels can be provided. PMID:25329473

  8. Real-time UV-visible spectroscopy analysis of purple membrane-polyacrylamide film formation taking into account Fano line shapes and scattering.

    PubMed

    Gomariz, María; Blaya, Salvador; Acebal, Pablo; Carretero, Luis

    2014-01-01

    We theoretically and experimentally analyze the formation of thick Purple Membrane (PM) polyacrylamide (PA) films by means of optical spectroscopy by considering the absorption of bacteriorhodopsin and scattering. We have applied semiclassical quantum mechanical techniques for the calculation of absorption spectra by taking into account the Fano effects on the ground state of bacteriorhodopsin. A model of the formation of PM-polyacrylamide films has been proposed based on the growth of polymeric chains around purple membrane. Experimentally, the temporal evolution of the polymerization process of acrylamide has been studied as function of the pH solution, obtaining a good correspondence to the proposed model. Thus, due to the formation of intermediate bacteriorhodopsin-doped nanogel, by controlling the polymerization process, an alternative methodology for the synthesis of bacteriorhodopsin-doped nanogels can be provided.

  9. Carbon dots rooted agarose hydrogel hybrid platform for optical detection and separation of heavy metal ions.

    PubMed

    Gogoi, Neelam; Barooah, Mayuri; Majumdar, Gitanjali; Chowdhury, Devasish

    2015-02-11

    A robust solid sensing platform for an on-site operational and accurate detection of heavy metal is still a challenge. We introduce chitosan based carbon dots rooted agarose hydrogel film as a hybrid solid sensing platform for detection of heavy metal ions. The fabrication of the solid sensing platform is centered on simple electrostatic interaction between the NH3+ group present in the carbon dots and the OH- groups present in agarose. Simply on dipping the hydrogel film strip into the heavy metal ion solution, in particular Cr6+, Cu2+, Fe3+, Pb2+, Mn2+, the strip displays a color change, viz., Cr6+→yellow, Cu2+→blue, Fe3+→brown, Pb2+→white, Mn2+→tan brown. The optical detection limit of the respective metal ion is found to be 1 pM for Cr6+, 0.5 μM for Cu2+, and 0.5 nM for Fe3+, Pb2+, and Mn2+ by studying the changes in UV-visible reflectance spectrum of the hydrogel film. Moreover, the hydrogel film finds applicability as an efficient filtration membrane for separation of these quintet heavy metal ions. The strategic fundamental feature of this sensing platform is the successful capability of chitosan to form colored chelates with transition metals. This proficient hybrid hydrogel solid sensing platform is thus the most suitable to employ as an on-site operational, portable, cheap colorimetric-optical detector of heavy metal ion with potential skill in their separation. Details of the possible mechanistic insight into the colorimetric detection and ion separation are also discussed.

  10. Purification of 6-phosphogluconate dehydrogenase from parsley (Petroselinum hortense) leaves and investigation of some kinetic properties.

    PubMed

    Demir, Hülya; Ciftçi, Mehmet; Küfrevioğlu, O Irfan

    2003-02-01

    In this study, 6-phosphogluconate dehydrogenase (E.C.1.1.44; 6PGD) was purified from parsley (Petroselinum hortense) leaves, and analysis of the kinetic behavior and some properties of the enzyme were investigated. The purification consisted of three steps that are preparation of homogenate ammonium sulfate fractionation and on DEAE-Sephadex A50 ion exchange. The enzyme was obtained with a yield of 49% and had a specific activity of 18.3 U (mg proteins)(-1) (Lehninger, A.L.; Nelson, D.L.; Cox, M.M. Principles of Biochemistry, 2nd Ed.; Worth Publishers Inc.: N.Y., 2000, 558-560). The overall purification was about 339-fold. A temperature of +4 degrees C was maintained during the purification process. Enzyme activity was spectrophotometrically measured according to the Beutler method at 340 mn. In order to control the purification of the enzyme, SDS-polyacrylamide gel electrophoresis was carried out in 4% and 10% acrylamide for stacking and running gel, respectively. SDS-polyacrylamide gel electrophoresis showed a single band for enzyme. The molecular weight was found to be 97.5 kDa by Sephadex G-150 gel filtration chromatography. A protein band corresponding to a subunit molecular weight of 24.1 kDa was obtained on SDS-polyacrylamide gel electrophoresis. For the enzymes, the stable pH, optimum pH, and optimum temperature were found as 8.0, 8.0, and 50 degrees C, respectively. In addition, KM and Vmax values for NADP+ and G6-P at optimum pH and 25 degrees C were determined by means of Lineweaver-Burk plots.

  11. Purification and investigation of some kinetic properties of glucose-6-phosphate dehydrogenase from parsley (Petroselinum hortense) leaves.

    PubMed

    Coban, T Abdül Kadir; Ciftçi, Mehmet; Küfrevioğlu, O Irfan

    2002-05-01

    In this study, glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP+ oxidoreductase, EC 1.1.1.49; G6PD) was purified from parsley (Petroselinum hortense) leaves, and analysis of the kinetic behavior and some properties of the enzyme were investigated. The purification consisted of three steps: preparation of homogenate, ammonium sulfate fractionation, and DEAE-Sephadex A50 ion exchange chromatography. The enzyme was obtained with a yield of 8.79% and had a specific activity of 2.146 U (mg protein)(-1). The overall purification was about 58-fold. Temperature of +4 degrees C was maintained during the purification process. Enzyme activity was spectrophotometrically measured according to the Beutler method, at 340 nm. In order to control the purification of enzyme, SDS-polyacrylamide gel electrophoresis was carried out in 4% and 10% acrylamide for stacking and running gel, respectively. SDS-polyacrylamide gel electrophoresis showed a single band for enzyme. The molecular weight was found to be 77.6 kDa by Sephadex G-150 gel filtration chromatography. A protein band corresponding to a molecular weight of 79.3 kDa was obtained on SDS-polyacrylamide gel electrophoresis. For the enzymes, the stable pH, optimum pH, and optimum temperature were found to be 6.0, 8.0, and 60 degrees C, respectively. Moreover, KM and Vmax values for NADP+ and G6-P at optimum pH and 25 degrees C were determined by means of Lineweaver-Burk graphs. Additionally, effects of streptomycin sulfate and tetracycline antibiotics were investigated for the enzyme activity of glucose-6-phosphate dehydrogenase in vitro.

  12. Morphology Modulation of Direct Inkjet Printing by Incorporating Polymers and Surfactants into a Sol-Gel Ink System.

    PubMed

    Zhu, Zhennan; Ning, Honglong; Cai, Wei; Wei, Jinglin; Zhou, Shangxiong; Yao, Rihui; Lu, Xubing; Zhang, Jianhua; Zhou, ZhongWei; Peng, Junbiao

    2018-06-05

    Many methods have been reported to prevent the nonuniformity of inkjet printing structures. Most of them depend on the balance of the capillary flow in the printing pattern during the evaporation of the solvent. However, as the relation of evaporation and capillary flow can obviously vary among different ink systems, it is difficult for a method to fit most of the situations. Therefore, it would be a promising way to eliminate any capillary flow before solvent evaporation so that morphology of the printing structure will not be affected by the evaporation behavior of the ink system. In this paper, a novel method of direct inkjet printing of a uniform metal oxide structure is reported. We introduce a polymer polyacrylamide and a surfactant FSO into a sol-gel ink system, and the new ink system can gel from the printing pattern edge to center as temperature increases because of the cross-linking of the polymer chains. By that means, transport of solute molecules and solvent molecules is limited. Meanwhile, the surfactant can ensure that the solute in the central liquid phase deposits uniformly by enhancing the Marangoni flow during the gelation process. The ZrO 2 film with uniform morphology was fabricated by drying and annealing the gelating film and afforded a leakage current density of 7.48 × 10 -7 A cm -2 at 1 MV and a breakdown field of 1.9 MV cm -1 at an annealing temperature of 250 °C.

  13. Effect of the presence of cationic polyacrylamide on the surface properties of aqueous alumina suspension-stability mechanism

    NASA Astrophysics Data System (ADS)

    Wiśniewska, Małgorzata; Chibowski, Stanisław; Urban, Teresa

    2014-11-01

    The effects of solution pH and the content of cationic groups in polyacrylamide (PAM) macromolecules on the stability mechanism of aqueous alumina suspension were investigated. The following experimental techniques were applied: spectrophotometry, potentiometric titration, microelectrophoresis, viscosimetry and turbidimetry. They enable determination of polymer adsorbed amount, surface charge density and zeta potential of solid particles in the presence and absence of PAM, as well as thickness of polymer adsorption layer, size of macromolecules in the solution and stability of the Al2O3-polymer systems, respectively. The obtained results indicate that adsorption of PAM increases with the increasing pH, whereas the thickness of polymeric adsorption layer decreases. Additionally, the greater the number of cationic groups in the PAM chains is, the higher adsorption was found. The polymer presence influences on the alumina suspension stability. At pH 3 and 6 the slight deterioration of stability conditions of solid particle covered with polyacrylamide was observed. At pH 9 the systems containing polymer are unstable, similarly to the suspension without PAM, but the mechanism of their destabilization is different.

  14. Forming giant-sized polymersomes using gel-assisted rehydration

    DOE PAGES

    Greene, Adrienne C.; Sasaki, Darryl Y.; Bachand, George D.

    2016-05-26

    Here, we present a protocol to rapidly form giant polymer vesicles ( pGVs). Briefly, polymer solutions are dehydrated on dried agarose films adhered to coverslips. Rehydration of the polymer films results in rapid formation of pGVs. This method greatly advances the preparation of synthetic giant vesicles for direct applications in biomimetic studies.

  15. Internal structure analysis of particle-double network gels used in a gel organ replica

    NASA Astrophysics Data System (ADS)

    Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

    2016-04-01

    In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

  16. Metabolic studies with NMR spectroscopy of the alga Dunaliella salina trapped within agarose beads.

    PubMed

    Bental, M; Pick, U; Avron, M; Degani, H

    1990-02-22

    A technique for the entrapment of the unicellular algae Dunaliella salina in agarose beads and their perfusion during NMR measurements is presented. The trapped cells maintained their ability to proliferate under normal growth conditions, and remained viable and stable under steady-state conditions for long periods during NMR measurements. Following osmotic shock in the dark, prominent changes were observed in the intracellular level of ATP and polyphosphates, but little to no changes in the intracellular pH or orthoposphate content. When cells were subjected to hyperosmotic shock, the ATP level decreased. The content of NMR-visible polyphosphates decreased as well, presumably due to the production of longer, NMR-invisible structures. Following hypoosmotic shock, the ATP content increased and longer polyphosphates were broken down to shorter, more mobile polymers.

  17. Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis.

    PubMed Central

    Haebel, S.; Jensen, C.; Andersen, S. O.; Roepstorff, P.

    1995-01-01

    Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15-kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) time-course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two-dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants. PMID:7795523

  18. Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis.

    PubMed

    Haebel, S; Jensen, C; Andersen, S O; Roepstorff, P

    1995-03-01

    Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15-kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) time-course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two-dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants.

  19. Potential application of immobilized streptokinase extracted from Streptococcus equinus VIT_VB2.

    PubMed

    Vaishnavi, B; Subathra Devi, C

    2017-11-26

    Streptokinase purified from Streptococcus equinus VIT_VB2 isolated from bovine milk sample was immobilized in various solid supports namely entrapment in agarose gel, calcium alginate beads and gelatin gel by cross-linking with formaldehyde. Immobilization of streptokinase in calcium alginate beads showed maximum efficiency (81.8 ± 1.06%) when compared with entrapment with agarose gel (55.6 ± 2.17%) and cross-linked gelatin formaldehyde gel (71.0 ± 1.54%). The purified SK activity was expressed maximum in calcium alginate (1%) and gelatin gel (0.25%) with 1292.68 ± 1.33 and 1121.9 ± 1.2 U mL -1 , respectively. Similarly, SK entrapped in gelatin gel and calcium alginate showed maximum in vitro blood clot lysis activity with 77.67 ± 2.64% and 76.16 ± 2.72%, respectively. The immobilized SK in gelatin gel showed complete clot lysis within 15 min; hence, this application of the study could be used in the treatment of superficial thrombophlebitis, phlebitis, and venous thrombosis. These beads were used for three repeated cycles to check the conversion of substrates into their products, and we concluded that SK can be immobilized in the suitable matrices. Therefore, this helps in the drug-delivery strategies in highly efficient way, moreover, economically competent process in the pharmaceutics.

  20. Introducing Students to Protein Analysis Techniques: Separation and Comparative Analysis of Gluten Proteins in Various Wheat Strains

    ERIC Educational Resources Information Center

    Pirinelli, Alyssa L.; Trinidad, Jonathan C.; Pohl, Nicola L. B.

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) is commonly taught in undergraduate laboratory classes as a traditional method to analyze proteins. An experiment has been developed to teach these basic protein gel skills in the context of gluten protein isolation from various types of wheat flour. A further goal is to relate this technique to current…

  1. Development of Two Analytical Methods Based on Reverse Phase Chromatographic and SDS-PAGE Gel for Assessment of Deglycosylation Yield in N-Glycan Mapping.

    PubMed

    Eckard, Anahita D; Dupont, David R; Young, Johnie K

    2018-01-01

    N -lined glycosylation is one of the critical quality attributes (CQA) for biotherapeutics impacting the safety and activity of drug product. Changes in pattern and level of glycosylation can significantly alter the intrinsic properties of the product and, therefore, have to be monitored throughout its lifecycle. Therefore fast, precise, and unbiased N -glycan mapping assay is desired. To ensure these qualities, using analytical methods that evaluate completeness of deglycosylation is necessary. For quantification of deglycosylation yield, methods such as reduced liquid chromatography-mass spectrometry (LC-MS) and reduced capillary gel electrophoresis (CGE) have been commonly used. Here we present development of two additional methods to evaluate deglycosylation yield: one based on LC using reverse phase (RP) column and one based on reduced sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE gel) with offline software (GelAnalyzer). With the advent of rapid deglycosylation workflows in the market for N -glycan profiling replacing overnight incubation, we have aimed to quantify the level of deglycosylation in a selected rapid deglycosylation workflow. Our results have shown well resolved peaks of glycosylated and deglycosylated protein species with RP-LC method allowing simple quantification of deglycosylation yield of protein with high confidence. Additionally a good correlation, ≥0.94, was found between deglycosylation yields estimated by RP-LC method and that of reduced SDS-PAGE gel method with offline software. Evaluation of rapid deglycosylation protocol from GlycanAssure™ HyPerformance assay kit performed on fetuin and RNase B has shown complete deglycosylation within the recommended protocol time when evaluated with these techniques. Using this kit, N -glycans from NIST mAb were prepared in 1.4 hr and analyzed by hydrophilic interaction chromatography (HILIC) ultrahigh performance LC (UHPLC) equipped with a fluorescence detector (FLD

  2. Heat-mediated, ultra-rapid electrophoretic transfer of high and low molecular weight proteins to nitrocellulose membranes.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2002-08-01

    Here, we report an ultra-rapid method for the transfer of high and low molecular weight proteins to nitrocellulose membranes following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In this procedure, the electro-transfer was performed with heated (70-75 degrees C) normal transfer buffer from which methanol had been omitted. Complete transfer of high and low molecular weight proteins (a purified protein, molecular weight protein standards and proteins from a human tissue extract) could be carried out in 10 min for a 0.75-mm, 7% SDS-PAGE gel. For 10% and 12.5% gels (0.75 mm), the corresponding time was 15 min. In the case of 1.5-mm gels, a complete transfer could be carried out in 20 min for 7%, 10% and 12.5% gels. The permeability of the gel is increased by heat, such that the proteins trapped in the polyacrylamide gel matrix can be easily transferred to the membrane. When the heat-mediated transfer method was compared with a conventional transfer protocol, under similar conditions, we found that the latter method transferred minimal low molecular weight proteins while retaining most of the high molecular weight proteins in the gel. In summary, this procedure is very rapid, avoids the use of methanol and is particularly useful for the transfer of high molecular weight proteins.

  3. Crystallization from Gels

    NASA Astrophysics Data System (ADS)

    Narayana Kalkura, S.; Natarajan, Subramanian

    Among the various crystallization techniques, crystallization in gels has found wide applications in the fields of biomineralization and macromolecular crystallization in addition to crystallizing materials having nonlinear optical, ferroelectric, ferromagnetic, and other properties. Furthermore, by using this method it is possible to grow single crystals with very high perfection that are difficult to grow by other techniques. The gel method of crystallization provides an ideal technique to study crystal deposition diseases, which could lead to better understanding of their etiology. This chapter focuses on crystallization in gels of compounds that are responsible for crystal deposition diseases. The introduction is followed by a description of the various gels used, the mechanism of gelling, and the fascinating phenomenon of Liesegang ring formation, along with various gel growth techniques. The importance and scope of study on crystal deposition diseases and the need for crystal growth experiments using gel media are stressed. The various crystal deposition diseases, viz. (1) urolithiasis, (2) gout or arthritis, (3) cholelithiasis and atherosclerosis, and (4) pancreatitis and details regarding the constituents of the crystal deposits responsible for the pathological mineralization are discussed. Brief accounts of the theories of the formation of urinary stones and gallstones and the role of trace elements in urinary stone formation are also given. The crystallization in gels of (1) the urinary stone constituents, viz. calcium oxalate, calcium phosphates, uric acid, cystine, etc., (2) the constituents of the gallstones, viz. cholesterol, calcium carbonate, etc., (3) the major constituent of the pancreatic calculi, viz., calcium carbonate, and (4) cholic acid, a steroidal hormone are presented. The effect of various organic and inorganic ions, trace elements, and extracts from cereals, herbs, and fruits on the crystallization of major urinary stone and gallstone

  4. Active DNA gels

    NASA Astrophysics Data System (ADS)

    Saleh, Omar A.; Fygenson, Deborah K.; Bertrand, Olivier J. N.; Park, Chang Young

    2013-02-01

    Research into the mechanics and fluctuations of living cells has revealed the key role played by the cytoskeleton, a gel of stiff filaments driven out of equilibrium by force-generating motor proteins. Inspired by the extraordinary mechanical functions that the cytoskeleton imparts to the cell, we sought to create an artificial gel with similar characteristics. We identified DNA, and DNA-based motor proteins, as functional counterparts to the constituents of the cytoskeleton. We used DNA selfassembly to create a gel, and characterized its fluctuations and mechanics both before and after activation by the motor. We found that certain aspects of the DNA gel quantitatively match those of cytoskeletal networks, indicating the universal features of motor-driven, non-equilibrium networks.

  5. Comprehensive protein profiling by multiplexed capillary zone electrophoresis using cross-linked polyacrylamide coated capillaries.

    PubMed

    Liu, Shaorong; Gao, Lin; Pu, Qiaosheng; Lu, Joann J; Wang, Xingjia

    2006-02-01

    We have recently developed a new process to create cross-linked polyacrylamide (CPA) coatings on capillary walls to suppress protein-wall interactions. Here, we demonstrate CPA-coated capillaries for high-efficiency (>2 x 10(6) plates per meter) protein separations by capillary zone electrophoresis (CZE). Because CPA virtually eliminates electroosmotic flow, positive and negative proteins cannot be analyzed in a single run. A "one-sample-two-separation" approach is developed to achieve a comprehensive protein analysis. High throughput is achieved through a multiplexed CZE system.

  6. Differential quantification of SIgA and SC by two-directional rocket method.

    PubMed Central

    Kosaka, T; Asahina, T; Kobayashi, N

    1980-01-01

    The two-directional rocket method, a newly modified method for quantitative immunoelectrophoresis, was used as the assay for separating SC and SIgA, which have identical antigenicity but differ in mobility. This method proved to be sufficiently simple and sensitive to enable simultaneous assay of SC and SIgA in saliva. The method employs electrophoresis into antibody-containing agarose/agar gel in the presence of heparin-Ca EDTA. The height of the precipitation peaks formed in two directions is proportional to the concentration of the antigens. Concomitant use of agarose which has little electroendosmosis and agar which has high electroendosmosis facilitated cathodic migration of SIgA. Transfer of SC from beta-region to alpha 1-region without influencing the mobilities of SIgA, albumin or IgG was obtained by addition of heparin-Ca EDTA to agarose/agar gel. This effect of heparin-Ca EDTA is vulnerable to changes of pH of the gel, but is almost completely independent of change in composition or concentration of the gel. The function of heparin as a polyanion may be resonsible for it. Carbamylation of antibody was used to accelerate a clear-cut resolution of the cathodic rockets. This technique was found to be a method of choice for analysis of SIgA and SC in large numbers. In using this method as a screening assay for detection of primary immunodeficiency, by studying saliva samples collected from 3 month old infants on the occasion of regular check-up over a 2 year period, two cases of isolated IgA immunodeficiency and two cases of hypoglobulinaemia were discovered in 12,000 infants. Images Figure 1 Figure 7 PMID:6776036

  7. Lectin from embryos and oocytes of Xenopus laevis. Purification and properties.

    PubMed

    Roberson, M M; Barondes, S H

    1982-07-10

    Soluble extracts of Xenopus laevis blastula stage embryos, oocytes, and adult liver contain lectin activities detected by agglutination of trypsinized, glutaraldehyde-fixed rabbit erythrocytes. Lectin from the embryos and oocytes was purified by affinity chromatography on a column derivatized with melibiose. Trace contaminants were removed either by preparative isoelectric focusing or by gel filtration. Based on its behavior on Sepharose 6B the purified oocyte lectin has an apparent molecular weight of approximately 480,000. On sodium dodecyl sulfate polyacrylamide gel electrophoresis under reducing conditions there were two major bands with molecular weight ranges of about 43,000 and 45,000, with diffuse trails. Since the purified lectin contains about 20% saccharides by weight and since both bands are glycosylated, diffuseness might be due to variable glycosylation. Heterogeneity was indicated by isoelectric focusing in polyacrylamide gels, which showed four protein bands with isoelectric points ranging from 4.4 to 4.9. Lectins from both embryos and oocytes comprised about 1 to 2% of the total soluble protein and could not be distinguished by sodium dodecyl sulfate polyacrylamide gel electrophoresis. However, the specific hemagglutination activity of the purified oocyte lectin was, on the average, 7-fold higher. Levels in crude extracts of liver were 3 orders of magnitude lower than those from oocytes. The hemagglutination activities of the lectins from embryos, oocytes, and adult liver required Ca2+ and were blocked by similar concentrations of both alpha- and beta-galactosides.

  8. Isolation, purification, and partial characterization of Brucella abortus matrix protein.

    PubMed Central

    Moriyon, I; Berman, D T

    1983-01-01

    Peptidoglycan sacculi with peptidoglycan-associated proteins were prepared from cell envelopes of Brucella abortus by extraction with sodium dodecyl sulfate (SDS) at 50 degrees C. On extraction of these preparations with SDS at 100 degrees C, a protein was obtained whose removal from peptidoglycan was confirmed by electron microscopy. Incubation of the 50 degrees C SDS-extracted cell envelopes with 50 mM MgCl2 in SDS-2-beta-mercaptoethanol at 37 degrees C also extracted the protein, along with lipopolysaccharide. At temperatures below 60 degrees C, the protein did not bind SDS strongly and had an apparent molecular weight greater than 92,000 in SDS-polyacrylamide gel electrophoresis. At higher temperatures, SDS bound strongly, and the apparent molecular weight was 38,000. Urea at 5 M did not alter the electrophoretic mobility of this 38,000-molecular-weight form. Immunoelectrophoresis in detergents with antisera to cell envelopes, carbohydrate staining of SDS-polyacrylamide gels, and production of anti-lipopolysaccharide antibodies by mice immunized with the purified protein indicated that lipopolysaccharide was present in free and protein-bound forms. Sequential gel filtration in SDS-EDTA and SDS-NaCl removed most lipopolysaccharide. After further purification by preparative SDS-polyacrylamide gel electrophoresis, a gas-liquid chromatographic analysis showed residual lipid tightly associated with the protein. The results suggested that the interactions between matrix proteins and other outer membrane components are stronger in B. abortus than in Escherichia coli, which was used as a control throughout. Images PMID:6401696

  9. Immobilization of a Commercial Lipase from Penicillium camembertii (Lipase G) by Different Strategies

    PubMed Central

    Mendes, Adriano A.; Freitas, Larissa; de Carvalho, Ana Karine F.; de Oliveira, Pedro C.; de Castro, Heizir F.

    2011-01-01

    The objective of this work was to select the most suitable procedure to immobilize lipase from Penicillium camembertii (Lipase G). Different techniques and supports were evaluated, including physical adsorption on hydrophobic supports octyl-agarose, poly(hydroxybutyrate) and Amberlite resin XAD-4; ionic adsorption on the anionic exchange resin MANAE-agarose and covalent attachment on glyoxyl-agarose, MANAE-agarose cross-linked with glutaraldehyde, MANAE-agarose-glutaraldehyde, and epoxy-silica-polyvinyl alcohol composite. Among the tested protocols, the highest hydrolytic activity (128.2 ± 8.10 IU·g−1 of support) was achieved when the lipase was immobilized on epoxy-SiO2-PVA using hexane as coupling medium. Lipase immobilized by ionic adsorption on MANAE-agarose also gave satisfactory result, attaining 55.6 ± 2.60 IU·g−1 of support. In this procedure, the maximum loading of immobilized enzyme was 9.3 mg·g−1 of gel, and the highest activity (68.8 ± 2.70 IU·g−1 of support) was obtained when 20 mg of protein·g−1 was offered. Immobilization carried out in aqueous medium by physical adsorption on hydrophobic supports and covalent attachment on MANAE-agarose-glutaraldehyde and glyoxyl-agarose was shown to be unfeasible for Lipase G. Thermal stability tests revealed that the immobilized derivative on epoxy-SiO2-PVA composite using hexane as coupling medium had a slight higher thermal stability than the free lipase. PMID:21811674

  10. Application of melanin-free ink as a new antioxidative gel enhancer in sardine surimi gel.

    PubMed

    Vate, Naveen Kumar; Benjakul, Soottawat; Agustini, Tri Winarni

    2015-08-30

    The squid ink that is discarded as waste during processing can be effectively utilised as a gel enhancer in surimi gels, especially those prepared from dark-fleshed fish which have poor gel properties. It also acts as an antioxidant, inhibiting lipid oxidation. This investigation aimed to study the effect of melanin-free ink (MFI) from splendid squid (Loligo formosana) on properties and oxidative stability of surimi gel from sardine (Sardinella albella). MFI (0-0.1 g kg(-1) surimi) increased the breaking force and deformation of sardine surimi gel in a dose-dependent manner (P < 0.05). The addition of MFI had no effect on whiteness of surimi gels (P > 0.05). The expressible moisture content of gels decreased as the levels of MFI increased (P < 0.05). Based on a microstructure study, gel added with MFI at a level of 0.08 g kg(-1) surimi was denser and finer than that of the control (without MFI). Surimi gels with MFI had lower peroxide values, thiobarbituric acid reactive substances, nonanal and 2-decenal. MFI could improve the properties of sardine surimi gel. Additionally, it was able to prevent lipid oxidation in surimi gels during refrigerated storage. © 2014 Society of Chemical Industry.

  11. The anomalous gel migration of a stable cruciform: temperature and salt dependence, and some comparisons with curved DNA.

    PubMed Central

    Diekmann, S; Lilley, D M

    1987-01-01

    We have made an analysis of the gel electrophoretic properties of a pseudo-cruciform fragment, a linear DNA molecule containing a stable cruciform. The migration of this construct was analysed in polyacrylamide gels at a various temperatures in the range 5 degrees to 55 degrees C, and in the presence of NaCl, MgCl2 or ethidium bromide. The magnitude of the anomalous migration (retardation) was almost temperature independent up to 40 degrees C, but decreased strongly beyond this point, extrapolating to normal migration at 70 degrees C. Addition of salts reduced the anomaly. This took the form of a continuous reduction in anomalous migration with the addition of NaCl up to 60 mM, while with MgCl2 there was a sharp reduction in the anomaly to a constant value which is reached by 10 mM. Under these conditions, moreover, the migration of the fragment became almost temperature-independent over the entire range. These results have been interpreted to reflect the influence of ion binding at the four-way junction on the relative disposition of the cruciform arms. The detailed electrophoretic properties of the pseudo-cruciform are in marked contrast to those of sequence-directed curved DNA fragments. In particular, the response to the addition of 1 microgram/ml ethidium bromide offers a convenient method for distinguishing between anomalous retardation arising from curvature (greatly reduced anomaly) or a cruciform junction (enhanced anomaly). Images PMID:3039465

  12. Studies on the "Aerobic" Acetyl-Coenzyme A Synthetase of Saccharomyces Cerevisiae: Purification, Crystallization, and Physical Properties of the Enzyme

    NASA Technical Reports Server (NTRS)

    Satyanarayana, T.; Klein, Harold P.

    1976-01-01

    A procedure for the purification of a stable acetyl-coenzyme A synthetase (ACS) from aerobic cells of Saccharomyces cerevisiae is presented. The steps include differential centrifugation, solubilization of the bound enzyme from the crude mitochondrial fraction, ammonium sulfate fractionation, crystallization to constant specific activity from ammonium sulfate solutions followed by Bio-Gel A-1.5 m column chromatography. The resulting enzyme preparation is homogeneous as judged by chromatography on Bio-Gel columns, QAE-Sephadex A-50 anion exchange columns, analytical ultracentrifugal studies, and polyacrylamide gel electrophoresis. Sedimentation velocity runs revealed a single symmetric peak with an s(sub (20,w)) value of 10.6. The molecular weight of the native enzyme, as determined by gel filtration and analytical ultracentrifugation, is 250,000 +/- 500. In polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, the molecular weight of the single polypeptide chain is 83,000 +/- 500. The purified enzyme is inhibited by palmityl-coenzyme A with a Hill interaction coefficient, n, of 2.88. These studies indicate that the ACS of aerobic Saccharomyces cerevisiae is composed of three subunits of identical or nearly identical size.

  13. Evaluation of radiochromic gel dosimetry and polymer gel dosimetry in a clinical dose verification

    NASA Astrophysics Data System (ADS)

    Vandecasteele, Jan; De Deene, Yves

    2013-09-01

    A quantitative comparison of two full three-dimensional (3D) gel dosimetry techniques was assessed in a clinical setting: radiochromic gel dosimetry with an in-house developed optical laser CT scanner and polymer gel dosimetry with magnetic resonance imaging (MRI). To benchmark both gel dosimeters, they were exposed to a 6 MV photon beam and the depth dose was compared against a diamond detector measurement that served as golden standard. Both gel dosimeters were found accurate within 4% accuracy. In the 3D dose matrix of the radiochromic gel, hotspot dose deviations up to 8% were observed which are attributed to the fabrication procedure. The polymer gel readout was shown to be sensitive to B0 field and B1 field non-uniformities as well as temperature variations during scanning. The performance of the two gel dosimeters was also evaluated for a brain tumour IMRT treatment. Both gel measured dose distributions were compared against treatment planning system predicted dose maps which were validated independently with ion chamber measurements and portal dosimetry. In the radiochromic gel measurement, two sources of deviations could be identified. Firstly, the dose in a cluster of voxels near the edge of the phantom deviated from the planned dose. Secondly, the presence of dose hotspots in the order of 10% related to inhomogeneities in the gel limit the clinical acceptance of this dosimetry technique. Based on the results of the micelle gel dosimeter prototype presented here, chemical optimization will be subject of future work. Polymer gel dosimetry is capable of measuring the absolute dose in the whole 3D volume within 5% accuracy. A temperature stabilization technique is incorporated to increase the accuracy during short measurements, however keeping the temperature stable during long measurement times in both calibration phantoms and the volumetric phantom is more challenging. The sensitivity of MRI readout to minimal temperature fluctuations is demonstrated which

  14. Chemical improvement of chitosan-modified beads for the immobilization of Enterococcus faecium DBFIQ E36 L-arabinose isomerase through multipoint covalent attachment approach.

    PubMed

    Manzo, Ricardo M; de Sousa, Marylane; Fenoglio, Cecilia L; Gonçalves, Luciana Rocha Barro; Mammarella, Enrique J

    2015-10-01

    D-tagatose is produced from D-galactose by the enzyme L-arabinose isomerase (L-AI) in a commercially viable bioprocess. An active and stable biocatalyst was obtained by modifying chitosan gel structure through reaction with TNBS, D-fructose or DMF, among others. This led to a significant improvement in L-AI immobilization via multipoint covalent attachment approach. Synthetized derivatives were compared with commercial supports such as Eupergit(®) C250L and glyoxal-agarose. The best chitosan derivative for L-AI immobilization was achieved by reacting 4 % (w/v) D-fructose with 3 % (w/v) chitosan at 50 °C for 4 h. When compared to the free enzyme, the glutaraldehyde-activated chitosan biocatalyst showed an apparent activity of 88.4 U g (gel) (-1) with a 211-fold stabilization factor while the glyoxal-agarose biocatalyst gave an apparent activity of 161.8 U g (gel) (-1) with an 85-fold stabilization factor. Hence, chitosan derivatives were comparable to commercial resins, thus becoming a viable low-cost strategy to obtain high active L-AI insolubilized derivatives.

  15. [Sniffing Position and i-gel Rotation Approach for i-gel Insertion under General Anesthesia].

    PubMed

    Takahashi, Yoshihiro; Murashima, Koji; Kayashima, Kenji

    2016-04-01

    Insertion assistance techniques, such as the sniffing position (SP) and i-gel? rotation approach (RA), are recommended in the i-gel supraglottic airway device insertion manual. The usefulness of these techniques was evaluated, in this study, under general anesthesia. In 50 adult patients, the i-gel was inserted with the patient in the mild-SP with 5 degrees head extention at first attempt. When resistance was encountered during insertion or airway patency was not obtained after insertion, the i-gel was re-inserted with the patient in the full-SP with maximum head extention during second attempt. When re-insertion failed, the i-gel was inserted with the patient in the full-SP and by using the i-gel RA during third attempt. Airway patency was established in the mild-SP in 36 of 50 patients, in the full-SP in 11 of the remaining 14, and in the full-SP with the i-gel RA in the remaining 3. The average insertion time was 24.0 s during the first attempt, 22.2 s during the second, and 18.2 s during the third. No major complications were observed. Both the full-SP and the i-gel RA can be used for i-gel insertion.

  16. [Polymer Gel Dosimeter].

    PubMed

    Hayashi, Shin-Ichiro

    2017-01-01

    With rapid advances being made in radiotherapy treatment, three-dimensional (3D) dose measurement techniques of great precision are required more than ever before. It is expected that 3D polymer gel dosimeters will satisfy clinical needs for an effective detector that can measure the complex 3D dose distributions. Polymer gel dosimeters are devices that utilize the radiation-induced polymerization reactions of vinyl monomers in a gel to store information about radiation dose. The 3D absorbed dose distribution can be deduced from the resulting polymer distribution using several imaging modalities, such as MRI, X-ray and optical CTs. In this article, the fundamental characteristics of polymer gel dosimeter are reviewed and some challenging keys are also suggested for the widely spread in clinical use.

  17. Metal-silica sol-gel materials

    NASA Technical Reports Server (NTRS)

    Stiegman, Albert E. (Inventor)

    2002-01-01

    The present invention relates to a single phase metal-silica sol-gel glass formed by the co-condensation of a transition metal with silicon atoms where the metal atoms are uniformly distributed within the sol-gel glass as individual metal centers. Any transition metal may be used in the sol-gel glasses. The present invention also relates to sensor materials where the sensor material is formed using the single phase metal-silica sol-gel glasses. The sensor materials may be in the form of a thin film or may be attached to an optical fiber. The present invention also relates to a method of sensing chemicals using the chemical sensors by monitoring the chromatic change of the metal-silica sol-gel glass when the chemical binds to the sensor. The present invention also relates to oxidation catalysts where a metal-silica sol-gel glass catalyzes the reaction. The present invention also relates to a method of performing oxidation reactions using the metal-silica sol-gel glasses. The present invention also relates to organopolymer metal-silica sol-gel composites where the pores of the metal-silica sol-gel glasses are filled with an organic polymer polymerized by the sol-gel glass.

  18. In vivo remineralization of dentin using an agarose hydrogel biomimetic mineralization system

    NASA Astrophysics Data System (ADS)

    Han, Min; Li, Quan-Li; Cao, Ying; Fang, Hui; Xia, Rong; Zhang, Zhi-Hong

    2017-02-01

    A novel agarose hydrogel biomimetic mineralization system loaded with calcium and phosphate was used to remineralize dentin and induce the oriented densely parallel packed HA layer on defective dentin surface in vivo in a rabbit model. Firstly, the enamel of the labial surface of rabbits’ incisor was removed and the dentin was exposed to oral environment. Secondly, the hydrogel biomimetic mineralization system was applied to the exposed dentin surface by using a custom tray. Finally, the teeth were extracted and evaluated by scanning electron microscopy, X-ray diffraction, and nanoindentation test after a certain time of mineralization intervals. The regenerated tissue on the dentin surface was composed of highly organised HA crystals. Densely packed along the c axis, these newly precipitated HA crystals were perpendicular to the underlying dental surface with a tight bond. The demineralized dentin was remineralized and dentinal tubules were occluded by the grown HA crystals. The nanohardness and elastic modulus of the regenerated tissue were similar to natural dentin. The results indicated a potential clinical use for repairing dentin-exposed related diseases, such as erosion, wear, and dentin hypersensitivity.

  19. Probing adsorption of polyacrylamide-based polymers on anisotropic Basal planes of kaolinite using quartz crystal microbalance.

    PubMed

    Alagha, Lana; Wang, Shengqun; Yan, Lujie; Xu, Zhenghe; Masliyah, Jacob

    2013-03-26

    Quartz crystal microbalance with dissipation (QCM-D) was applied to investigate the adsorption characteristics of polyacrylamide-based polymers (PAMs) on anisotropic basal planes of kaolinite. Kaolinite basal planes were differentiated by depositing kaolinite nanoparticles (KNPs) on silica and alumina sensors in solutions of controlled pH values. Adsorption of an in-house synthesized organic-inorganic Al(OH)3-PAM (Al-PAM) as an example of cationic hybrid PAM and a commercially available partially hydrolyzed polyacrylamide (MF1011) as an example of anionic PAM was studied. Cationic Al-PAM was found to adsorb irreversibly and preferentially on tetrahedral silica basal planes of kaolinite. In contrast, anionic MF1011 adsorbed strongly on aluminum-hydroxy basal planes, while its adsorption on tetrahedral silica basal planes was weak and reversible. Adsorption study revealed that both electrostatic attraction and hydrogen-bonding mechanisms contribute to adsorption of PAMs on kaolinite. The adsorbed Al-PAM layer was able to release trapped water overtime and became more compact, while MF1011 film became more dissipative as backbones stretched out from kaolinite surface with minimal overlapping. Experimental results obtained from this study provide clear insights into the phenomenon that governs flocculation-based solid-liquid separation processes using multicomponent flocculants of anionic and cationic nature.

  20. A brief review of other notable protein blotting methods.

    PubMed

    Kurien, Biji T; Scofield, R Hal

    2009-01-01

    A plethora of methods have been used for transferring proteins from the gel to the membrane. These include centrifuge blotting, electroblotting of proteins to Teflon tape and membranes for N- and C-terminal sequence analysis, multiple tissue blotting, a two-step transfer of low and high molecular weight proteins, blotting of Coomassie Brilliant Blue (CBB)-stained proteins from polyacrylamide gels to transparencies, acid electroblotting onto activated glass, membrane-array method for the detection of human intestinal bacteria in fecal samples, protein microarray using a new black cellulose nitrate support, electrotransfer using square wave alternating voltage for enhanced protein recovery, polyethylene glycol-mediated significant enhancement of the immunoblotting transfer, parallel protein chemical processing before and during western blot and the molecular scanner concept, electronic western blot of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-identified polypeptides from parallel processed gel-separated proteins, semidry electroblotting of peptides and proteins from acid-urea polyacrylamide gels, transfer of silver-stained proteins from polyacrylamide gels to polyvinylidene difluoride (PVDF) membranes, and the display of K(+) channel proteins on a solid nitrocellulose support for assaying toxin binding. The quantification of proteins bound to PVDF membranes by elution of CBB, clarification of immunoblots on PVDF for transmission densitometry, gold coating of nonconductive membranes before MALDI tandem mass spectrometric analysis to prevent charging effect for analysis of peptides from PVDF membranes, and a simple method for coating native polysaccharides onto nitrocellulose are some of the methods involving either the manipulation of membranes with transferred proteins or just a passive transfer of antigens to membranes. All these methods are briefly reviewed in this chapter.

  1. Direct Force Measurements on Neurofilaments: Gel Expanded to Gel Condensed Transition

    NASA Astrophysics Data System (ADS)

    Beck, R.; Deek, J.; Jones, J. B.; Safinya, C. R.

    2010-03-01

    Neurofilaments (NFs)--the major cytoskeletal constituent of axons in vertebrates, consist of three subunit proteins assembled to form filaments with protruding unstructured C-terminus sidearms. Liquid crystal gel networks of sidearm-mediated NF assemblies play a key role in the mechanical while disruptions of this network, due to over-accumulation or incorrect sidearm interactions, are a hallmark of motor neuron diseases. Using synchrotron SAXS [1,2] and microscopy techniques [1,3] we report a direct force measurement of reconstituted NF-gels under osmotic pressure (P), which revealed the role of subunit sidearms on structure and interaction of NFs. With increasing P, near physiological condition, the gels undergo an abrupt nonreversible gel expanded to gel condensed transition that indicates sidearm-mediated attractions between NFs. This attraction is consistent with an electrostatic model of interpenetrating chains.[4pt] [1] J.B. Jones, C.R. Safinya, Biophys. J. 95, 823 (2008);[0pt] [2] R. Beck et al., Nature Mat. (2009) in press;[0pt] [3] H. Hess et al. Langmuir 24, 8397 (2008)

  2. Thermal stabilization of glucose oxidase and glucoamylase by physical entrapment.

    PubMed Central

    Basaveswara Rao, V; Sastri, N V; Subba Rao, P V

    1981-01-01

    Physical entrapment was used as an approach to achieve thermal stabilization of enzymes. The t 1/2 values for the thermoinactivation of glucose oxidase and glucoamylase were increased several-fold by their entrapment in polyacrylamide gels. In polyacrylate gels the individual enzymes behaved differently, probably owing to microenvironmental effects arising by the polyelectrolyte nature of the carrier. PMID:6796045

  3. How-To-Do-It: Recombinant DNA Technology in the High School Biology Laboratory.

    ERIC Educational Resources Information Center

    Myers, Richard

    1988-01-01

    Describes a basic biotechnology investigation that includes restriction and ligation of plasmid DNA, transformation of bacteria and cloning of these bacterial cells. Discusses laboratory procedures and another activity in the identification of unknown plasmids by studying agarose gel electrophoresis photographs. (CW)

  4. Practical Molecular Biology for Students: An Integrated Approach to Teaching Basic Techniques.

    ERIC Educational Resources Information Center

    Hames, B. David; And Others

    1990-01-01

    An activity that introduces students to the correct handling of bacterial recombinants, antibiotic sensitivity testing, insertional inactivation, plasmid DNA isolation, restriction endonuclease digestion, agarose gel electrophoresis, Southern blotting, hybridization, and autoradiography is presented. A list of needed materials, procedures, safety…

  5. Chemical Degradation of Polyacrylamide during Hydraulic Fracturing

    NASA Astrophysics Data System (ADS)

    Xiong, B.; Tasker, T.; Miller, Z.; Roman-White, S.; Farina, B.; Piechowicz, B.; Burgos, W.; Joshi, P.; Zhu, L.; Gorski, C.; Zydney, A.; Kumar, M.

    2017-12-01

    Polyacrylamide (PAM) based friction reducers are a primary ingredient of slickwater hydraulic fracturing fluids. Little is known regarding the fate of these polymers under downhole conditions, which could have important environmental impacts including strategies for reuse or treatment of flowback water. The objective of this study was to evaluate the chemical degradation of high molecular weight PAM, including the effects of shale, oxygen, temperature, pressure, and salinity. Data were obtained with a slickwater fracturing fluid exposed to both a shale sample collected from a Marcellus shale outcrop and to Marcellus core samples at high pressures/temperatures (HPT) simulating downhole conditions. Based on size exclusion chromatography analyses, the peak molecular weight of the PAM was reduced by two orders of magnitude, from roughly 10 MDa to 200 kDa under typical HPT fracturing conditions. The rate of degradation was independent of pressure and salinity but increased significantly at high temperatures and in the presence of oxygen dissolved in fracturing fluid. Results were consistent with a free radical chain scission mechanism, supported by measurements of sub-M hydroxyl radical concentrations. The shale sample adsorbed some PAM ( 30%), but importantly it catalyzed the chemical degradation of PAM, likely due to dissolution of Fe2+ at low pH. These results provide the first evidence of radical-induced degradation of PAM under HPT hydraulic fracturing conditions without additional oxidative breaker.

  6. Chemical Degradation of Polyacrylamide during Hydraulic Fracturing.

    PubMed

    Xiong, Boya; Miller, Zachary; Roman-White, Selina; Tasker, Travis; Farina, Benjamin; Piechowicz, Bethany; Burgos, William D; Joshi, Prachi; Zhu, Liang; Gorski, Christopher A; Zydney, Andrew L; Kumar, Manish

    2018-01-02

    Polyacrylamide (PAM) based friction reducers are a primary ingredient of slickwater hydraulic fracturing fluids. Little is known regarding the fate of these polymers under downhole conditions, which could have important environmental impacts including decisions on strategies for reuse or treatment of flowback water. The objective of this study was to evaluate the chemical degradation of high molecular weight PAM, including the effects of shale, oxygen, temperature, pressure, and salinity. Data were obtained with a slickwater fracturing fluid exposed to both a shale sample collected from a Marcellus outcrop and to Marcellus core samples at high pressures/temperatures (HPT) simulating downhole conditions. Based on size exclusion chromatography analyses, the peak molecular weight of the PAM was reduced by 2 orders of magnitude, from roughly 10 MDa to 200 kDa under typical HPT fracturing conditions. The rate of degradation was independent of pressure and salinity but increased significantly at high temperatures and in the presence of oxygen dissolved in fracturing fluids. Results were consistent with a free radical chain scission mechanism, supported by measurements of sub-μM hydroxyl radical concentrations. The shale sample adsorbed some PAM (∼30%), but importantly it catalyzed the chemical degradation of PAM, likely due to dissolution of Fe 2+ at low pH. These results provide the first evidence of radical-induced degradation of PAM under HPT hydraulic fracturing conditions without additional oxidative breaker.

  7. Agarose-chitosan-C18 film micro-solid phase extraction combined with high performance liquid chromatography for the determination of phenanthrene and pyrene in chrysanthemum tea samples.

    PubMed

    Ng, Nyuk Ting; Sanagi, Mohd Marsin; Wan Ibrahim, Wan Nazihah; Wan Ibrahim, Wan Aini

    2017-05-01

    Agarose-chitosan-immobilized octadecylsilyl-silica (C 18 ) film micro-solid phase extraction (μSPE) was developed and applied for the determination of phenanthrene (PHE) and pyrene (PYR) in chrysanthemum tea samples using high performance liquid chromatography-ultraviolet detection (HPLC-UV). The film of blended agarose and chitosan allows good dispersion of C 18 , prevents the leaching of C 18 during application and enhances the film mechanical stability. Important μSPE parameters were optimized including amount of sorbent loading, extraction time, desorption solvent and desorption time. The matrix match calibration curves showed good linearity (r⩾0.994) over a concentration range of 1-500ppb. Under the optimized conditions, the proposed method showed good limits of detection (0.549-0.673ppb), good analyte recoveries (100.8-105.99%) and good reproducibilities (RSDs⩽13.53%, n=3) with preconcentration factors of 4 and 72 for PHE and PYR, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Free forming of the gel by 3D gel printer SWIM-ER

    NASA Astrophysics Data System (ADS)

    Okada, Koji; Tase, Taishi; Saito, Azusa; Makino, Masato; Gong, Jin; Kawakami, Masaru; Furukawa, Hidemitsu

    2015-04-01

    Gels, soft and wet materials, have unique properties such as material permeability, biocompatibility and low friction, which are hardly found in hard and dry materials. These superior characteristics of hydrogels promise to expand the medical applications. In recent years, the optical 3D gel printer named SWIM-ER (Soft and Wet Industrial - Easy Realizer) was developed by our team in order to fabricate tough gels with free form. We are aiming to create artificial blood vessel of the gel material by 3D gel printer. Artificial blood vessel is expected to be used for vascular surgery practice. The artificial blood vessel made by 3D gel printer can be create to free form on the basis of the biological data of the patient. Therefore, we believe it is possible to contribute to increasing the success rate and safety of vascular surgery by creating artificial blood vessel with 3D gel printer. The modeling method of SWIM-ER is as follow. Pregel solution is polymerized by one-point UV irradiation with optical fiber. The irradiation area is controlled by computer program, so that exact 3D free forming is realized. In this study, synthesis conditions are re-examined in order to improve the degree of freedom of fabrication. The dimensional accuracy in height direction is improved by increasing the cross linker concentration. We examined the relationship of resolution to the pitch and UV irradiation time in order to improve the modeling accuracy.

  9. Conducting Polymeric Hydrogel Electrolyte Based on Carboxymethylcellulose and Polyacrylamide/Polyaniline for Supercapacitor Applications

    NASA Astrophysics Data System (ADS)

    Suganya, N.; Jaisankar, V.; Sivakumar, E. K. T.

    Conducting polymer hydrogels represent a unique class of materials that possess enormous application in flexible electronic devices. In the present work, conducting carboxymethylcellulose (CMC)-co-polyacrylamide (PAAm)/polyaniline was synthesized by a two-step interpenetrating network solution polymerization technique. The synthesized CMC-co-PAAm/polyaniline with interpenetrating network structure was prepared by in situ polymerization of aniline to enhance conductivity. The molecular structure and morphology of the copolymer hydrogels were characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. The novel conducting polymer hydrogels show good electrical and electrochemical behavior, which makes them potentially useful in electronic devices such as supercapacitors, biosensors, bioelectronics, solar cells and memory devices.

  10. Purification and partial characterization of an aminopeptidase from the midgut tissue of Dysdercus peruvianus.

    PubMed

    Costa, Inês A; Samuels, Richard I; Bifano, Thaís D; Terra, Walter R; Silva, Carlos P

    2011-03-01

    The surface of midgut cells in Hemiptera is ensheathed by a lipoprotein membrane (the perimicrovillar membrane), which delimits a closed compartment with the microvillar membrane, the so-called perimicrovillar space. In Dysdercus peruvianus midgut perimicrovillar space a soluble aminopeptidase maybe involved in the digestion of oligopeptides and proteins ingested in the diet. This D. peruvianus aminopeptidase was purified to homogeneity by ion-exchange chromatography on an Econo-Q column, hydrophobic interaction chromatography on phenyl-agarose column and preparative polyacrylamide gel electrophoresis. The results suggested that there is a single molecular species of aminopeptidase in D. peruvianus midgut. Molecular mass values for the aminopeptidase were estimated to be 106kDa (gel filtration) and 55kDa (SDS-PAGE), suggesting that the enzyme occurs as a dimer under native conditions. Kinetic data showed that D. peruvianus aminopeptidase hydrolyzes the synthetic substrates LpNA, RpNA, AβNA and AsnMCA (K(m)s 0.65, 0.14, 0.68 and 0.74mM, respectively). The aminopeptidase activity upon LpNA was inhibited by EDTA and 1,10-phenanthroline, indicating the importance of metal ions in enzyme catalysis. One partial sequence of BLAST-identified aminopeptidase was found by random sequencing of the D. peruvianus midgut cDNA library. Semi-quantitative RT-PCR analysis showed that the aminopeptidase genes were expressed throughout the midgut epithelium, in the epithelia of V1, V2 and V3, Malphigian tubules and fat body, but it was not expressed in the salivary glands. These results are important in furthering our understanding of the digestive process in this pest species. Copyright © 2010 Elsevier Inc. All rights reserved.

  11. Plasma lipoproteins and the synthesis and turnover of plasma triglyceride in normal and genetically obese mice

    PubMed Central

    Salmon, D. Michael W.; Hems, Douglas A.

    1973-01-01

    1. Lipoproteins in the plasma of mice were characterized by agarose-gel chromatography and polyacrylamide-gel electrophoresis: genetically obese (ob/ob) mice exhibited hyperlipoproteinaemia (compared with lean mice), largely owing to an increase in the concentration of cholesterol in high-density lipoprotein. Plasma concentrations of triglyceride and phospholipid were not markedly increased in genetically obese mice. 2. The formation of glycerolipids in liver and plasma was investigated with 14C-labelled precursors. The synthesis of hepatic triglyceride and phospholipid from glucose or palmitate was enhanced in ob/ob mice, compared with lean mice. The rate of entry of triglyceride into plasma, calculated from the time-course of incorporation of 14C from [14C]palmitate into plasma triglyceride, was increased in ob/ob mice (0.5μmol of fatty acid/min, compared with 0.2 in lean mice). 3. The removal from plasma of murine lipoprotein triglyceride-[14C]fatty acid was increased in ob/ob mice (half-time 2.2min, compared with 7.2min in lean mice). Similar results were obtained with an injected lipid emulsion (Intralipid). 4. From these measurements, estimates of the rates of turnover of plasma triglyceride in mice (fed on a mixed diet, female, 3 months old) are about 1.0μmol of fatty acid/min in ob/ob mice, and 0.25 in lean mice. 5. The major precursor of hepatic and plasma triglyceride in lean and ob/ob mice was calculated to be plasma free fatty acid. 6. These results are discussed, in connexion with the role of the liver in triglyceride metabolism in mice, especially in relation to genetic obesity. PMID:4360712

  12. Differences in unwinding of supercoiled DNA induced by the two enantiomers of anti-benzo[a]pyrene diol epoxide.

    PubMed Central

    Xu, R; Birke, S; Carberry, S E; Geacintov, N E; Swenberg, C E; Harvey, R G

    1992-01-01

    The unwinding of supercoiled phi X174 RFI DNA induced by the tumorigenic (+) and non-tumorigenic (-) enantiomers of trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) has been investigated by agarose slab-gel and ethidium titration tube gel electrophoresis. The differences in adduct conformations were verified by flow linear dichroism techniques. Both enantiomers cause a reversible unwinding by the formation of noncovalent intercalative complexes. The effects of covalently bound BPDE residues on the electrophoretic mobilities of the RF I DNA form in agarose gels were investigated in detail in the range of binding ratios rb approximately 0.0-0.06 (covalently bound BPDE residues/nucleotide). In this range of rb values, there is a striking difference in the mobilities of (+)-BPDE- and (-)-BPDE-adducted phi X174 DNA in agarose slab-gels, the covalently bound (+)-BPDE residues causing a significantly greater retardation than (-)-BPDE residues. Increasing the level of covalent adducts beyond rb approximately 0.06 in the case of the (+)-BPDE enantiomer, leads to further unwinding and a minimum in the mobilities (corresponding to comigration of the nicked form and the covalently closed relaxed modified form) at rb 0.10 +/- 0.01; at still higher rb values, rewinding of the modified DNA in the opposite sense is observed. From the minimum in the mobility, a mean unwinding angle (per BPDE residue) of theta = 12 +/- 1.5 degrees is determined, which is in good agreement the value of theta = 11 +/- 1.8 degrees obtained by the tube gel titration method. Using this latter method, values of theta = 6.8 +/- 1.7 degrees for (-)-BPDE-phi X174 adducts are observed. It is concluded that agarose slab gel techniques are not suitable for determining unwinding angles for (-)-BPDE-modified phi X174 DNA because the alterations in the tertiary structures for rb < 0.06 are too small to cause sufficiently large changes in the electrophoretic mobilities. The major trans

  13. Adsorption properties of the nanozirconia/anionic polyacrylamide system-Effects of surfactant presence, solution pH and polymer carboxyl groups content

    NASA Astrophysics Data System (ADS)

    Wiśniewska, Małgorzata; Chibowski, Stanisław; Urban, Teresa

    2016-05-01

    The adsorption mechanism of anionic polyacrylamide (PAM) on the nanozirconia surface was examined. The effects of solution pH, carboxyl groups content in macromolecules and anionic surfactant (sodium dodecyl sulfate-SDS) addition were determined. The more probable structure of polymer adsorption layer was characterized based on the data obtained from spectrophotometry, viscosimetry and potentiometric titration methods. The adsorbed amount of polymer, size of macromolecules in the solution and surface charge density of ZrO2 particles in the absence and presence of PAM were assessed, respectively. Analysis of these results indicated that the increase of solution pH and content of carboxyl groups in the polymeric chains lead to more expanded conformations of adsorbing macromolecules. As a result, the adsorption of anionic polyacrylamide decreased. The SDS presence caused the significant increase of PAM adsorbed amount at pH 3, whereas at pH 6 and 9 the surfactant addition resulted in reduction of polymer adsorption level.

  14. Real-time nested multiplex PCR for the detection of herpes simplex virus types 1 and 2 and varicella zoster virus.

    PubMed

    O'Neill, Hugh J; Wyatt, Dorothy E; Coyle, Peter V; McCaughey, Conall; Mitchell, Frederick

    2003-12-01

    One hundred forty-nine specimens were tested in a LightCycler nested multiplex polymerase chain reaction (LCnmPCR) for Herpes simplex virus (HSV)1, HSV2, and VZV. Eighty-one were from genitourinary medicine (GUM) patients and the other 68 specimens were from other patients with skin lesions. The results were compared to a conventional multiplex nested PCR (nmPCR) using agarose gel electrophoresis. Twenty-five specimens were positive in both assays for HSV1 and 29 were positive for VZV. For HSV2 there were 27 positive in the LCnmPCR and 26 positive in the nmPCR assay. The melting temperatures (Tms) of each target were different with a mean of 84.75 degrees C for HSV1, 88.57 degrees C for HSV2, and 83.62 degrees C for VZV. The melting curves of positive specimens directly overlaid the melting curves of the positive controls in the assay. The LCnmPCR assay is a convenient alternative to conventional PCR using agarose gel electrophoresis. It improves specimen turnaround time by eliminating the need for gel electrophoresis, transillumination, and gel photography. It also shows increased sensitivity for HSV2 over our standard assay. This LCnmPCR reduces further the possibility of amplicon contamination with nested PCR protocols. Copyright 2003 Wiley-Liss, Inc.

  15. Identification of Fur, Aconitase, and Other Proteins Expressed by Mycobacterium tuberculosis under Conditions of Low and High Concentrations of Iron by Combined Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    PubMed Central

    Wong, Diane K.; Lee, Bai-Yu; Horwitz, Marcus A.; Gibson, Bradford W.

    1999-01-01

    Iron plays a critical role in the pathophysiology of Mycobacterium tuberculosis. To gain a better understanding of iron regulation by this organism, we have used two-dimensional (2-D) gel electrophoresis, mass spectrometry, and database searching to study protein expression in M. tuberculosis under conditions of high and low iron concentration. Proteins in cellular extracts from M. tuberculosis Erdman strain grown under low-iron (1 μM) and high-iron (70 μM) conditions were separated by 2-D polyacrylamide gel electrophoresis, which allowed high-resolution separation of several hundred proteins, as visualized by Coomassie staining. The expression of at least 15 proteins was induced, and the expression of at least 12 proteins was decreased under low-iron conditions. In-gel trypsin digestion was performed on these differentially expressed proteins, and the digestion mixtures were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry to determine the molecular masses of the resulting tryptic peptides. Partial sequence data on some of the peptides were obtained by using after source decay and/or collision-induced dissociation. The fragmentation data were used to search computerized peptide mass and protein sequence databases for known proteins. Ten iron-regulated proteins were identified, including Fur and aconitase proteins, both of which are known to be regulated by iron in other bacterial systems. Our study shows that, where large protein sequence databases are available from genomic studies, the combined use of 2-D gel electrophoresis, mass spectrometry, and database searching to analyze proteins expressed under defined environmental conditions is a powerful tool for identifying expressed proteins and their physiologic relevance. PMID:9864233

  16. Instrumental texture profile analysis of gelatin gel extracted from grouper skin and commercial (bovine and porcine) gelatin gels.

    PubMed

    Rahman, Mohammad Shafiur; Al-Mahrouqi, Abdullah Issa

    2009-01-01

    Mechanical compression was used to study the gelling characteristics of gelatin gels. Texture profile analysis (TPA) showed that the hardness of fish and mammalian gelatin increased significantly as the concentrations of gels increased. TPA attributes of 10% fish skin gel showed significant differences from those obtained from 20% and 30% gels. In bovine and porcine cases, such generic trends were not observed. Mechanical characteristics of 10% gels of gelatin from fish skin, determined from one cycle compression, were significantly lower than other sources of gelatin gels, while bovine and porcine gels did not show any significant differences. In the case of TPA, hardness of bovine gelatin gel was highest at 41 N for 10% gel, followed by porcine (30 N) then fish skin (5 N) gelatin gels. The gels prepared from different sources did not show any generic trends when all other mechanical attributes were considered.

  17. Compatibility between weak gel and microorganisms in weak gel-assisted microbial enhanced oil recovery.

    PubMed

    Qi, Yi-Bin; Zheng, Cheng-Gang; Lv, Cheng-Yuan; Lun, Zeng-Min; Ma, Tao

    2018-03-20

    To investigate weak gel-assisted microbial flooding in Block Wang Long Zhuang in the Jiangsu Oilfield, the compatibility of weak gel and microbe was evaluated using laboratory experiments. Bacillus sp. W5 was isolated from the formation water in Block Wang Long Zhuang. The rate of oil degradation reached 178 mg/day, and the rate of viscosity reduction reached 75.3%. Strain W5 could produce lipopeptide with a yield of 1254 mg/L. Emulsified crude oil was dispersed in the microbial degradation system, and the average diameter of the emulsified oil particles was 18.54 μm. Bacillus sp. W5 did not affect the rheological properties of the weak gel, and the presence of the weak gel did not significantly affect bacterial reproduction (as indicated by an unchanged microbial biomass), emulsification (surface tension is 35.56 mN/m and average oil particles size is 21.38 μm), oil degradation (162 mg/day) and oil viscosity reduction (72.7%). Core-flooding experiments indicated oil recovery of 23.6% when both weak gel and Bacillus sp. W5 were injected into the system, 14.76% when only the weak gel was injected, and 9.78% with strain W5 was injected without the weak gel. The results demonstrate good compatibility between strains W5 and the weak gel and highlight the application potential of weak gel-assisted microbial flooding. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  18. Application of polyacrylamide (PAM) through lay-flat polyethylene 1 tubing: effects on infiltration, erosion, N and P transport, and corn yield

    USDA-ARS?s Scientific Manuscript database

    Polyacrylamides (PAMs), when applied as a soil amendment, purportedly improve soil infiltration, decrease erosion, and reduce off-site agrochemical transport. The effect of PAM on infiltration, erosion, agrochemical transport, and crop yield when applied in-furrow to Mid-South production systems has...

  19. Supramolecular Gel-Templated In Situ Synthesis and Assembly of CdS Quantum Dots Gels

    NASA Astrophysics Data System (ADS)

    Zhu, Lili; He, Jie; Wang, Xiaoliang; Li, Dawei; He, Haibing; Ren, Lianbing; Jiang, Biwang; Wang, Yong; Teng, Chao; Xue, Gi; Tao, Huchun

    2017-01-01

    Although many studies have attempted to develop strategies for spontaneously organizing nanoparticles (NPs) into three-dimensional (3D) geometries, it remains a fascinating challenge. In this study, a method for in situ synthesis and self-assembly of a CdS quantum dots (QDs) gel using a Cd supramolecular gel as a scaffold was demonstrated. During the QDs formation process, the Cd ions that constituted the Cd gels served as the precursors of the CdS QDs, and the oleic acid (OA) that ligated with the Cd in the supramolecular gels was capped on the surface of the CdS QDs in the form of carboxylate. The OA-stabilized CdS QDs were in situ synthesized in the entangled self-assembled fibrillar networks (SAFIN) of the Cd gels through reactions between the gelator and H2S. As a result, the QDs exactly replicated the framework of the SAFIN in the CdS QD gels instead of simply assembling along the SAFIN of the supramolecular gels. Moreover, the CdS QDs showed extraordinary sensitivity in the fluorescence detection of IO4 - anions. The facile one-step method developed here is a new approach to assembling nanostructured materials into 3D architectures and has general implications for the design of low molecular mass gelators to bring desired functionality to the developed supramolecular gels.

  20. Influence of pre-cooking protein paste gelation conditions and post-cooking gel storage conditions on gel texture.

    PubMed

    Paker, Ilgin; Matak, Kristen E

    2016-01-15

    Gelation conditions affect the setting of myofibrillar fish protein gels. Therefore the impact of widely applied pre-cooking gelation time/temperature strategies and post-cooking period on the texture and color of final protein gels was determined. Four pre-cooking gelation strategies (no setting time, 30 min at 25 °C, 1 h at 40 °C or 24 h at 4 °C) were applied to protein pastes (fish protein concentrate and standard functional additives). After cooking, texture and color were analyzed either directly or after 24 h at 4 °C on gels adjusted to 25 °C. No-set gels were harder, gummier and chewier (P < 0.05) when analyzed immediately after cooling; however, gel chewiness, cohesiveness and firmness indicated by Kramer force benefited from 24 h at 4 °C gel setting when stored post-cooking. Gel-setting conditions had a greater (P < 0.05) effect on texture when directly analyzed and most changes occurred in no-set gels. There were significant (P < 0.05) changes between directly analyzed and post-cooking stored gels in texture and color, depending on the pre-cooking gelation strategy. Pre-cooking gelation conditions will affect final protein gel texture and color, with gel stability benefiting from a gel-setting period. However, post-cooking storage may have a greater impact on final gels, with textural attributes becoming more consistent between all samples. © 2015 Society of Chemical Industry.